Starting phenix.real_space_refine
on Sun Aug 24 10:20:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sxb_40830/08_2025/8sxb_40830_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sxb_40830/08_2025/8sxb_40830.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sxb_40830/08_2025/8sxb_40830_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sxb_40830/08_2025/8sxb_40830_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sxb_40830/08_2025/8sxb_40830.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sxb_40830/08_2025/8sxb_40830.map"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.066
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      35      5.16       5
     C    5971      2.51       5
     N    1544      2.21       5
     O    1649      1.98       5
     H    9405      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 18604
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 18576
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1152, 18576
          Classifications: {'peptide': 1152}
          Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 1117}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'P2E': 1}
          Classifications: {'undetermined': 1, 'water': 1}
          Link IDs: {None: 1}
  Time building chain proxies: 3.44, per 1000 atoms: 0.18
  Number of scatterers: 18604
  At special positions: 0
  Unit cell: (81.83, 96.025, 144.455, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      35     16.00
     O    1649      8.00
     N    1544      7.00
     C    5971      6.00
     H    9405      1.00
    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: 1.84
  Conformation dependent library (CDL) restraints added in 836.1 milliseconds
  
  Enol-peptide restraints added in 1.4 microseconds
  

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2176

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 5 sheets defined
      73.7% alpha, 7.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.58
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1368 through 1371
    Processing helix  chain 'A' and resid 1372 through 1394
      removed outlier: 4.085A  pdb=" N   LEU A1380 " --> pdb=" O   LEU A1376 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   TYR A1383 " --> pdb=" O   GLU A1379 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1399 through 1414
      removed outlier: 5.867A  pdb=" N   LYS A1410 " --> pdb=" O   LYS A1406 " (cutoff:3.500A)
      removed outlier: 5.796A  pdb=" N   SER A1411 " --> pdb=" O   CYS A1407 " (cutoff:3.500A)
      removed outlier: 4.252A  pdb=" N   VAL A1414 " --> pdb=" O   LYS A1410 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1415 through 1442
      removed outlier: 3.834A  pdb=" N   THR A1419 " --> pdb=" O   LEU A1415 " (cutoff:3.500A)
      Proline residue:  A1430  - end of helix
      removed outlier: 3.578A  pdb=" N   TYR A1439 " --> pdb=" O   LYS A1435 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   PHE A1440 " --> pdb=" O   ILE A1436 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1447 through 1501
      removed outlier: 4.103A  pdb=" N   ARG A1500 " --> pdb=" O   ARG A1496 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1504 through 1509
      removed outlier: 3.661A  pdb=" N   LYS A1508 " --> pdb=" O   ALA A1505 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1510 through 1520
      removed outlier: 3.542A  pdb=" N   LEU A1517 " --> pdb=" O   GLN A1513 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   LEU A1518 " --> pdb=" O   ILE A1514 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1521 through 1523
      No H-bonds generated for 'chain 'A' and resid 1521 through 1523'
    Processing helix  chain 'A' and resid 1524 through 1532
      removed outlier: 3.780A  pdb=" N   THR A1529 " --> pdb=" O   PHE A1525 " (cutoff:3.500A)
      removed outlier: 4.602A  pdb=" N   ILE A1530 " --> pdb=" O   ASP A1526 " (cutoff:3.500A)
      removed outlier: 4.501A  pdb=" N   PHE A1531 " --> pdb=" O   GLN A1527 " (cutoff:3.500A)
      removed outlier: 4.181A  pdb=" N   LEU A1532 " --> pdb=" O   VAL A1528 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1533 through 1554
      Proline residue:  A1539  - end of helix
      removed outlier: 3.582A  pdb=" N   GLU A1552 " --> pdb=" O   LEU A1548 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1556 through 1602
      removed outlier: 4.009A  pdb=" N   GLY A1560 " --> pdb=" O   SER A1556 " (cutoff:3.500A)
      Proline residue:  A1569  - end of helix
      removed outlier: 3.950A  pdb=" N   ALA A1587 " --> pdb=" O   SER A1583 " (cutoff:3.500A)
      removed outlier: 4.405A  pdb=" N   PHE A1588 " --> pdb=" O   LYS A1584 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1602 through 1609
    Processing helix  chain 'A' and resid 1611 through 1662
      removed outlier: 4.760A  pdb=" N   SER A1648 " --> pdb=" O   PHE A1644 " (cutoff:3.500A)
      removed outlier: 4.898A  pdb=" N   LYS A1649 " --> pdb=" O   PHE A1645 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1667 through 1685
    Processing helix  chain 'A' and resid 1687 through 1711
      removed outlier: 3.540A  pdb=" N   VAL A1701 " --> pdb=" O   SER A1697 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1770 through 1779
    Processing helix  chain 'A' and resid 1809 through 1815
    Processing helix  chain 'A' and resid 1820 through 1831
      removed outlier: 3.797A  pdb=" N   LYS A1826 " --> pdb=" O   GLU A1822 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1833 through 1840
    Processing helix  chain 'A' and resid 1842 through 1845
    Processing helix  chain 'A' and resid 1856 through 1871
      removed outlier: 3.601A  pdb=" N   ALA A1868 " --> pdb=" O   ASN A1864 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   GLN A1871 " --> pdb=" O   ARG A1867 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1881 through 1885
    Processing helix  chain 'A' and resid 1886 through 1897
    Processing helix  chain 'A' and resid 1913 through 1920
      removed outlier: 4.778A  pdb=" N   LYS A1918 " --> pdb=" O   GLN A1915 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2017 through 2027
      removed outlier: 3.807A  pdb=" N   TYR A2021 " --> pdb=" O   GLY A2017 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2030 through 2065
      removed outlier: 3.526A  pdb=" N   ILE A2034 " --> pdb=" O   HIS A2030 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   ASP A2052 " --> pdb=" O   TYR A2048 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   LEU A2065 " --> pdb=" O   GLN A2061 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2080 through 2128
      removed outlier: 3.657A  pdb=" N   PHE A2107 " --> pdb=" O   SER A2103 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2129 through 2136
      removed outlier: 4.050A  pdb=" N   PHE A2133 " --> pdb=" O   PRO A2129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2137 through 2154
      removed outlier: 3.974A  pdb=" N   ARG A2144 " --> pdb=" O   ARG A2140 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   PHE A2145 " --> pdb=" O   ILE A2141 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   ILE A2149 " --> pdb=" O   PHE A2145 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2154 through 2181
      removed outlier: 3.891A  pdb=" N   LEU A2158 " --> pdb=" O   ASP A2154 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   GLN A2169 " --> pdb=" O   GLN A2165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2184 through 2230
      Proline residue:  A2190  - end of helix
      removed outlier: 3.869A  pdb=" N   GLU A2204 " --> pdb=" O   ARG A2200 " (cutoff:3.500A)
      removed outlier: 4.170A  pdb=" N   THR A2205 " --> pdb=" O   TYR A2201 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   SER A2218 " --> pdb=" O   SER A2214 " (cutoff:3.500A)
      Proline residue:  A2219  - end of helix
    Processing helix  chain 'A' and resid 2230 through 2235
    Processing helix  chain 'A' and resid 2239 through 2290
      removed outlier: 3.603A  pdb=" N   PHE A2247 " --> pdb=" O   PHE A2243 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   ARG A2271 " --> pdb=" O   TRP A2267 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   LEU A2288 " --> pdb=" O   ALA A2284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2295 through 2335
      removed outlier: 3.626A  pdb=" N   LEU A2309 " --> pdb=" O   TYR A2305 " (cutoff:3.500A)
      removed outlier: 4.387A  pdb=" N   MET A2310 " --> pdb=" O   ALA A2306 " (cutoff:3.500A)
      removed outlier: 5.082A  pdb=" N   GLY A2311 " --> pdb=" O   LEU A2307 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   MET A2312 " --> pdb=" O   THR A2308 " (cutoff:3.500A)
      removed outlier: 4.673A  pdb=" N   GLN A2314 " --> pdb=" O   MET A2310 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   TRP A2315 " --> pdb=" O   GLY A2311 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ALA A2321 " --> pdb=" O   VAL A2317 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   ILE A2328 " --> pdb=" O   GLU A2324 " (cutoff:3.500A)
      removed outlier: 4.564A  pdb=" N   SER A2329 " --> pdb=" O   ASN A2325 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   VAL A2330 " --> pdb=" O   MET A2326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2336 through 2339
      removed outlier: 3.968A  pdb=" N   LEU A2339 " --> pdb=" O   TYR A2336 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 2336 through 2339'
    Processing helix  chain 'A' and resid 2400 through 2409
      removed outlier: 3.978A  pdb=" N   ILE A2405 " --> pdb=" O   LYS A2401 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2426 through 2428
      No H-bonds generated for 'chain 'A' and resid 2426 through 2428'
    Processing helix  chain 'A' and resid 2429 through 2436
      removed outlier: 3.724A  pdb=" N   LYS A2436 " --> pdb=" O   ASP A2432 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2450 through 2456
    Processing helix  chain 'A' and resid 2462 through 2473
    Processing helix  chain 'A' and resid 2475 through 2481
    Processing helix  chain 'A' and resid 2484 through 2488
    Processing helix  chain 'A' and resid 2491 through 2495
    Processing helix  chain 'A' and resid 2498 through 2513
      removed outlier: 3.798A  pdb=" N   VAL A2505 " --> pdb=" O   GLN A2501 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2523 through 2527
    Processing helix  chain 'A' and resid 2528 through 2543
      removed outlier: 4.737A  pdb=" N   LEU A2534 " --> pdb=" O   ARG A2530 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   PHE A2543 " --> pdb=" O   ILE A2539 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2554 through 2558
    Processing helix  chain 'A' and resid 2577 through 2584
    Processing helix  chain 'A' and resid 2587 through 2597
      removed outlier: 3.864A  pdb=" N   GLY A2597 " --> pdb=" O   VAL A2593 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2597 through 2617
    Processing sheet with id=AA1, first strand: chain 'A' and resid 1748 through 1755
      removed outlier: 6.376A  pdb=" N   GLN A1749 " --> pdb=" O   THR A1736 " (cutoff:3.500A)
      removed outlier: 5.776A  pdb=" N   THR A1736 " --> pdb=" O   GLN A1749 " (cutoff:3.500A)
      removed outlier: 4.654A  pdb=" N   LEU A1751 " --> pdb=" O   ASP A1734 " (cutoff:3.500A)
      removed outlier: 5.431A  pdb=" N   VAL A1732 " --> pdb=" O   SER A1790 " (cutoff:3.500A)
      removed outlier: 7.655A  pdb=" N   SER A1790 " --> pdb=" O   VAL A1732 " (cutoff:3.500A)
      removed outlier: 5.429A  pdb=" N   ASP A1734 " --> pdb=" O   GLN A1788 " (cutoff:3.500A)
      removed outlier: 5.328A  pdb=" N   GLN A1788 " --> pdb=" O   ASP A1734 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 1795 through 1798
      removed outlier: 6.509A  pdb=" N   ALA A1796 " --> pdb=" O   LEU A1877 " (cutoff:3.500A)
      removed outlier: 7.788A  pdb=" N   ASP A1879 " --> pdb=" O   ALA A1796 " (cutoff:3.500A)
      removed outlier: 7.388A  pdb=" N   VAL A1798 " --> pdb=" O   ASP A1879 " (cutoff:3.500A)
      removed outlier: 6.336A  pdb=" N   LEU A1760 " --> pdb=" O   GLN A1922 " (cutoff:3.500A)
      removed outlier: 7.738A  pdb=" N   LEU A1924 " --> pdb=" O   LEU A1760 " (cutoff:3.500A)
      removed outlier: 6.365A  pdb=" N   ALA A1762 " --> pdb=" O   LEU A1924 " (cutoff:3.500A)
      removed outlier: 7.587A  pdb=" N   LEU A1926 " --> pdb=" O   ALA A1762 " (cutoff:3.500A)
      removed outlier: 6.510A  pdb=" N   VAL A1764 " --> pdb=" O   LEU A1926 " (cutoff:3.500A)
      removed outlier: 6.641A  pdb=" N   ILE A1923 " --> pdb=" O   LYS A1934 " (cutoff:3.500A)
      removed outlier: 4.637A  pdb=" N   LYS A1934 " --> pdb=" O   ILE A1923 " (cutoff:3.500A)
      removed outlier: 7.086A  pdb=" N   ILE A1925 " --> pdb=" O   VAL A1932 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1807 through 1808
      removed outlier: 3.727A  pdb=" N   GLY A1807 " --> pdb=" O   ILE A1848 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 2378 through 2385
      removed outlier: 6.696A  pdb=" N   LYS A2379 " --> pdb=" O   ASN A2367 " (cutoff:3.500A)
      removed outlier: 6.283A  pdb=" N   ASN A2367 " --> pdb=" O   LYS A2379 " (cutoff:3.500A)
      removed outlier: 5.189A  pdb=" N   LEU A2381 " --> pdb=" O   ASN A2365 " (cutoff:3.500A)
      removed outlier: 5.505A  pdb=" N   PHE A2363 " --> pdb=" O   TRP A2419 " (cutoff:3.500A)
      removed outlier: 7.007A  pdb=" N   TRP A2419 " --> pdb=" O   PHE A2363 " (cutoff:3.500A)
      removed outlier: 4.994A  pdb=" N   ASN A2365 " --> pdb=" O   LYS A2417 " (cutoff:3.500A)
      removed outlier: 4.781A  pdb=" N   LYS A2417 " --> pdb=" O   ASN A2365 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 2438 through 2440
      removed outlier: 6.321A  pdb=" N   SER A2438 " --> pdb=" O   ILE A2519 " (cutoff:3.500A)
      removed outlier: 7.511A  pdb=" N   ASP A2521 " --> pdb=" O   SER A2438 " (cutoff:3.500A)
      removed outlier: 7.201A  pdb=" N   ILE A2440 " --> pdb=" O   ASP A2521 " (cutoff:3.500A)
      removed outlier: 6.166A  pdb=" N   LEU A2518 " --> pdb=" O   LEU A2549 " (cutoff:3.500A)
      removed outlier: 7.721A  pdb=" N   ILE A2551 " --> pdb=" O   LEU A2518 " (cutoff:3.500A)
      removed outlier: 6.246A  pdb=" N   ILE A2520 " --> pdb=" O   ILE A2551 " (cutoff:3.500A)
      removed outlier: 6.477A  pdb=" N   LYS A2390 " --> pdb=" O   LYS A2563 " (cutoff:3.500A)
      removed outlier: 7.732A  pdb=" N   MET A2565 " --> pdb=" O   LYS A2390 " (cutoff:3.500A)
      removed outlier: 6.293A  pdb=" N   GLY A2392 " --> pdb=" O   MET A2565 " (cutoff:3.500A)
      removed outlier: 7.567A  pdb=" N   LEU A2567 " --> pdb=" O   GLY A2392 " (cutoff:3.500A)
      removed outlier: 6.722A  pdb=" N   VAL A2394 " --> pdb=" O   LEU A2567 " (cutoff:3.500A)

    619 hydrogen bonds defined for protein.
    1785 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: 4.53

  Time building geometry restraints manager: 2.61 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 9392
        1.03 -     1.23: 37
        1.23 -     1.42: 3862
        1.42 -     1.62: 5447
        1.62 -     1.81: 57
  Bond restraints: 18795
  Sorted by residual:
  bond pdb=" C1  P2E A2701 "
       pdb=" O1  P2E A2701 "
    ideal  model  delta    sigma   weight residual
    1.247  1.209  0.038 2.00e-02 2.50e+03 3.67e+00
  bond pdb=" C1  P2E A2701 "
       pdb=" O2  P2E A2701 "
    ideal  model  delta    sigma   weight residual
    1.250  1.212  0.038 2.00e-02 2.50e+03 3.56e+00
  bond pdb=" CB  THR A1686 "
       pdb=" CG2 THR A1686 "
    ideal  model  delta    sigma   weight residual
    1.521  1.470  0.051 3.30e-02 9.18e+02 2.43e+00
  bond pdb=" C   ALA A2343 "
       pdb=" N   PRO A2344 "
    ideal  model  delta    sigma   weight residual
    1.331  1.349 -0.018 1.21e-02 6.83e+03 2.13e+00
  bond pdb=" C2  P2E A2701 "
       pdb=" C3  P2E A2701 "
    ideal  model  delta    sigma   weight residual
    1.519  1.545 -0.026 2.00e-02 2.50e+03 1.72e+00
  ... (remaining 18790 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.22: 30343
        1.22 -     2.44: 3376
        2.44 -     3.66: 258
        3.66 -     4.88: 38
        4.88 -     6.10: 14
  Bond angle restraints: 34029
  Sorted by residual:
  angle pdb=" N   HIS A1478 "
        pdb=" CA  HIS A1478 "
        pdb=" C   HIS A1478 "
      ideal   model   delta    sigma   weight residual
     111.36  115.11   -3.75 1.09e+00 8.42e-01 1.18e+01
  angle pdb=" N   TRP A2345 "
        pdb=" CA  TRP A2345 "
        pdb=" C   TRP A2345 "
      ideal   model   delta    sigma   weight residual
     111.36  114.64   -3.28 1.09e+00 8.42e-01 9.06e+00
  angle pdb=" N   GLY A2175 "
        pdb=" CA  GLY A2175 "
        pdb=" C   GLY A2175 "
      ideal   model   delta    sigma   weight residual
     112.50  115.88   -3.38 1.16e+00 7.43e-01 8.50e+00
  angle pdb=" N   GLY A2172 "
        pdb=" CA  GLY A2172 "
        pdb=" C   GLY A2172 "
      ideal   model   delta    sigma   weight residual
     112.73  116.06   -3.33 1.20e+00 6.94e-01 7.69e+00
  angle pdb=" CA  HIS A1473 "
        pdb=" CB  HIS A1473 "
        pdb=" CG  HIS A1473 "
      ideal   model   delta    sigma   weight residual
     113.80  111.09    2.71 1.00e+00 1.00e+00 7.35e+00
  ... (remaining 34024 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.93: 8083
       17.93 -    35.85: 371
       35.85 -    53.78: 149
       53.78 -    71.71: 155
       71.71 -    89.64: 10
  Dihedral angle restraints: 8768
    sinusoidal: 4763
      harmonic: 4005
  Sorted by residual:
  dihedral pdb=" CA  ALA A2343 "
           pdb=" C   ALA A2343 "
           pdb=" N   PRO A2344 "
           pdb=" CA  PRO A2344 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -153.98  -26.02     0      5.00e+00 4.00e-02 2.71e+01
  dihedral pdb=" CA  CYS A2546 "
           pdb=" C   CYS A2546 "
           pdb=" N   THR A2547 "
           pdb=" CA  THR A2547 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.01   24.99     0      5.00e+00 4.00e-02 2.50e+01
  dihedral pdb=" CA  GLU A2522 "
           pdb=" C   GLU A2522 "
           pdb=" N   ALA A2523 "
           pdb=" CA  ALA A2523 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.53  -24.47     0      5.00e+00 4.00e-02 2.39e+01
  ... (remaining 8765 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 1066
       0.056 -    0.113: 323
       0.113 -    0.169: 76
       0.169 -    0.225: 12
       0.225 -    0.282: 3
  Chirality restraints: 1480
  Sorted by residual:
  chirality pdb=" CA  PHE A1656 "
            pdb=" N   PHE A1656 "
            pdb=" C   PHE A1656 "
            pdb=" CB  PHE A1656 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 1.98e+00
  chirality pdb=" C15 P2E A2701 "
            pdb=" C14 P2E A2701 "
            pdb=" C16 P2E A2701 "
            pdb=" O5  P2E A2701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.23    2.49   -0.26 2.00e-01 2.50e+01 1.75e+00
  chirality pdb=" CA  PHE A1672 "
            pdb=" N   PHE A1672 "
            pdb=" C   PHE A1672 "
            pdb=" CB  PHE A1672 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.50e+00
  ... (remaining 1477 not shown)

  Planarity restraints: 2698
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A1794 "   -0.097 9.50e-02 1.11e+02   4.91e-02 3.17e+01
        pdb=" NE  ARG A1794 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  ARG A1794 "   -0.006 2.00e-02 2.50e+03
        pdb=" NH1 ARG A1794 "   -0.043 2.00e-02 2.50e+03
        pdb=" NH2 ARG A1794 "    0.063 2.00e-02 2.50e+03
        pdb="HH11 ARG A1794 "    0.000 2.00e-02 2.50e+03
        pdb="HH12 ARG A1794 "    0.049 2.00e-02 2.50e+03
        pdb="HH21 ARG A1794 "    0.002 2.00e-02 2.50e+03
        pdb="HH22 ARG A1794 "   -0.063 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS A1473 "   -0.037 2.00e-02 2.50e+03   3.44e-02 2.67e+01
        pdb=" CG  HIS A1473 "    0.066 2.00e-02 2.50e+03
        pdb=" ND1 HIS A1473 "    0.020 2.00e-02 2.50e+03
        pdb=" CD2 HIS A1473 "    0.012 2.00e-02 2.50e+03
        pdb=" CE1 HIS A1473 "    0.038 2.00e-02 2.50e+03
        pdb=" NE2 HIS A1473 "   -0.010 2.00e-02 2.50e+03
        pdb=" HD1 HIS A1473 "   -0.023 2.00e-02 2.50e+03
        pdb=" HD2 HIS A1473 "   -0.028 2.00e-02 2.50e+03
        pdb=" HE1 HIS A1473 "   -0.039 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A1500 "    0.221 9.50e-02 1.11e+02   7.95e-02 2.56e+01
        pdb=" NE  ARG A1500 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ  ARG A1500 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH1 ARG A1500 "    0.008 2.00e-02 2.50e+03
        pdb=" NH2 ARG A1500 "   -0.063 2.00e-02 2.50e+03
        pdb="HH11 ARG A1500 "   -0.000 2.00e-02 2.50e+03
        pdb="HH12 ARG A1500 "   -0.018 2.00e-02 2.50e+03
        pdb="HH21 ARG A1500 "   -0.001 2.00e-02 2.50e+03
        pdb="HH22 ARG A1500 "    0.061 2.00e-02 2.50e+03
  ... (remaining 2695 not shown)

  Histogram of nonbonded interaction distances:
        1.54 -     2.15: 656
        2.15 -     2.76: 35365
        2.76 -     3.38: 52906
        3.38 -     3.99: 65962
        3.99 -     4.60: 105814
  Nonbonded interactions: 260703
  Sorted by model distance:
  nonbonded pdb="HH21 ARG A2127 "
            pdb=" O   GLU A2342 "
     model   vdw
     1.540 2.450
  nonbonded pdb=" HZ1 LYS A1497 "
            pdb=" OE1 GLU A1714 "
     model   vdw
     1.554 2.450
  nonbonded pdb=" HG1 THR A1589 "
            pdb=" OE2 GLU A1626 "
     model   vdw
     1.564 2.450
  nonbonded pdb=" O   ALA A1616 "
            pdb=" HG1 THR A1620 "
     model   vdw
     1.564 2.450
  nonbonded pdb=" OD2 ASP A2052 "
            pdb=" HH  TYR A2305 "
     model   vdw
     1.580 2.450
  ... (remaining 260698 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.580
  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:             0.090
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     19.540
  Find NCS groups from input model:        0.070
  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:7.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.590
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
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      :  0.006   0.051   9390  Z= 0.260
  Angle     :  0.833   6.103  12724  Z= 0.528
  Chirality :  0.058   0.282   1480
  Planarity :  0.009   0.109   1584
  Dihedral  : 12.608  89.636   3441
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 0.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    Favored  : 98.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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 aren not related in a simple way.
  whole: -0.86 (0.22), residues: 1144
  helix: -0.90 (0.16), residues: 750
  sheet:  0.48 (0.56), residues: 78
  loop :  0.57 (0.36), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.025   0.002   ARG A1670 
 TYR   0.027   0.006   TYR A1412 
 PHE   0.020   0.003   PHE A1805 
 TRP   0.029   0.005   TRP A2054 
 HIS   0.025   0.003   HIS A1473 

Details of bonding type rmsd
  covalent geometry    : bond        0.00569 ( 9390)
  covalent geometry    : angle       0.83346 (12724)
  hydrogen bonds       : bond        0.20149 (  619)
  hydrogen bonds       : angle       7.64235 ( 1785)

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1596 MET cc_start: 0.7961 (tpt) cc_final: 0.7753 (tpt)
REVERT: A 1632 ARG cc_start: 0.7530 (mtt-85) cc_final: 0.7012 (mmt180)
REVERT: A 2451 MET cc_start: 0.7417 (tpt) cc_final: 0.7206 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 143
  average time/residue: 1.2051
  time to fit residues: 184.1464
Evaluate side-chains
  79 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 108 optimal weight:   10.0000
   chunk 49 optimal weight:   20.0000
   chunk 97 optimal weight:    2.9990
   chunk 113 optimal weight:    8.9990
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    5.9990
   chunk 100 optimal weight:    5.9990
   overall best weight:    1.7588

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

Flipped N/Q/H residues before XYZ refinement:
A2254 HIS
A2442 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4431 r_free = 0.4431 target = 0.205009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.139018 restraints weight = 33285.642|
|-----------------------------------------------------------------------------|
r_work (start): 0.3666 rms_B_bonded: 2.16
r_work: 0.3553 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3440 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7950
moved from start:          0.2353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   9390  Z= 0.184
  Angle     :  0.606   4.994  12724  Z= 0.339
  Chirality :  0.041   0.147   1480
  Planarity :  0.005   0.061   1584
  Dihedral  :  5.824  40.105   1277
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 2.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  :  6.61 %
    Favored  : 92.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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 aren not related in a simple way.
  whole:  0.88 (0.24), residues: 1144
  helix:  0.76 (0.18), residues: 750
  sheet:  0.06 (0.55), residues: 78
  loop :  0.64 (0.35), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A2502 
 TYR   0.015   0.002   TYR A2590 
 PHE   0.019   0.002   PHE A1672 
 TRP   0.012   0.002   TRP A2053 
 HIS   0.010   0.002   HIS A1473 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 ( 9390)
  covalent geometry    : angle       0.60606 (12724)
  hydrogen bonds       : bond        0.06277 (  619)
  hydrogen bonds       : angle       4.89604 ( 1785)

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 85
  time to evaluate  : 0.515 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1442 ASN cc_start: 0.7037 (m110) cc_final: 0.6719 (t0)
REVERT: A 1632 ARG cc_start: 0.7660 (mtt-85) cc_final: 0.6782 (mmt180)
REVERT: A 2217 ARG cc_start: 0.8203 (ttm170) cc_final: 0.7857 (ttm170)
REVERT: A 2259 PHE cc_start: 0.7242 (OUTLIER) cc_final: 0.6853 (t80)
REVERT: A 2402 SER cc_start: 0.8094 (OUTLIER) cc_final: 0.7881 (p)
REVERT: A 2421 ASP cc_start: 0.8122 (t0) cc_final: 0.6867 (t0)
REVERT: A 2485 LYS cc_start: 0.7543 (mtmt) cc_final: 0.6941 (pttt)
REVERT: A 2502 ARG cc_start: 0.6621 (mtm-85) cc_final: 0.6198 (mtt90)
  outliers start: 13
  outliers final: 4
  residues processed: 90
  average time/residue: 1.1877
  time to fit residues: 115.5335
Evaluate side-chains
  73 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 67
  time to evaluate  : 0.529 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1643 SER
Chi-restraints excluded: chain A residue 2206 SER
Chi-restraints excluded: chain A residue 2229 GLN
Chi-restraints excluded: chain A residue 2259 PHE
Chi-restraints excluded: chain A residue 2402 SER
Chi-restraints excluded: chain A residue 2486 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 26 optimal weight:    0.7980
   chunk 59 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 95 optimal weight:    0.9990
   chunk 58 optimal weight:    0.5980
   chunk 0 optimal weight:    4.9990
   chunk 18 optimal weight:    0.8980
   chunk 63 optimal weight:    0.6980
   chunk 9 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A2442 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4441 r_free = 0.4441 target = 0.205994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.140154 restraints weight = 33213.509|
|-----------------------------------------------------------------------------|
r_work (start): 0.3692 rms_B_bonded: 2.17
r_work: 0.3578 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3459 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.3459
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7938
moved from start:          0.3000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   9390  Z= 0.119
  Angle     :  0.498   4.927  12724  Z= 0.273
  Chirality :  0.038   0.138   1480
  Planarity :  0.004   0.071   1584
  Dihedral  :  4.954  36.336   1277
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 2.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  :  8.21 %
    Favored  : 90.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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 aren not related in a simple way.
  whole:  1.74 (0.25), residues: 1144
  helix:  1.49 (0.19), residues: 755
  sheet:  0.31 (0.56), residues: 83
  loop :  0.82 (0.36), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A2127 
 TYR   0.010   0.001   TYR A2590 
 PHE   0.014   0.001   PHE A2018 
 TRP   0.009   0.001   TRP A2053 
 HIS   0.018   0.002   HIS A2357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 9390)
  covalent geometry    : angle       0.49809 (12724)
  hydrogen bonds       : bond        0.05268 (  619)
  hydrogen bonds       : angle       4.40400 ( 1785)

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 80
  time to evaluate  : 0.491 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1442 ASN cc_start: 0.6943 (m110) cc_final: 0.6593 (t0)
REVERT: A 2016 VAL cc_start: 0.7458 (OUTLIER) cc_final: 0.7154 (m)
REVERT: A 2217 ARG cc_start: 0.8236 (ttm170) cc_final: 0.7950 (ttm170)
REVERT: A 2259 PHE cc_start: 0.7394 (OUTLIER) cc_final: 0.6901 (t80)
REVERT: A 2485 LYS cc_start: 0.7490 (mtmt) cc_final: 0.6877 (pttt)
REVERT: A 2502 ARG cc_start: 0.6404 (mtm-85) cc_final: 0.5963 (mtt90)
REVERT: A 2542 LYS cc_start: 0.7997 (mmmt) cc_final: 0.7623 (mmtt)
  outliers start: 12
  outliers final: 3
  residues processed: 84
  average time/residue: 0.9230
  time to fit residues: 84.3551
Evaluate side-chains
  73 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 68
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1660 VAL
Chi-restraints excluded: chain A residue 2016 VAL
Chi-restraints excluded: chain A residue 2259 PHE
Chi-restraints excluded: chain A residue 2415 GLU
Chi-restraints excluded: chain A residue 2486 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 71 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 84 optimal weight:    2.9990
   chunk 92 optimal weight:    6.9990
   chunk 86 optimal weight:    2.9990
   chunk 111 optimal weight:    8.9990
   chunk 24 optimal weight:    1.9990
   chunk 17 optimal weight:    0.6980
   chunk 97 optimal weight:    0.9980
   chunk 85 optimal weight:    0.6980
   chunk 69 optimal weight:    0.4980
   overall best weight:    0.7782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4441 r_free = 0.4441 target = 0.206343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.140517 restraints weight = 33378.512|
|-----------------------------------------------------------------------------|
r_work (start): 0.3681 rms_B_bonded: 2.18
r_work: 0.3576 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3457 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.3457
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7831
moved from start:          0.3230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   9390  Z= 0.113
  Angle     :  0.471   4.748  12724  Z= 0.258
  Chirality :  0.037   0.135   1480
  Planarity :  0.004   0.038   1584
  Dihedral  :  4.761  35.269   1277
  Min Nonbonded Distance : 2.256

Molprobity Statistics.
  All-atom Clashscore : 2.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  :  8.71 %
    Favored  : 90.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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 aren not related in a simple way.
  whole:  1.99 (0.25), residues: 1144
  helix:  1.70 (0.19), residues: 755
  sheet:  0.43 (0.58), residues: 83
  loop :  0.83 (0.36), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A2127 
 TYR   0.010   0.001   TYR A2590 
 PHE   0.014   0.001   PHE A2018 
 TRP   0.009   0.001   TRP A2053 
 HIS   0.006   0.001   HIS A1473 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 ( 9390)
  covalent geometry    : angle       0.47139 (12724)
  hydrogen bonds       : bond        0.04909 (  619)
  hydrogen bonds       : angle       4.26159 ( 1785)

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 70
  time to evaluate  : 0.523 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1442 ASN cc_start: 0.6887 (m110) cc_final: 0.6526 (t0)
REVERT: A 2016 VAL cc_start: 0.7372 (OUTLIER) cc_final: 0.7138 (m)
REVERT: A 2217 ARG cc_start: 0.8129 (ttm170) cc_final: 0.7859 (ttm170)
REVERT: A 2259 PHE cc_start: 0.7334 (OUTLIER) cc_final: 0.6825 (t80)
REVERT: A 2456 ASP cc_start: 0.6973 (t0) cc_final: 0.6636 (t0)
REVERT: A 2485 LYS cc_start: 0.7399 (mtmt) cc_final: 0.6830 (pttt)
REVERT: A 2502 ARG cc_start: 0.6318 (mtm-85) cc_final: 0.5947 (mtt90)
  outliers start: 12
  outliers final: 4
  residues processed: 75
  average time/residue: 0.9381
  time to fit residues: 77.5704
Evaluate side-chains
  70 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 64
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1643 SER
Chi-restraints excluded: chain A residue 1660 VAL
Chi-restraints excluded: chain A residue 2016 VAL
Chi-restraints excluded: chain A residue 2206 SER
Chi-restraints excluded: chain A residue 2259 PHE
Chi-restraints excluded: chain A residue 2486 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 53 optimal weight:   20.0000
   chunk 79 optimal weight:    0.8980
   chunk 102 optimal weight:   10.0000
   chunk 65 optimal weight:    2.9990
   chunk 43 optimal weight:    6.9990
   chunk 111 optimal weight:   10.0000
   chunk 67 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 36 optimal weight:    6.9990
   chunk 14 optimal weight:    3.9990
   chunk 68 optimal weight:    2.9990
   overall best weight:    2.3788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4376 r_free = 0.4376 target = 0.200855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.133576 restraints weight = 33271.387|
|-----------------------------------------------------------------------------|
r_work (start): 0.3609 rms_B_bonded: 2.21
r_work: 0.3513 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3396 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.3396
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7930
moved from start:          0.3466

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   9390  Z= 0.212
  Angle     :  0.557   5.466  12724  Z= 0.310
  Chirality :  0.041   0.153   1480
  Planarity :  0.004   0.048   1584
  Dihedral  :  5.880  56.335   1277
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 3.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  :  8.61 %
    Favored  : 89.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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 aren not related in a simple way.
  whole:  1.51 (0.25), residues: 1144
  helix:  1.30 (0.18), residues: 760
  sheet:  0.52 (0.58), residues: 85
  loop :  0.63 (0.36), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A2509 
 TYR   0.012   0.002   TYR A1383 
 PHE   0.024   0.002   PHE A1672 
 TRP   0.012   0.002   TRP A2053 
 HIS   0.015   0.002   HIS A1473 

Details of bonding type rmsd
  covalent geometry    : bond        0.00497 ( 9390)
  covalent geometry    : angle       0.55702 (12724)
  hydrogen bonds       : bond        0.05847 (  619)
  hydrogen bonds       : angle       4.48477 ( 1785)

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 70
  time to evaluate  : 0.510 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1442 ASN cc_start: 0.6907 (m110) cc_final: 0.6664 (t0)
REVERT: A 1704 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7541 (mtm180)
REVERT: A 2016 VAL cc_start: 0.7414 (OUTLIER) cc_final: 0.7170 (m)
REVERT: A 2217 ARG cc_start: 0.8213 (ttm170) cc_final: 0.7969 (ttm170)
REVERT: A 2259 PHE cc_start: 0.7350 (OUTLIER) cc_final: 0.6866 (t80)
REVERT: A 2485 LYS cc_start: 0.7369 (mtmt) cc_final: 0.6780 (pttt)
REVERT: A 2502 ARG cc_start: 0.6544 (mtm-85) cc_final: 0.6180 (mtt90)
  outliers start: 17
  outliers final: 6
  residues processed: 80
  average time/residue: 1.0631
  time to fit residues: 93.0533
Evaluate side-chains
  76 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 67
  time to evaluate  : 0.500 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1643 SER
Chi-restraints excluded: chain A residue 1660 VAL
Chi-restraints excluded: chain A residue 1704 ARG
Chi-restraints excluded: chain A residue 2016 VAL
Chi-restraints excluded: chain A residue 2154 ASP
Chi-restraints excluded: chain A residue 2206 SER
Chi-restraints excluded: chain A residue 2259 PHE
Chi-restraints excluded: chain A residue 2445 VAL
Chi-restraints excluded: chain A residue 2486 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9990
   chunk 61 optimal weight:    2.9990
   chunk 97 optimal weight:    0.8980
   chunk 49 optimal weight:   20.0000
   chunk 36 optimal weight:   20.0000
   chunk 51 optimal weight:    6.9990
   chunk 78 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 104 optimal weight:    0.7980
   chunk 13 optimal weight:    1.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
A2442 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4393 r_free = 0.4393 target = 0.202731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.135956 restraints weight = 33220.499|
|-----------------------------------------------------------------------------|
r_work (start): 0.3624 rms_B_bonded: 2.23
r_work: 0.3528 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3414 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.3414
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
moved from start:          0.3657

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9390  Z= 0.135
  Angle     :  0.482   5.787  12724  Z= 0.263
  Chirality :  0.038   0.140   1480
  Planarity :  0.004   0.045   1584
  Dihedral  :  4.787  39.460   1277
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 3.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  :  8.91 %
    Favored  : 89.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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 aren not related in a simple way.
  whole:  1.83 (0.25), residues: 1144
  helix:  1.60 (0.19), residues: 757
  sheet:  0.57 (0.58), residues: 85
  loop :  0.61 (0.36), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A2127 
 TYR   0.008   0.001   TYR A2305 
 PHE   0.016   0.002   PHE A2018 
 TRP   0.012   0.001   TRP A2053 
 HIS   0.008   0.001   HIS A1473 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 9390)
  covalent geometry    : angle       0.48213 (12724)
  hydrogen bonds       : bond        0.05040 (  619)
  hydrogen bonds       : angle       4.23828 ( 1785)

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 71
  time to evaluate  : 0.426 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1442 ASN cc_start: 0.6804 (m110) cc_final: 0.6519 (t0)
REVERT: A 1698 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7829 (mm-30)
REVERT: A 1704 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7448 (mtm180)
REVERT: A 2016 VAL cc_start: 0.7334 (OUTLIER) cc_final: 0.7087 (m)
REVERT: A 2217 ARG cc_start: 0.8134 (ttm170) cc_final: 0.7875 (ttm170)
REVERT: A 2229 GLN cc_start: 0.7168 (mp10) cc_final: 0.6791 (mp10)
REVERT: A 2259 PHE cc_start: 0.7228 (OUTLIER) cc_final: 0.6745 (t80)
REVERT: A 2456 ASP cc_start: 0.7075 (t0) cc_final: 0.6663 (t0)
REVERT: A 2485 LYS cc_start: 0.7298 (mtmt) cc_final: 0.6721 (pttt)
REVERT: A 2502 ARG cc_start: 0.6412 (mtm-85) cc_final: 0.6118 (mtt90)
  outliers start: 14
  outliers final: 3
  residues processed: 77
  average time/residue: 1.1917
  time to fit residues: 99.5533
Evaluate side-chains
  72 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 66
  time to evaluate  : 0.489 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1643 SER
Chi-restraints excluded: chain A residue 1704 ARG
Chi-restraints excluded: chain A residue 2016 VAL
Chi-restraints excluded: chain A residue 2206 SER
Chi-restraints excluded: chain A residue 2259 PHE
Chi-restraints excluded: chain A residue 2445 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 66 optimal weight:    0.6980
   chunk 92 optimal weight:    6.9990
   chunk 55 optimal weight:   10.0000
   chunk 37 optimal weight:    8.9990
   chunk 64 optimal weight:    1.9990
   chunk 97 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 49 optimal weight:    7.9990
   chunk 70 optimal weight:    1.9990
   chunk 40 optimal weight:    0.4980
   chunk 85 optimal weight:    0.9980
   overall best weight:    1.2384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4393 r_free = 0.4393 target = 0.202818 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.135849 restraints weight = 33521.034|
|-----------------------------------------------------------------------------|
r_work (start): 0.3625 rms_B_bonded: 2.22
r_work: 0.3530 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3416 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.3416
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
moved from start:          0.3827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9390  Z= 0.132
  Angle     :  0.474   6.146  12724  Z= 0.258
  Chirality :  0.037   0.140   1480
  Planarity :  0.004   0.042   1584
  Dihedral  :  4.642  37.021   1277
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 3.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  :  9.51 %
    Favored  : 89.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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 aren not related in a simple way.
  whole:  1.97 (0.25), residues: 1144
  helix:  1.72 (0.19), residues: 759
  sheet:  0.57 (0.59), residues: 85
  loop :  0.68 (0.37), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A2127 
 TYR   0.008   0.001   TYR A2057 
 PHE   0.017   0.001   PHE A1672 
 TRP   0.011   0.001   TRP A2053 
 HIS   0.008   0.001   HIS A1473 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 9390)
  covalent geometry    : angle       0.47392 (12724)
  hydrogen bonds       : bond        0.04877 (  619)
  hydrogen bonds       : angle       4.15601 ( 1785)

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 68
  time to evaluate  : 0.512 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1442 ASN cc_start: 0.6785 (m110) cc_final: 0.6492 (t0)
REVERT: A 1698 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7786 (mm-30)
REVERT: A 1704 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.7406 (mtm180)
REVERT: A 2016 VAL cc_start: 0.7393 (OUTLIER) cc_final: 0.7145 (m)
REVERT: A 2217 ARG cc_start: 0.8120 (ttm170) cc_final: 0.7684 (ttm170)
REVERT: A 2229 GLN cc_start: 0.7221 (mp10) cc_final: 0.6851 (mp10)
REVERT: A 2259 PHE cc_start: 0.7189 (OUTLIER) cc_final: 0.6679 (t80)
REVERT: A 2456 ASP cc_start: 0.7057 (t0) cc_final: 0.6660 (t0)
REVERT: A 2485 LYS cc_start: 0.7266 (mtmt) cc_final: 0.6713 (pttt)
  outliers start: 12
  outliers final: 3
  residues processed: 74
  average time/residue: 1.1368
  time to fit residues: 91.7883
Evaluate side-chains
  71 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 65
  time to evaluate  : 0.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1643 SER
Chi-restraints excluded: chain A residue 1704 ARG
Chi-restraints excluded: chain A residue 2016 VAL
Chi-restraints excluded: chain A residue 2206 SER
Chi-restraints excluded: chain A residue 2259 PHE
Chi-restraints excluded: chain A residue 2445 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 2 optimal weight:    2.9990
   chunk 105 optimal weight:    5.9990
   chunk 50 optimal weight:    3.9990
   chunk 94 optimal weight:    0.9990
   chunk 64 optimal weight:    1.9990
   chunk 53 optimal weight:   10.0000
   chunk 14 optimal weight:    2.9990
   chunk 112 optimal weight:    9.9990
   chunk 87 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 37 optimal weight:   20.0000
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
A1664 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4370 r_free = 0.4370 target = 0.200460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.133246 restraints weight = 33307.433|
|-----------------------------------------------------------------------------|
r_work (start): 0.3608 rms_B_bonded: 2.22
r_work: 0.3506 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3389 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7954
moved from start:          0.3925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   9390  Z= 0.207
  Angle     :  0.533   6.201  12724  Z= 0.294
  Chirality :  0.040   0.148   1480
  Planarity :  0.004   0.047   1584
  Dihedral  :  4.931  40.990   1277
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 3.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  :  9.61 %
    Favored  : 88.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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 aren not related in a simple way.
  whole:  1.44 (0.25), residues: 1144
  helix:  1.30 (0.18), residues: 766
  sheet:  0.59 (0.58), residues: 85
  loop :  0.38 (0.37), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A2271 
 TYR   0.012   0.002   TYR A1383 
 PHE   0.021   0.002   PHE A1672 
 TRP   0.012   0.002   TRP A2053 
 HIS   0.013   0.002   HIS A1473 

Details of bonding type rmsd
  covalent geometry    : bond        0.00487 ( 9390)
  covalent geometry    : angle       0.53349 (12724)
  hydrogen bonds       : bond        0.05607 (  619)
  hydrogen bonds       : angle       4.37599 ( 1785)

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 71
  time to evaluate  : 0.531 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1442 ASN cc_start: 0.6924 (m110) cc_final: 0.6709 (t0)
REVERT: A 1704 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7506 (mtm180)
REVERT: A 2016 VAL cc_start: 0.7494 (OUTLIER) cc_final: 0.7218 (m)
REVERT: A 2217 ARG cc_start: 0.8248 (ttm170) cc_final: 0.7827 (ttm170)
REVERT: A 2229 GLN cc_start: 0.7334 (mp10) cc_final: 0.6908 (mp10)
REVERT: A 2259 PHE cc_start: 0.7302 (OUTLIER) cc_final: 0.6783 (t80)
REVERT: A 2502 ARG cc_start: 0.6467 (mtm-85) cc_final: 0.6226 (mtt90)
  outliers start: 14
  outliers final: 5
  residues processed: 79
  average time/residue: 1.1561
  time to fit residues: 99.6964
Evaluate side-chains
  74 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 66
  time to evaluate  : 0.495 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1643 SER
Chi-restraints excluded: chain A residue 1660 VAL
Chi-restraints excluded: chain A residue 1704 ARG
Chi-restraints excluded: chain A residue 2016 VAL
Chi-restraints excluded: chain A residue 2206 SER
Chi-restraints excluded: chain A residue 2259 PHE
Chi-restraints excluded: chain A residue 2445 VAL
Chi-restraints excluded: chain A residue 2486 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 57 optimal weight:    0.4980
   chunk 104 optimal weight:    4.9990
   chunk 98 optimal weight:    4.9990
   chunk 100 optimal weight:    0.9990
   chunk 23 optimal weight:    1.9990
   chunk 53 optimal weight:    5.9990
   chunk 93 optimal weight:    5.9990
   chunk 3 optimal weight:    0.0870
   chunk 28 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 95 optimal weight:    2.9990
   overall best weight:    0.8762

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4410 r_free = 0.4410 target = 0.203359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.146873 restraints weight = 33684.996|
|-----------------------------------------------------------------------------|
r_work (start): 0.3766 rms_B_bonded: 2.31
r_work: 0.3534 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3420 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.3420
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.4053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   9390  Z= 0.114
  Angle     :  0.464   6.276  12724  Z= 0.251
  Chirality :  0.037   0.136   1480
  Planarity :  0.003   0.043   1584
  Dihedral  :  4.577  36.330   1277
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 3.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  : 11.11 %
    Favored  : 87.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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 aren not related in a simple way.
  whole:  1.98 (0.25), residues: 1144
  helix:  1.72 (0.19), residues: 760
  sheet:  0.63 (0.58), residues: 85
  loop :  0.67 (0.37), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A2271 
 TYR   0.007   0.001   TYR A1609 
 PHE   0.016   0.001   PHE A2018 
 TRP   0.012   0.001   TRP A2053 
 HIS   0.007   0.001   HIS A1473 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 9390)
  covalent geometry    : angle       0.46430 (12724)
  hydrogen bonds       : bond        0.04724 (  619)
  hydrogen bonds       : angle       4.10280 ( 1785)

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 65
  time to evaluate  : 0.532 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1442 ASN cc_start: 0.6760 (m110) cc_final: 0.6523 (t0)
REVERT: A 1704 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7532 (mtm180)
REVERT: A 2016 VAL cc_start: 0.7524 (OUTLIER) cc_final: 0.7257 (m)
REVERT: A 2217 ARG cc_start: 0.8187 (ttm170) cc_final: 0.7759 (ttm170)
REVERT: A 2229 GLN cc_start: 0.7373 (mp10) cc_final: 0.7025 (mp10)
REVERT: A 2234 ILE cc_start: 0.6710 (pt) cc_final: 0.6323 (tt)
REVERT: A 2259 PHE cc_start: 0.7242 (OUTLIER) cc_final: 0.6739 (t80)
REVERT: A 2456 ASP cc_start: 0.7106 (t0) cc_final: 0.6714 (t0)
  outliers start: 9
  outliers final: 4
  residues processed: 70
  average time/residue: 1.1224
  time to fit residues: 86.1808
Evaluate side-chains
  70 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 63
  time to evaluate  : 0.499 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1643 SER
Chi-restraints excluded: chain A residue 1704 ARG
Chi-restraints excluded: chain A residue 2016 VAL
Chi-restraints excluded: chain A residue 2206 SER
Chi-restraints excluded: chain A residue 2259 PHE
Chi-restraints excluded: chain A residue 2445 VAL
Chi-restraints excluded: chain A residue 2486 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 72 optimal weight:    0.0980
   chunk 38 optimal weight:    0.9980
   chunk 62 optimal weight:    1.9990
   chunk 88 optimal weight:    0.1980
   chunk 32 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 84 optimal weight:    1.9990
   chunk 97 optimal weight:    1.9990
   chunk 94 optimal weight:    0.8980
   chunk 2 optimal weight:    1.9990
   overall best weight:    0.6382

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

Flipped N/Q/H residues before XYZ refinement:
A1429 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4424 r_free = 0.4424 target = 0.204838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.149032 restraints weight = 33444.765|
|-----------------------------------------------------------------------------|
r_work (start): 0.3788 rms_B_bonded: 2.34
r_work: 0.3572 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3463 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.3463
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7850
moved from start:          0.4230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   9390  Z= 0.102
  Angle     :  0.442   6.904  12724  Z= 0.237
  Chirality :  0.037   0.135   1480
  Planarity :  0.003   0.041   1584
  Dihedral  :  4.256  31.132   1277
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 3.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  0.50 %
    Allowed  : 11.61 %
    Favored  : 87.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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 aren not related in a simple way.
  whole:  2.34 (0.25), residues: 1144
  helix:  2.02 (0.19), residues: 759
  sheet:  0.64 (0.58), residues: 85
  loop :  0.76 (0.37), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A2502 
 TYR   0.006   0.001   TYR A2057 
 PHE   0.016   0.001   PHE A2018 
 TRP   0.010   0.001   TRP A2053 
 HIS   0.005   0.001   HIS A1473 

Details of bonding type rmsd
  covalent geometry    : bond        0.00213 ( 9390)
  covalent geometry    : angle       0.44181 (12724)
  hydrogen bonds       : bond        0.04271 (  619)
  hydrogen bonds       : angle       3.91277 ( 1785)

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 68
  time to evaluate  : 0.529 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1442 ASN cc_start: 0.6759 (m110) cc_final: 0.6439 (t0)
REVERT: A 1698 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7409 (mm-30)
REVERT: A 2016 VAL cc_start: 0.7532 (OUTLIER) cc_final: 0.7275 (m)
REVERT: A 2217 ARG cc_start: 0.8142 (ttm170) cc_final: 0.7727 (ttm170)
REVERT: A 2456 ASP cc_start: 0.7084 (t0) cc_final: 0.6717 (t0)
  outliers start: 5
  outliers final: 2
  residues processed: 70
  average time/residue: 1.0539
  time to fit residues: 81.4762
Evaluate side-chains
  69 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 66
  time to evaluate  : 0.503 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 2016 VAL
Chi-restraints excluded: chain A residue 2206 SER
Chi-restraints excluded: chain A residue 2486 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 114 optimal weight:    0.4980
   chunk 79 optimal weight:    2.9990
   chunk 103 optimal weight:    5.9990
   chunk 83 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 113 optimal weight:    8.9990
   chunk 62 optimal weight:    2.9990
   chunk 42 optimal weight:    9.9990
   chunk 59 optimal weight:    0.7980
   chunk 33 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   overall best weight:    1.6586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4402 r_free = 0.4402 target = 0.202559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.136760 restraints weight = 33685.115|
|-----------------------------------------------------------------------------|
r_work (start): 0.3644 rms_B_bonded: 2.20
r_work: 0.3531 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3414 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.3414
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7998
moved from start:          0.4221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9390  Z= 0.155
  Angle     :  0.480   6.008  12724  Z= 0.261
  Chirality :  0.038   0.143   1480
  Planarity :  0.004   0.043   1584
  Dihedral  :  4.500  39.777   1277
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 3.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  : 11.71 %
    Favored  : 87.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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 aren not related in a simple way.
  whole:  1.93 (0.25), residues: 1144
  helix:  1.70 (0.19), residues: 768
  sheet:  0.70 (0.57), residues: 85
  loop :  0.52 (0.37), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1582 
 TYR   0.009   0.001   TYR A2305 
 PHE   0.020   0.002   PHE A1672 
 TRP   0.011   0.001   TRP A2053 
 HIS   0.011   0.001   HIS A1473 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 9390)
  covalent geometry    : angle       0.47955 (12724)
  hydrogen bonds       : bond        0.04844 (  619)
  hydrogen bonds       : angle       4.07895 ( 1785)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6988.32 seconds
wall clock time: 118 minutes 58.37 seconds (7138.37 seconds total)