Starting phenix.real_space_refine
on Mon May 19 21:59:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sxb_40830/05_2025/8sxb_40830_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sxb_40830/05_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sxb_40830/05_2025/8sxb_40830.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sxb_40830/05_2025/8sxb_40830.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sxb_40830/05_2025/8sxb_40830_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sxb_40830/05_2025/8sxb_40830_trim.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 8.88, per 1000 atoms: 0.48
  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: 5.14
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  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: 1.52
  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: 7.59

  Time building geometry restraints manager: 6.08 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:             1.420
  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:             0.320
  Extract box with map and model:          0.750
  Check model and map are aligned:         0.130
  Set scattering table:                    0.180
  Process input model:                     41.740
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.060
  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:12.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   56.990
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.029   0.005   TRP A2054 
 HIS   0.025   0.003   HIS A1473 
 PHE   0.020   0.003   PHE A1805 
 TYR   0.027   0.006   TYR A1412 
 ARG   0.025   0.002   ARG A1670 

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

*********************** 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  : 1.394 
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 1632 ARG cc_start: 0.7530 (mtt-85) cc_final: 0.7013 (mmt180)
REVERT: A 2451 MET cc_start: 0.7417 (tpt) cc_final: 0.7205 (mmm)
REVERT: A 2542 LYS cc_start: 0.7886 (mmmt) cc_final: 0.7682 (mmmt)
  outliers start: 0
  outliers final: 0
  residues processed: 143
  average time/residue: 2.5311
  time to fit residues: 388.9268
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  : 1.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 97 optimal weight:    0.9980
   chunk 87 optimal weight:    3.9990
   chunk 48 optimal weight:    9.9990
   chunk 29 optimal weight:    0.9980
   chunk 58 optimal weight:    0.9980
   chunk 46 optimal weight:   20.0000
   chunk 90 optimal weight:    5.9990
   chunk 34 optimal weight:    2.9990
   chunk 54 optimal weight:    0.0370
   chunk 67 optimal weight:    1.9990
   chunk 104 optimal weight:    1.9990
   overall best weight:    1.0060

-------------------------------------------------------------------------------
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 = 0.4445 r_free = 0.4445 target = 0.206325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.140536 restraints weight = 33085.394|
|-----------------------------------------------------------------------------|
r_work (start): 0.3669 rms_B_bonded: 2.17
r_work: 0.3557 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3444 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
moved from start:          0.2163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   9390  Z= 0.158
  Angle     :  0.596   4.935  12724  Z= 0.336
  Chirality :  0.040   0.153   1480
  Planarity :  0.005   0.066   1584
  Dihedral  :  5.626  51.030   1277
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 2.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  :  7.01 %
    Favored  : 91.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.90 (0.24), residues: 1144
  helix:  0.77 (0.18), residues: 756
  sheet:  0.24 (0.56), residues: 78
  loop :  0.60 (0.35), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A2053 
 HIS   0.008   0.001   HIS A1473 
 PHE   0.014   0.002   PHE A1672 
 TYR   0.015   0.002   TYR A2590 
 ARG   0.007   0.000   ARG A2502 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06729 (  619)
  hydrogen bonds       : angle       5.02145 ( 1785)
  covalent geometry    : bond        0.00324 ( 9390)
  covalent geometry    : angle       0.59566 (12724)

*********************** 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
  97 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 86
  time to evaluate  : 1.309 
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 1632 ARG cc_start: 0.7545 (mtt-85) cc_final: 0.6636 (mmt180)
REVERT: A 2259 PHE cc_start: 0.7148 (OUTLIER) cc_final: 0.6807 (t80)
REVERT: A 2402 SER cc_start: 0.7991 (OUTLIER) cc_final: 0.7775 (p)
REVERT: A 2485 LYS cc_start: 0.7574 (mtmt) cc_final: 0.6965 (pttt)
REVERT: A 2502 ARG cc_start: 0.6523 (mtm-85) cc_final: 0.6071 (mtt90)
  outliers start: 11
  outliers final: 3
  residues processed: 89
  average time/residue: 2.3208
  time to fit residues: 224.0784
Evaluate side-chains
  74 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 69
  time to evaluate  : 1.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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
Chi-restraints excluded: chain A residue 2503 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 77 optimal weight:    4.9990
   chunk 95 optimal weight:    1.9990
   chunk 52 optimal weight:   10.0000
   chunk 19 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 100 optimal weight:    6.9990
   chunk 17 optimal weight:    0.8980
   chunk 73 optimal weight:    3.9990
   chunk 38 optimal weight:    6.9990
   chunk 68 optimal weight:    2.9990
   chunk 30 optimal weight:    0.6980
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
A1513 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4417 r_free = 0.4417 target = 0.203961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.137610 restraints weight = 33317.944|
|-----------------------------------------------------------------------------|
r_work (start): 0.3660 rms_B_bonded: 2.19
r_work: 0.3543 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3424 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.3424
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
moved from start:          0.2936

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= 0.170
  Angle     :  0.548   6.052  12724  Z= 0.303
  Chirality :  0.040   0.140   1480
  Planarity :  0.005   0.100   1584
  Dihedral  :  5.319  35.990   1277
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 2.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  :  7.61 %
    Favored  : 90.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.44 (0.24), residues: 1144
  helix:  1.24 (0.18), residues: 762
  sheet:  0.25 (0.53), residues: 83
  loop :  0.73 (0.36), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A2053 
 HIS   0.013   0.002   HIS A1473 
 PHE   0.025   0.002   PHE A1672 
 TYR   0.011   0.002   TYR A2305 
 ARG   0.006   0.001   ARG A2502 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05720 (  619)
  hydrogen bonds       : angle       4.56608 ( 1785)
  covalent geometry    : bond        0.00386 ( 9390)
  covalent geometry    : angle       0.54815 (12724)

*********************** 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
  98 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 81
  time to evaluate  : 1.504 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1442 ASN cc_start: 0.7001 (m110) cc_final: 0.6655 (t0)
REVERT: A 2016 VAL cc_start: 0.7362 (OUTLIER) cc_final: 0.7133 (m)
REVERT: A 2259 PHE cc_start: 0.7435 (OUTLIER) cc_final: 0.6963 (t80)
REVERT: A 2485 LYS cc_start: 0.7489 (mtmt) cc_final: 0.6875 (pttt)
REVERT: A 2502 ARG cc_start: 0.6449 (mtm-85) cc_final: 0.5904 (mtt90)
  outliers start: 17
  outliers final: 7
  residues processed: 88
  average time/residue: 1.9249
  time to fit residues: 186.9031
Evaluate side-chains
  77 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 68
  time to evaluate  : 1.356 
-------------------------------------------------------------------------------
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 2384 LEU
Chi-restraints excluded: chain A residue 2415 GLU
Chi-restraints excluded: chain A residue 2486 MET
Chi-restraints excluded: chain A residue 2503 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 66 optimal weight:    1.9990
   chunk 93 optimal weight:    6.9990
   chunk 48 optimal weight:   10.0000
   chunk 61 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9980
   chunk 53 optimal weight:   20.0000
   chunk 71 optimal weight:    0.9990
   chunk 40 optimal weight:    9.9990
   chunk 22 optimal weight:    1.9990
   chunk 55 optimal weight:    8.9990
   chunk 100 optimal weight:    6.9990
   overall best weight:    1.5988

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4417 r_free = 0.4417 target = 0.203989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.137633 restraints weight = 33182.768|
|-----------------------------------------------------------------------------|
r_work (start): 0.3661 rms_B_bonded: 2.16
r_work: 0.3545 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3430 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.3430
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8006
moved from start:          0.3205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9390  Z= 0.156
  Angle     :  0.512   4.870  12724  Z= 0.283
  Chirality :  0.039   0.136   1480
  Planarity :  0.004   0.046   1584
  Dihedral  :  5.232  39.848   1277
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 2.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  :  8.81 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.68 (0.25), residues: 1144
  helix:  1.42 (0.19), residues: 762
  sheet:  0.41 (0.55), residues: 85
  loop :  0.79 (0.37), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A2053 
 HIS   0.009   0.001   HIS A1473 
 PHE   0.018   0.002   PHE A1672 
 TYR   0.010   0.001   TYR A2590 
 ARG   0.005   0.000   ARG A2127 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05444 (  619)
  hydrogen bonds       : angle       4.42352 ( 1785)
  covalent geometry    : bond        0.00349 ( 9390)
  covalent geometry    : angle       0.51179 (12724)

*********************** 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
  84 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 69
  time to evaluate  : 1.324 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1442 ASN cc_start: 0.6947 (m110) cc_final: 0.6628 (t0)
REVERT: A 1704 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7605 (mtm180)
REVERT: A 2016 VAL cc_start: 0.7438 (OUTLIER) cc_final: 0.7197 (m)
REVERT: A 2217 ARG cc_start: 0.8256 (ttm170) cc_final: 0.7975 (ttm170)
REVERT: A 2259 PHE cc_start: 0.7426 (OUTLIER) cc_final: 0.6964 (t80)
REVERT: A 2485 LYS cc_start: 0.7398 (mtmt) cc_final: 0.6832 (pttt)
REVERT: A 2502 ARG cc_start: 0.6546 (mtm-85) cc_final: 0.6112 (mtt90)
  outliers start: 15
  outliers final: 7
  residues processed: 77
  average time/residue: 1.9603
  time to fit residues: 166.7678
Evaluate side-chains
  76 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 66
  time to evaluate  : 1.985 
-------------------------------------------------------------------------------
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 2298 GLN
Chi-restraints excluded: chain A residue 2384 LEU
Chi-restraints excluded: chain A residue 2486 MET
Chi-restraints excluded: chain A residue 2503 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 2 optimal weight:    2.9990
   chunk 105 optimal weight:    0.6980
   chunk 9 optimal weight:    2.9990
   chunk 90 optimal weight:    2.9990
   chunk 69 optimal weight:    0.9990
   chunk 85 optimal weight:    0.8980
   chunk 6 optimal weight:    0.8980
   chunk 54 optimal weight:   20.0000
   chunk 46 optimal weight:   10.0000
   chunk 8 optimal weight:    0.8980
   chunk 30 optimal weight:    1.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4434 r_free = 0.4434 target = 0.205720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.139937 restraints weight = 33356.701|
|-----------------------------------------------------------------------------|
r_work (start): 0.3684 rms_B_bonded: 2.17
r_work: 0.3573 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3456 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.3456
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7947
moved from start:          0.3513

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= 0.114
  Angle     :  0.466   5.510  12724  Z= 0.253
  Chirality :  0.037   0.143   1480
  Planarity :  0.004   0.040   1584
  Dihedral  :  4.669  37.544   1277
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 3.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  :  8.71 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.02 (0.25), residues: 1144
  helix:  1.75 (0.19), residues: 759
  sheet:  0.41 (0.57), residues: 85
  loop :  0.76 (0.36), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A2053 
 HIS   0.006   0.001   HIS A1472 
 PHE   0.017   0.001   PHE A2018 
 TYR   0.008   0.001   TYR A1609 
 ARG   0.002   0.000   ARG A2502 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04713 (  619)
  hydrogen bonds       : angle       4.14236 ( 1785)
  covalent geometry    : bond        0.00240 ( 9390)
  covalent geometry    : angle       0.46550 (12724)

*********************** 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
  88 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 72
  time to evaluate  : 1.492 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1442 ASN cc_start: 0.6872 (m110) cc_final: 0.6531 (t0)
REVERT: A 1704 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7564 (mtm110)
REVERT: A 2016 VAL cc_start: 0.7391 (OUTLIER) cc_final: 0.7147 (m)
REVERT: A 2217 ARG cc_start: 0.8213 (ttm170) cc_final: 0.7976 (ttm170)
REVERT: A 2259 PHE cc_start: 0.7344 (OUTLIER) cc_final: 0.6826 (t80)
REVERT: A 2456 ASP cc_start: 0.7103 (t0) cc_final: 0.6730 (t0)
REVERT: A 2485 LYS cc_start: 0.7293 (mtmt) cc_final: 0.6746 (pttt)
REVERT: A 2502 ARG cc_start: 0.6446 (mtm-85) cc_final: 0.6152 (mtt90)
  outliers start: 16
  outliers final: 2
  residues processed: 80
  average time/residue: 1.8718
  time to fit residues: 166.5183
Evaluate side-chains
  70 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 65
  time to evaluate  : 1.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 2503 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 52 optimal weight:   10.0000
   chunk 71 optimal weight:    1.9990
   chunk 45 optimal weight:    8.9990
   chunk 103 optimal weight:    0.9980
   chunk 95 optimal weight:    4.9990
   chunk 90 optimal weight:    5.9990
   chunk 82 optimal weight:    1.9990
   chunk 4 optimal weight:    0.8980
   chunk 38 optimal weight:    0.8980
   chunk 21 optimal weight:    2.9990
   chunk 83 optimal weight:    0.9980
   overall best weight:    1.1582

-------------------------------------------------------------------------------
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 = 0.4408 r_free = 0.4408 target = 0.204027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.137411 restraints weight = 33486.060|
|-----------------------------------------------------------------------------|
r_work (start): 0.3651 rms_B_bonded: 2.22
r_work: 0.3557 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3437 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.3437
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7849
moved from start:          0.3648

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9390  Z= 0.128
  Angle     :  0.472   5.695  12724  Z= 0.257
  Chirality :  0.037   0.139   1480
  Planarity :  0.004   0.040   1584
  Dihedral  :  4.689  38.491   1277
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 3.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  :  9.11 %
    Favored  : 89.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.10 (0.25), residues: 1144
  helix:  1.80 (0.19), residues: 759
  sheet:  0.53 (0.59), residues: 85
  loop :  0.80 (0.37), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A2053 
 HIS   0.008   0.001   HIS A1473 
 PHE   0.016   0.001   PHE A2018 
 TYR   0.008   0.001   TYR A2057 
 ARG   0.002   0.000   ARG A2127 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04797 (  619)
  hydrogen bonds       : angle       4.13309 ( 1785)
  covalent geometry    : bond        0.00280 ( 9390)
  covalent geometry    : angle       0.47186 (12724)

*********************** 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
  81 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 68
  time to evaluate  : 1.342 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1442 ASN cc_start: 0.6833 (m110) cc_final: 0.6494 (t0)
REVERT: A 1704 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7460 (mtm180)
REVERT: A 2016 VAL cc_start: 0.7296 (OUTLIER) cc_final: 0.7046 (m)
REVERT: A 2217 ARG cc_start: 0.8167 (ttm170) cc_final: 0.7930 (ttm170)
REVERT: A 2229 GLN cc_start: 0.7148 (mp10) cc_final: 0.6738 (mp10)
REVERT: A 2259 PHE cc_start: 0.7302 (OUTLIER) cc_final: 0.6776 (t80)
REVERT: A 2456 ASP cc_start: 0.7030 (t0) cc_final: 0.6644 (t0)
REVERT: A 2485 LYS cc_start: 0.7275 (mtmt) cc_final: 0.6726 (pttt)
REVERT: A 2502 ARG cc_start: 0.6355 (mtm-85) cc_final: 0.6071 (mtt90)
  outliers start: 13
  outliers final: 5
  residues processed: 76
  average time/residue: 2.0559
  time to fit residues: 172.0828
Evaluate side-chains
  72 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 64
  time to evaluate  : 1.329 
-------------------------------------------------------------------------------
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 2384 LEU
Chi-restraints excluded: chain A residue 2486 MET
Chi-restraints excluded: chain A residue 2503 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 5 optimal weight:    0.9990
   chunk 61 optimal weight:    0.0970
   chunk 46 optimal weight:   10.0000
   chunk 17 optimal weight:    1.9990
   chunk 84 optimal weight:    1.9990
   chunk 85 optimal weight:    0.9980
   chunk 105 optimal weight:    5.9990
   chunk 41 optimal weight:    5.9990
   chunk 90 optimal weight:    5.9990
   chunk 2 optimal weight:    2.9990
   chunk 36 optimal weight:   20.0000
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4403 r_free = 0.4403 target = 0.203663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.137072 restraints weight = 33132.067|
|-----------------------------------------------------------------------------|
r_work (start): 0.3633 rms_B_bonded: 2.22
r_work: 0.3537 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3421 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.3421
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7793
moved from start:          0.3843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9390  Z= 0.128
  Angle     :  0.464   6.132  12724  Z= 0.253
  Chirality :  0.037   0.141   1480
  Planarity :  0.003   0.040   1584
  Dihedral  :  4.638  39.633   1277
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 3.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  :  9.41 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.12 (0.25), residues: 1144
  helix:  1.81 (0.19), residues: 763
  sheet:  0.52 (0.58), residues: 85
  loop :  0.83 (0.37), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A2053 
 HIS   0.009   0.001   HIS A1473 
 PHE   0.015   0.001   PHE A1672 
 TYR   0.008   0.001   TYR A2305 
 ARG   0.003   0.000   ARG A2127 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04741 (  619)
  hydrogen bonds       : angle       4.07573 ( 1785)
  covalent geometry    : bond        0.00281 ( 9390)
  covalent geometry    : angle       0.46447 (12724)

*********************** 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
  79 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 66
  time to evaluate  : 1.314 
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: 0.6813 (m110) cc_final: 0.6461 (t0)
REVERT: A 1704 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.7384 (mtm180)
REVERT: A 2016 VAL cc_start: 0.7337 (OUTLIER) cc_final: 0.7077 (m)
REVERT: A 2154 ASP cc_start: 0.7416 (OUTLIER) cc_final: 0.7211 (t70)
REVERT: A 2217 ARG cc_start: 0.8087 (ttm170) cc_final: 0.7842 (ttm170)
REVERT: A 2259 PHE cc_start: 0.7187 (OUTLIER) cc_final: 0.6663 (t80)
REVERT: A 2456 ASP cc_start: 0.7014 (t0) cc_final: 0.6630 (t0)
REVERT: A 2485 LYS cc_start: 0.7250 (mtmt) cc_final: 0.6707 (pttt)
  outliers start: 13
  outliers final: 3
  residues processed: 73
  average time/residue: 1.9845
  time to fit residues: 159.7463
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  : 1.316 
-------------------------------------------------------------------------------
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 2154 ASP
Chi-restraints excluded: chain A residue 2206 SER
Chi-restraints excluded: chain A residue 2259 PHE
Chi-restraints excluded: chain A residue 2503 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 49 optimal weight:   20.0000
   chunk 78 optimal weight:    3.9990
   chunk 1 optimal weight:    2.9990
   chunk 100 optimal weight:    7.9990
   chunk 47 optimal weight:   20.0000
   chunk 77 optimal weight:    0.9980
   chunk 50 optimal weight:    4.9990
   chunk 109 optimal weight:    8.9990
   chunk 87 optimal weight:    1.9990
   chunk 111 optimal weight:    4.9990
   chunk 88 optimal weight:    1.9990
   overall best weight:    2.3988

-------------------------------------------------------------------------------
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 = 0.4379 r_free = 0.4379 target = 0.201249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.134131 restraints weight = 33411.562|
|-----------------------------------------------------------------------------|
r_work (start): 0.3601 rms_B_bonded: 2.18
r_work: 0.3502 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3385 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.3385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
moved from start:          0.3900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   9390  Z= 0.202
  Angle     :  0.525   5.905  12724  Z= 0.289
  Chirality :  0.040   0.145   1480
  Planarity :  0.004   0.044   1584
  Dihedral  :  5.613  53.843   1277
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  :  9.91 %
    Favored  : 88.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.69 (0.25), residues: 1144
  helix:  1.46 (0.19), residues: 761
  sheet:  0.58 (0.58), residues: 85
  loop :  0.65 (0.37), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A2053 
 HIS   0.011   0.001   HIS A1473 
 PHE   0.020   0.002   PHE A1672 
 TYR   0.012   0.002   TYR A1383 
 ARG   0.003   0.001   ARG A1592 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05475 (  619)
  hydrogen bonds       : angle       4.29899 ( 1785)
  covalent geometry    : bond        0.00472 ( 9390)
  covalent geometry    : angle       0.52541 (12724)

*********************** 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
  83 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 68
  time to evaluate  : 1.339 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1442 ASN cc_start: 0.6845 (m110) cc_final: 0.6564 (t0)
REVERT: A 1704 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7404 (mtm180)
REVERT: A 2016 VAL cc_start: 0.7422 (OUTLIER) cc_final: 0.7155 (m)
REVERT: A 2154 ASP cc_start: 0.7507 (OUTLIER) cc_final: 0.7300 (t70)
REVERT: A 2217 ARG cc_start: 0.8108 (ttm170) cc_final: 0.7859 (ttm170)
REVERT: A 2229 GLN cc_start: 0.7312 (mp10) cc_final: 0.6927 (mp10)
REVERT: A 2259 PHE cc_start: 0.7314 (OUTLIER) cc_final: 0.6784 (t80)
REVERT: A 2456 ASP cc_start: 0.7070 (t0) cc_final: 0.6662 (t0)
REVERT: A 2485 LYS cc_start: 0.7259 (mtmt) cc_final: 0.6710 (pttt)
REVERT: A 2502 ARG cc_start: 0.6420 (mtm-85) cc_final: 0.6186 (mtt90)
  outliers start: 15
  outliers final: 6
  residues processed: 76
  average time/residue: 1.9712
  time to fit residues: 165.3212
Evaluate side-chains
  75 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 65
  time to evaluate  : 1.542 
-------------------------------------------------------------------------------
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 2154 ASP
Chi-restraints excluded: chain A residue 2206 SER
Chi-restraints excluded: chain A residue 2259 PHE
Chi-restraints excluded: chain A residue 2384 LEU
Chi-restraints excluded: chain A residue 2445 VAL
Chi-restraints excluded: chain A residue 2486 MET
Chi-restraints excluded: chain A residue 2503 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 46 optimal weight:   10.0000
   chunk 64 optimal weight:    0.9980
   chunk 39 optimal weight:   20.0000
   chunk 48 optimal weight:   10.0000
   chunk 80 optimal weight:    0.6980
   chunk 4 optimal weight:    1.9990
   chunk 105 optimal weight:    4.9990
   chunk 104 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 15 optimal weight:    0.5980
   chunk 78 optimal weight:    3.9990
   overall best weight:    1.2584

-------------------------------------------------------------------------------
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 = 0.4411 r_free = 0.4411 target = 0.203260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.145978 restraints weight = 33666.984|
|-----------------------------------------------------------------------------|
r_work (start): 0.3760 rms_B_bonded: 2.58
r_work: 0.3531 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3419 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.3419
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7956
moved from start:          0.4001

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= 0.131
  Angle     :  0.477   6.315  12724  Z= 0.258
  Chirality :  0.037   0.138   1480
  Planarity :  0.004   0.042   1584
  Dihedral  :  4.849  40.541   1277
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  : 10.81 %
    Favored  : 88.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.95 (0.25), residues: 1144
  helix:  1.67 (0.19), residues: 761
  sheet:  0.65 (0.58), residues: 85
  loop :  0.71 (0.37), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A2053 
 HIS   0.008   0.001   HIS A1473 
 PHE   0.016   0.001   PHE A2018 
 TYR   0.008   0.001   TYR A1609 
 ARG   0.004   0.000   ARG A2271 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04887 (  619)
  hydrogen bonds       : angle       4.13747 ( 1785)
  covalent geometry    : bond        0.00286 ( 9390)
  covalent geometry    : angle       0.47655 (12724)

*********************** 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  : 1.492 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1442 ASN cc_start: 0.6818 (m110) cc_final: 0.6558 (t0)
REVERT: A 1704 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.7556 (mtm180)
REVERT: A 2016 VAL cc_start: 0.7537 (OUTLIER) cc_final: 0.7263 (m)
REVERT: A 2217 ARG cc_start: 0.8191 (ttm170) cc_final: 0.7962 (ttm170)
REVERT: A 2229 GLN cc_start: 0.7421 (mp10) cc_final: 0.7072 (mp10)
REVERT: A 2234 ILE cc_start: 0.6808 (pt) cc_final: 0.6391 (tt)
REVERT: A 2259 PHE cc_start: 0.7278 (OUTLIER) cc_final: 0.6778 (t80)
REVERT: A 2456 ASP cc_start: 0.7121 (t0) cc_final: 0.6726 (t0)
REVERT: A 2485 LYS cc_start: 0.7252 (mtmt) cc_final: 0.6694 (pttt)
  outliers start: 9
  outliers final: 4
  residues processed: 70
  average time/residue: 1.9443
  time to fit residues: 151.3874
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  : 1.426 
-------------------------------------------------------------------------------
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 2486 MET
Chi-restraints excluded: chain A residue 2503 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 90 optimal weight:    0.8980
   chunk 39 optimal weight:   20.0000
   chunk 63 optimal weight:    1.9990
   chunk 41 optimal weight:    4.9990
   chunk 31 optimal weight:    2.9990
   chunk 3 optimal weight:    0.4980
   chunk 53 optimal weight:    9.9990
   chunk 95 optimal weight:    2.9990
   chunk 114 optimal weight:    5.9990
   chunk 110 optimal weight:   10.0000
   chunk 93 optimal weight:    2.9990
   overall best weight:    1.8786

-------------------------------------------------------------------------------
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 = 0.4399 r_free = 0.4399 target = 0.202028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.144633 restraints weight = 33626.165|
|-----------------------------------------------------------------------------|
r_work (start): 0.3743 rms_B_bonded: 2.53
r_work: 0.3512 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3401 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.3401
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7965
moved from start:          0.4047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9390  Z= 0.173
  Angle     :  0.504   5.863  12724  Z= 0.276
  Chirality :  0.039   0.142   1480
  Planarity :  0.004   0.044   1584
  Dihedral  :  4.739  39.250   1277
  Min Nonbonded Distance : 2.260

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 10.61 %
    Favored  : 88.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.56 (0.25), residues: 1144
  helix:  1.37 (0.18), residues: 780
  sheet:  0.63 (0.57), residues: 85
  loop :  0.47 (0.38), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A2053 
 HIS   0.011   0.001   HIS A1473 
 PHE   0.019   0.002   PHE A2018 
 TYR   0.009   0.001   TYR A1383 
 ARG   0.003   0.000   ARG A2271 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05202 (  619)
  hydrogen bonds       : angle       4.22344 ( 1785)
  covalent geometry    : bond        0.00398 ( 9390)
  covalent geometry    : angle       0.50414 (12724)

********************** 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: 10
    poor density    : 63
  time to evaluate  : 1.609 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1442 ASN cc_start: 0.6899 (m110) cc_final: 0.6607 (t0)
REVERT: A 1704 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7535 (mtm180)
REVERT: A 2016 VAL cc_start: 0.7595 (OUTLIER) cc_final: 0.7321 (m)
REVERT: A 2217 ARG cc_start: 0.8195 (ttm170) cc_final: 0.7965 (ttm170)
REVERT: A 2229 GLN cc_start: 0.7416 (mp10) cc_final: 0.7031 (mp10)
REVERT: A 2234 ILE cc_start: 0.6832 (pt) cc_final: 0.6447 (tt)
REVERT: A 2259 PHE cc_start: 0.7289 (OUTLIER) cc_final: 0.6767 (t80)
REVERT: A 2456 ASP cc_start: 0.7184 (t0) cc_final: 0.6785 (t0)
REVERT: A 2485 LYS cc_start: 0.7252 (mtmt) cc_final: 0.6684 (pttt)
  outliers start: 10
  outliers final: 5
  residues processed: 68
  average time/residue: 1.9022
  time to fit residues: 143.6413
Evaluate side-chains
  71 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 63
  time to evaluate  : 1.353 
-------------------------------------------------------------------------------
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
Chi-restraints excluded: chain A residue 2503 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 108 optimal weight:    8.9990
   chunk 19 optimal weight:    1.9990
   chunk 37 optimal weight:   20.0000
   chunk 16 optimal weight:    1.9990
   chunk 55 optimal weight:    4.9990
   chunk 2 optimal weight:    1.9990
   chunk 15 optimal weight:    0.5980
   chunk 71 optimal weight:    1.9990
   chunk 92 optimal weight:    0.9980
   chunk 91 optimal weight:    0.9990
   chunk 110 optimal weight:    0.9990
   overall best weight:    1.1186

-------------------------------------------------------------------------------
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 = 0.4414 r_free = 0.4414 target = 0.203517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.145352 restraints weight = 33507.996|
|-----------------------------------------------------------------------------|
r_work (start): 0.3748 rms_B_bonded: 3.41
r_work: 0.3538 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3419 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3419
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
moved from start:          0.4144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9390  Z= 0.125
  Angle     :  0.463   5.863  12724  Z= 0.250
  Chirality :  0.037   0.135   1480
  Planarity :  0.003   0.042   1584
  Dihedral  :  4.536  36.838   1277
  Min Nonbonded Distance : 2.306

Molprobity Statistics.
  All-atom Clashscore : 3.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 10.61 %
    Favored  : 88.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.90 (0.25), residues: 1144
  helix:  1.66 (0.19), residues: 774
  sheet:  0.63 (0.57), residues: 85
  loop :  0.56 (0.38), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A2053 
 HIS   0.008   0.001   HIS A1473 
 PHE   0.017   0.001   PHE A2018 
 TYR   0.007   0.001   TYR A2305 
 ARG   0.002   0.000   ARG A2271 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04700 (  619)
  hydrogen bonds       : angle       4.06150 ( 1785)
  covalent geometry    : bond        0.00275 ( 9390)
  covalent geometry    : angle       0.46282 (12724)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 12870.22 seconds
wall clock time: 220 minutes 30.11 seconds (13230.11 seconds total)