Starting phenix.real_space_refine
on Mon Oct 14 22:35:23 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxb_40830/10_2024/8sxb_40830_trim.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxb_40830/10_2024/8sxb_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxb_40830/10_2024/8sxb_40830.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxb_40830/10_2024/8sxb_40830.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxb_40830/10_2024/8sxb_40830_trim.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxb_40830/10_2024/8sxb_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-5477/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: 8.91, 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: 4.78
  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: 1.63
  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: 7.77

  Time building geometry restraints manager: 5.79 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:             1.920
  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:             0.330
  Extract box with map and model:          0.670
  Check model and map are aligned:         0.140
  Set scattering table:                    0.170
  Process input model:                     41.220
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.050
  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:11.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   56.530
-------------------------------------------------------------------------------
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= 0.367
  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 

*********************** 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 fitting.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 1.379 
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: 2.6523
  time to fit residues: 408.9883
Evaluate side-chains
  79 residues out of total 999 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 1.426 
-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7951
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= 0.206
  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 

*********************** 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 fitting.
    rotamer outliers: 11
    poor density    : 86
  time to evaluate  : 1.495 
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: 0.7396 (mtt-85) cc_final: 0.6879 (mmt180)
REVERT: A 2259 PHE cc_start: 0.7278 (OUTLIER) cc_final: 0.6924 (t80)
REVERT: A 2402 SER cc_start: 0.8107 (OUTLIER) cc_final: 0.7879 (p)
REVERT: A 2485 LYS cc_start: 0.7514 (mtmt) cc_final: 0.6952 (pttt)
REVERT: A 2502 ARG cc_start: 0.6718 (mtm-85) cc_final: 0.6271 (mtt90)
  outliers start: 11
  outliers final: 3
  residues processed: 89
  average time/residue: 2.3917
  time to fit residues: 232.1082
Evaluate side-chains
  74 residues out of total 999 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 69
  time to evaluate  : 1.362 
-------------------------------------------------------------------------------
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 58 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 86 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   chunk 104 optimal weight:    4.9990
   chunk 113 optimal weight:   10.0000
   chunk 93 optimal weight:    6.9990
   chunk 103 optimal weight:    0.6980
   chunk 35 optimal weight:   20.0000
   chunk 83 optimal weight:    2.9990
   overall best weight:    1.5386

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7980
moved from start:          0.2967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9390  Z= 0.228
  Angle     :  0.539   7.519  12724  Z= 0.297
  Chirality :  0.039   0.139   1480
  Planarity :  0.005   0.101   1584
  Dihedral  :  5.194  35.535   1277
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 2.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  :  7.71 %
    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 (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:  1.51 (0.24), residues: 1144
  helix:  1.31 (0.18), residues: 762
  sheet:  0.18 (0.52), residues: 85
  loop :  0.76 (0.36), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A2053 
 HIS   0.012   0.002   HIS A1473 
 PHE   0.021   0.002   PHE A1672 
 TYR   0.011   0.001   TYR A2305 
 ARG   0.003   0.000   ARG A1390 

*********************** 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
  99 residues out of total 999 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 82
  time to evaluate  : 1.414 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1442 ASN cc_start: 0.7002 (m110) cc_final: 0.6662 (t0)
REVERT: A 2016 VAL cc_start: 0.7461 (OUTLIER) cc_final: 0.7211 (m)
REVERT: A 2259 PHE cc_start: 0.7439 (OUTLIER) cc_final: 0.6961 (t80)
REVERT: A 2485 LYS cc_start: 0.7456 (mtmt) cc_final: 0.6885 (pttt)
REVERT: A 2502 ARG cc_start: 0.6547 (mtm-85) cc_final: 0.6002 (mtt90)
  outliers start: 17
  outliers final: 7
  residues processed: 89
  average time/residue: 2.0221
  time to fit residues: 199.4263
Evaluate side-chains
  77 residues out of total 999 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 68
  time to evaluate  : 1.440 
-------------------------------------------------------------------------------
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 103 optimal weight:    0.0470
   chunk 78 optimal weight:    2.9990
   chunk 54 optimal weight:   20.0000
   chunk 11 optimal weight:    1.9990
   chunk 49 optimal weight:   20.0000
   chunk 70 optimal weight:    0.9980
   chunk 104 optimal weight:    4.9990
   chunk 111 optimal weight:    9.9990
   chunk 99 optimal weight:    5.9990
   chunk 29 optimal weight:    1.9990
   chunk 92 optimal weight:   10.0000
   overall best weight:    1.6084

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
moved from start:          0.3215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9390  Z= 0.225
  Angle     :  0.508   4.856  12724  Z= 0.281
  Chirality :  0.038   0.138   1480
  Planarity :  0.004   0.046   1584
  Dihedral  :  5.146  39.855   1277
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 2.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  :  8.61 %
    Favored  : 89.89 %
  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:  1.71 (0.25), residues: 1144
  helix:  1.46 (0.19), residues: 759
  sheet:  0.40 (0.56), residues: 85
  loop :  0.79 (0.37), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A2053 
 HIS   0.008   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 

*********************** 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
  86 residues out of total 999 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 71
  time to evaluate  : 1.321 
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: 0.7000 (m110) cc_final: 0.6694 (t0)
REVERT: A 1704 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7541 (mtm180)
REVERT: A 2016 VAL cc_start: 0.7517 (OUTLIER) cc_final: 0.7260 (m)
REVERT: A 2217 ARG cc_start: 0.8144 (ttm170) cc_final: 0.7911 (ttm170)
REVERT: A 2259 PHE cc_start: 0.7440 (OUTLIER) cc_final: 0.6967 (t80)
REVERT: A 2456 ASP cc_start: 0.7039 (t0) cc_final: 0.6658 (t0)
REVERT: A 2485 LYS cc_start: 0.7367 (mtmt) cc_final: 0.6838 (pttt)
REVERT: A 2502 ARG cc_start: 0.6614 (mtm-85) cc_final: 0.6199 (mtt90)
  outliers start: 15
  outliers final: 7
  residues processed: 78
  average time/residue: 2.0389
  time to fit residues: 176.4275
Evaluate side-chains
  75 residues out of total 999 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 65
  time to evaluate  : 1.401 
-------------------------------------------------------------------------------
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 63 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 82 optimal weight:    1.9990
   chunk 45 optimal weight:    7.9990
   chunk 94 optimal weight:    4.9990
   chunk 76 optimal weight:    3.9990
   chunk 0 optimal weight:    3.9990
   chunk 56 optimal weight:    2.9990
   chunk 99 optimal weight:    4.9990
   chunk 28 optimal weight:    1.9990
   chunk 37 optimal weight:    0.5980
   overall best weight:    1.9188

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

Flipped N/Q/H residues before XYZ refinement:
A2357 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8014
moved from start:          0.3505

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= 0.261
  Angle     :  0.521   5.811  12724  Z= 0.288
  Chirality :  0.039   0.148   1480
  Planarity :  0.004   0.047   1584
  Dihedral  :  5.612  49.834   1277
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 3.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  :  8.91 %
    Favored  : 89.39 %
  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:  1.61 (0.25), residues: 1144
  helix:  1.40 (0.19), residues: 759
  sheet:  0.43 (0.57), residues: 85
  loop :  0.66 (0.36), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A2053 
 HIS   0.011   0.001   HIS A1473 
 PHE   0.018   0.002   PHE A1672 
 TYR   0.010   0.001   TYR A2084 
 ARG   0.002   0.000   ARG A2332 

*********************** 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
  82 residues out of total 999 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 65
  time to evaluate  : 1.506 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1442 ASN cc_start: 0.6946 (m110) cc_final: 0.6699 (t0)
REVERT: A 1704 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7592 (mtm180)
REVERT: A 2016 VAL cc_start: 0.7554 (OUTLIER) cc_final: 0.7281 (m)
REVERT: A 2259 PHE cc_start: 0.7378 (OUTLIER) cc_final: 0.6910 (t80)
REVERT: A 2485 LYS cc_start: 0.7328 (mtmt) cc_final: 0.6788 (pttt)
REVERT: A 2502 ARG cc_start: 0.6593 (mtm-85) cc_final: 0.6266 (mtt90)
  outliers start: 17
  outliers final: 6
  residues processed: 75
  average time/residue: 2.0916
  time to fit residues: 174.0357
Evaluate side-chains
  72 residues out of total 999 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 63
  time to evaluate  : 1.388 
-------------------------------------------------------------------------------
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 2384 LEU
Chi-restraints excluded: chain A residue 2486 MET
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 100 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 111 optimal weight:    9.9990
   chunk 92 optimal weight:    7.9990
   chunk 51 optimal weight:   10.0000
   chunk 9 optimal weight:    2.9990
   chunk 36 optimal weight:   20.0000
   chunk 58 optimal weight:    1.9990
   chunk 107 optimal weight:    7.9990
   overall best weight:    1.9788

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.3722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9390  Z= 0.261
  Angle     :  0.514   5.421  12724  Z= 0.282
  Chirality :  0.039   0.144   1480
  Planarity :  0.004   0.048   1584
  Dihedral  :  4.912  40.620   1277
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 3.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  :  9.21 %
    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 (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:  1.50 (0.25), residues: 1144
  helix:  1.38 (0.19), residues: 758
  sheet:  0.49 (0.57), residues: 85
  loop :  0.40 (0.36), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A2053 
 HIS   0.012   0.001   HIS A1473 
 PHE   0.018   0.002   PHE A1672 
 TYR   0.009   0.001   TYR A1383 
 ARG   0.002   0.000   ARG A2127 

*********************** 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
  89 residues out of total 999 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 71
  time to evaluate  : 1.352 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1704 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.7554 (mtm180)
REVERT: A 2016 VAL cc_start: 0.7664 (OUTLIER) cc_final: 0.7380 (m)
REVERT: A 2259 PHE cc_start: 0.7373 (OUTLIER) cc_final: 0.6883 (t80)
REVERT: A 2456 ASP cc_start: 0.7183 (t0) cc_final: 0.6774 (t0)
REVERT: A 2485 LYS cc_start: 0.7300 (mtmt) cc_final: 0.6764 (pttt)
REVERT: A 2502 ARG cc_start: 0.6577 (mtm-85) cc_final: 0.6332 (mtt90)
  outliers start: 18
  outliers final: 8
  residues processed: 82
  average time/residue: 2.2869
  time to fit residues: 206.4916
Evaluate side-chains
  77 residues out of total 999 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 66
  time to evaluate  : 1.561 
-------------------------------------------------------------------------------
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 2229 GLN
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 2445 VAL
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 12 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 81 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 93 optimal weight:    3.9990
   chunk 110 optimal weight:    7.9990
   chunk 69 optimal weight:    0.9990
   chunk 67 optimal weight:    1.9990
   chunk 51 optimal weight:    8.9990
   chunk 68 optimal weight:    0.5980
   chunk 44 optimal weight:    3.9990
   overall best weight:    1.5188

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

Flipped N/Q/H residues before XYZ refinement:
** A1442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8008
moved from start:          0.3889

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9390  Z= 0.214
  Angle     :  0.492   6.070  12724  Z= 0.270
  Chirality :  0.038   0.140   1480
  Planarity :  0.004   0.048   1584
  Dihedral  :  4.774  38.826   1277
  Min Nonbonded Distance : 2.112

Molprobity Statistics.
  All-atom Clashscore : 3.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 10.41 %
    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:  1.64 (0.25), residues: 1144
  helix:  1.48 (0.19), residues: 764
  sheet:  0.57 (0.58), residues: 85
  loop :  0.42 (0.37), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A2053 
 HIS   0.010   0.001   HIS A1473 
 PHE   0.018   0.002   PHE A2018 
 TYR   0.008   0.001   TYR A1609 
 ARG   0.003   0.000   ARG A2271 

*********************** 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
  82 residues out of total 999 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 69
  time to evaluate  : 1.398 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1704 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7526 (mtm180)
REVERT: A 2016 VAL cc_start: 0.7653 (OUTLIER) cc_final: 0.7364 (m)
REVERT: A 2259 PHE cc_start: 0.7337 (OUTLIER) cc_final: 0.6831 (t80)
REVERT: A 2456 ASP cc_start: 0.7130 (t0) cc_final: 0.6724 (t0)
REVERT: A 2485 LYS cc_start: 0.7261 (mtmt) cc_final: 0.6741 (pttt)
  outliers start: 13
  outliers final: 5
  residues processed: 75
  average time/residue: 1.8338
  time to fit residues: 154.2354
Evaluate side-chains
  74 residues out of total 999 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 66
  time to evaluate  : 1.482 
-------------------------------------------------------------------------------
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 2229 GLN
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 2503 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 66 optimal weight:    0.9980
   chunk 33 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9980
   chunk 70 optimal weight:    1.9990
   chunk 75 optimal weight:    3.9990
   chunk 54 optimal weight:   30.0000
   chunk 10 optimal weight:    1.9990
   chunk 87 optimal weight:    0.2980
   chunk 100 optimal weight:    7.9990
   chunk 106 optimal weight:    0.3980
   chunk 96 optimal weight:    2.9990
   overall best weight:    0.9382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7978
moved from start:          0.4008

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= 0.160
  Angle     :  0.457   6.037  12724  Z= 0.247
  Chirality :  0.037   0.136   1480
  Planarity :  0.003   0.045   1584
  Dihedral  :  4.520  35.411   1277
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 3.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 10.41 %
    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:  2.02 (0.25), residues: 1144
  helix:  1.76 (0.19), residues: 757
  sheet:  0.62 (0.58), residues: 85
  loop :  0.67 (0.37), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A2053 
 HIS   0.007   0.001   HIS A1473 
 PHE   0.016   0.001   PHE A2018 
 TYR   0.007   0.001   TYR A2305 
 ARG   0.003   0.000   ARG A2271 

*********************** 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
  74 residues out of total 999 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 64
  time to evaluate  : 1.349 
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: 0.6885 (m110) cc_final: 0.6617 (t0)
REVERT: A 1698 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7232 (mm-30)
REVERT: A 1704 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7530 (mtm180)
REVERT: A 2016 VAL cc_start: 0.7642 (OUTLIER) cc_final: 0.7349 (m)
REVERT: A 2259 PHE cc_start: 0.7295 (OUTLIER) cc_final: 0.6776 (t80)
REVERT: A 2456 ASP cc_start: 0.7168 (t0) cc_final: 0.6791 (t0)
REVERT: A 2485 LYS cc_start: 0.7254 (mtmt) cc_final: 0.6714 (pttt)
  outliers start: 10
  outliers final: 4
  residues processed: 70
  average time/residue: 1.9141
  time to fit residues: 149.9017
Evaluate side-chains
  69 residues out of total 999 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 62
  time to evaluate  : 1.413 
-------------------------------------------------------------------------------
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 2229 GLN
Chi-restraints excluded: chain A residue 2259 PHE
Chi-restraints excluded: chain A residue 2445 VAL
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 103 optimal weight:    2.9990
   chunk 106 optimal weight:    5.9990
   chunk 62 optimal weight:    0.9990
   chunk 44 optimal weight:    2.9990
   chunk 81 optimal weight:    0.9980
   chunk 31 optimal weight:    2.9990
   chunk 93 optimal weight:    6.9990
   chunk 97 optimal weight:    0.9980
   chunk 102 optimal weight:    7.9990
   chunk 67 optimal weight:    1.9990
   chunk 109 optimal weight:   10.0000
   overall best weight:    1.5986

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8007
moved from start:          0.4068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9390  Z= 0.222
  Angle     :  0.484   5.854  12724  Z= 0.264
  Chirality :  0.038   0.139   1480
  Planarity :  0.004   0.044   1584
  Dihedral  :  4.637  39.740   1277
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 10.21 %
    Favored  : 88.49 %
  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:  1.71 (0.25), residues: 1144
  helix:  1.51 (0.19), residues: 774
  sheet:  0.68 (0.58), residues: 85
  loop :  0.45 (0.38), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A2053 
 HIS   0.010   0.001   HIS A1473 
 PHE   0.018   0.002   PHE A1672 
 TYR   0.009   0.001   TYR A2305 
 ARG   0.003   0.000   ARG A2211 

*********************** 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
  78 residues out of total 999 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 65
  time to evaluate  : 1.363 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1442 ASN cc_start: 0.6859 (m110) cc_final: 0.6621 (t0)
REVERT: A 1704 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7530 (mtm180)
REVERT: A 2016 VAL cc_start: 0.7686 (OUTLIER) cc_final: 0.7403 (m)
REVERT: A 2259 PHE cc_start: 0.7336 (OUTLIER) cc_final: 0.6806 (t80)
REVERT: A 2456 ASP cc_start: 0.7242 (t0) cc_final: 0.6841 (t0)
REVERT: A 2485 LYS cc_start: 0.7262 (mtmt) cc_final: 0.6715 (pttt)
  outliers start: 13
  outliers final: 5
  residues processed: 70
  average time/residue: 1.8162
  time to fit residues: 143.0331
Evaluate side-chains
  70 residues out of total 999 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 62
  time to evaluate  : 1.446 
-------------------------------------------------------------------------------
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 2229 GLN
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 66 optimal weight:    0.9980
   chunk 51 optimal weight:    9.9990
   chunk 75 optimal weight:    1.9990
   chunk 114 optimal weight:    5.9990
   chunk 105 optimal weight:    2.9990
   chunk 91 optimal weight:    4.9990
   chunk 9 optimal weight:    2.9990
   chunk 70 optimal weight:    1.9990
   chunk 55 optimal weight:    6.9990
   chunk 72 optimal weight:    0.0050
   chunk 97 optimal weight:    0.6980
   overall best weight:    1.1398

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          0.4142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9390  Z= 0.171
  Angle     :  0.464   5.912  12724  Z= 0.251
  Chirality :  0.037   0.136   1480
  Planarity :  0.003   0.043   1584
  Dihedral  :  4.498  37.217   1277
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 3.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  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:  1.86 (0.25), residues: 1144
  helix:  1.64 (0.19), residues: 774
  sheet:  0.68 (0.57), residues: 85
  loop :  0.50 (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   0.008   0.001   TYR A2305 
 ARG   0.002   0.000   ARG A2127 

********************** 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
  72 residues out of total 999 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 62
  time to evaluate  : 1.438 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1442 ASN cc_start: 0.6905 (m110) cc_final: 0.6635 (t0)
REVERT: A 1704 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7520 (mtm180)
REVERT: A 2016 VAL cc_start: 0.7732 (OUTLIER) cc_final: 0.7456 (m)
REVERT: A 2234 ILE cc_start: 0.6814 (pt) cc_final: 0.6526 (tt)
REVERT: A 2259 PHE cc_start: 0.7312 (OUTLIER) cc_final: 0.6780 (t80)
REVERT: A 2456 ASP cc_start: 0.7208 (t0) cc_final: 0.6815 (t0)
REVERT: A 2485 LYS cc_start: 0.7177 (mtmt) cc_final: 0.6612 (pttt)
  outliers start: 10
  outliers final: 7
  residues processed: 67
  average time/residue: 1.8907
  time to fit residues: 142.0564
Evaluate side-chains
  72 residues out of total 999 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 62
  time to evaluate  : 1.498 
-------------------------------------------------------------------------------
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 2229 GLN
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 84 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 91 optimal weight:    4.9990
   chunk 38 optimal weight:   20.0000
   chunk 93 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 80 optimal weight:    0.6980
   chunk 5 optimal weight:    0.4980
   overall best weight:    1.4386

-------------------------------------------------------------------------------
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 = 0.4404 r_free = 0.4404 target = 0.202651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.144225 restraints weight = 33604.489|
|-----------------------------------------------------------------------------|
r_work (start): 0.3731 rms_B_bonded: 3.40
r_work: 0.3522 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3411 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.3411
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
moved from start:          0.4195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9390  Z= 0.204
  Angle     :  0.477   5.425  12724  Z= 0.259
  Chirality :  0.038   0.139   1480
  Planarity :  0.004   0.044   1584
  Dihedral  :  4.548  39.032   1277
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 3.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 10.71 %
    Favored  : 88.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.84 (0.25), residues: 1144
  helix:  1.61 (0.19), residues: 768
  sheet:  0.71 (0.57), residues: 85
  loop :  0.52 (0.37), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A2053 
 HIS   0.009   0.001   HIS A1473 
 PHE   0.018   0.002   PHE A1672 
 TYR   0.008   0.001   TYR A2305 
 ARG   0.002   0.000   ARG A2127 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5623.92 seconds
wall clock time: 117 minutes 0.74 seconds (7020.74 seconds total)