Starting phenix.real_space_refine
on Fri Feb  6 02:17:03 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9mfw_48240/02_2026/9mfw_48240.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9mfw_48240/02_2026/9mfw_48240.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9mfw_48240/02_2026/9mfw_48240.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9mfw_48240/02_2026/9mfw_48240.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9mfw_48240/02_2026/9mfw_48240.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9mfw_48240/02_2026/9mfw_48240.map"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.029
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       9      5.49       5
     S      98      5.16       5
     C   13471      2.51       5
     N    3496      2.21       5
     O    3963      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 21037
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 20925
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2583, 20925
          Classifications: {'peptide': 2583}
          Link IDs: {'PCIS': 1, 'PTRANS': 68, 'TRANS': 2513}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 112
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 112
          Unusual residues: {'ADP': 3, 'ATP': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
  Time building chain proxies: 4.87, per 1000 atoms: 0.23
  Number of scatterers: 21037
  At special positions: 0
  Unit cell: (119.784, 161.448, 167.958, 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      98     16.00
     P       9     15.00
     O    3963      8.00
     N    3496      7.00
     C   13471      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.10
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  5158 Ramachandran restraints generated.
    2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4930

  Finding SS restraints...
    Secondary structure from input PDB file:
      113 helices and 13 sheets defined
      64.6% alpha, 6.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1241 through 1251
    Processing helix  chain 'A' and resid 1257 through 1274
      removed outlier: 4.010A  pdb=" N   ASP A1273 " --> pdb=" O   LEU A1269 " (cutoff:3.500A)
      removed outlier: 4.111A  pdb=" N   GLU A1274 " --> pdb=" O   ARG A1270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1276 through 1282
    Processing helix  chain 'A' and resid 1282 through 1298
      removed outlier: 4.018A  pdb=" N   LYS A1286 " --> pdb=" O   PHE A1282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1298 through 1306
    Processing helix  chain 'A' and resid 1311 through 1322
    Processing helix  chain 'A' and resid 1328 through 1334
      removed outlier: 3.705A  pdb=" N   LYS A1334 " --> pdb=" O   ASN A1330 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1338 through 1344
    Processing helix  chain 'A' and resid 1350 through 1378
      removed outlier: 3.542A  pdb=" N   LEU A1354 " --> pdb=" O   ASN A1350 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   ILE A1367 " --> pdb=" O   LYS A1363 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   SER A1370 " --> pdb=" O   VAL A1366 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1397 through 1415
      removed outlier: 4.356A  pdb=" N   LEU A1401 " --> pdb=" O   GLU A1397 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1424 through 1457
      removed outlier: 3.880A  pdb=" N   GLU A1447 " --> pdb=" O   VAL A1443 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1462 through 1469
    Processing helix  chain 'A' and resid 1469 through 1494
      removed outlier: 3.721A  pdb=" N   ASP A1494 " --> pdb=" O   ALA A1490 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1496 through 1502
      removed outlier: 3.522A  pdb=" N   ILE A1500 " --> pdb=" O   ILE A1497 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1505 through 1534
    Processing helix  chain 'A' and resid 1536 through 1541
      removed outlier: 4.314A  pdb=" N   LEU A1540 " --> pdb=" O   ARG A1536 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   GLY A1541 " --> pdb=" O   PHE A1537 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1536 through 1541'
    Processing helix  chain 'A' and resid 1541 through 1551
    Processing helix  chain 'A' and resid 1556 through 1561
      removed outlier: 3.517A  pdb=" N   LYS A1560 " --> pdb=" O   GLN A1557 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1603 through 1632
      removed outlier: 3.648A  pdb=" N   TRP A1607 " --> pdb=" O   GLN A1603 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   THR A1613 " --> pdb=" O   ASN A1609 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   LYS A1616 " --> pdb=" O   ASP A1612 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   ASP A1632 " --> pdb=" O   GLY A1628 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1636 through 1641
      removed outlier: 4.365A  pdb=" N   SER A1641 " --> pdb=" O   GLU A1637 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1644 through 1667
    Processing helix  chain 'A' and resid 1668 through 1690
      removed outlier: 4.259A  pdb=" N   TYR A1672 " --> pdb=" O   GLN A1668 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ASN A1688 " --> pdb=" O   LEU A1684 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   LYS A1689 " --> pdb=" O   ASP A1685 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1691 through 1718
      removed outlier: 4.331A  pdb=" N   LYS A1697 " --> pdb=" O   ASN A1693 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   GLU A1704 " --> pdb=" O   ALA A1700 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1720 through 1731
    Processing helix  chain 'A' and resid 1772 through 1788
      removed outlier: 3.910A  pdb=" N   GLN A1788 " --> pdb=" O   ASP A1784 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1801 through 1814
    Processing helix  chain 'A' and resid 1827 through 1842
      removed outlier: 3.527A  pdb=" N   LEU A1831 " --> pdb=" O   ASP A1827 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1854 through 1875
    Processing helix  chain 'A' and resid 1909 through 1913
    Processing helix  chain 'A' and resid 1925 through 1937
    Processing helix  chain 'A' and resid 1941 through 1960
    Processing helix  chain 'A' and resid 1969 through 1987
      removed outlier: 3.631A  pdb=" N   LEU A1973 " --> pdb=" O   GLY A1969 " (cutoff:3.500A)
      removed outlier: 4.663A  pdb=" N   SER A1981 " --> pdb=" O   LEU A1977 " (cutoff:3.500A)
      Proline residue:  A1982  - end of helix
    Processing helix  chain 'A' and resid 1990 through 2002
      removed outlier: 3.796A  pdb=" N   VAL A1994 " --> pdb=" O   GLY A1990 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2003 through 2006
      removed outlier: 3.632A  pdb=" N   LEU A2006 " --> pdb=" O   LEU A2003 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 2003 through 2006'
    Processing helix  chain 'A' and resid 2007 through 2022
    Processing helix  chain 'A' and resid 2030 through 2045
      removed outlier: 4.220A  pdb=" N   ILE A2034 " --> pdb=" O   ASN A2030 " (cutoff:3.500A)
      removed outlier: 4.640A  pdb=" N   GLN A2036 " --> pdb=" O   LYS A2032 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2050 through 2065
      removed outlier: 3.805A  pdb=" N   LYS A2065 " --> pdb=" O   TYR A2061 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2079 through 2096
    Processing helix  chain 'A' and resid 2110 through 2115
    Processing helix  chain 'A' and resid 2128 through 2139
    Processing helix  chain 'A' and resid 2159 through 2165
      removed outlier: 3.765A  pdb=" N   ALA A2165 " --> pdb=" O   GLU A2161 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2166 through 2171
    Processing helix  chain 'A' and resid 2203 through 2210
    Processing helix  chain 'A' and resid 2221 through 2239
      removed outlier: 4.244A  pdb=" N   ASN A2239 " --> pdb=" O   GLU A2235 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2242 through 2255
    Processing helix  chain 'A' and resid 2258 through 2271
      removed outlier: 3.600A  pdb=" N   ASN A2264 " --> pdb=" O   ALA A2260 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2279 through 2298
      removed outlier: 3.722A  pdb=" N   LYS A2283 " --> pdb=" O   ARG A2279 " (cutoff:3.500A)
      removed outlier: 4.926A  pdb=" N   GLU A2285 " --> pdb=" O   PHE A2281 " (cutoff:3.500A)
      removed outlier: 4.330A  pdb=" N   THR A2286 " --> pdb=" O   ASN A2282 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   TYR A2298 " --> pdb=" O   LEU A2294 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2299 through 2302
    Processing helix  chain 'A' and resid 2306 through 2327
    Processing helix  chain 'A' and resid 2332 through 2346
    Processing helix  chain 'A' and resid 2381 through 2385
      removed outlier: 3.585A  pdb=" N   VAL A2385 " --> pdb=" O   ALA A2382 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2394 through 2410
    Processing helix  chain 'A' and resid 2423 through 2434
      removed outlier: 4.197A  pdb=" N   ASN A2434 " --> pdb=" O   ASN A2430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2450 through 2460
      removed outlier: 3.760A  pdb=" N   ILE A2454 " --> pdb=" O   THR A2450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2500 through 2513
    Processing helix  chain 'A' and resid 2547 through 2554
    Processing helix  chain 'A' and resid 2564 through 2580
    Processing helix  chain 'A' and resid 2581 through 2587
      removed outlier: 6.407A  pdb=" N   GLU A2584 " --> pdb=" O   LEU A2581 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   PHE A2585 " --> pdb=" O   VAL A2582 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   ARG A2586 " --> pdb=" O   PRO A2583 " (cutoff:3.500A)
      removed outlier: 5.487A  pdb=" N   SER A2587 " --> pdb=" O   GLU A2584 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 2581 through 2587'
    Processing helix  chain 'A' and resid 2588 through 2607
      removed outlier: 3.630A  pdb=" N   PHE A2592 " --> pdb=" O   TYR A2588 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2618 through 2636
      removed outlier: 3.747A  pdb=" N   LEU A2622 " --> pdb=" O   SER A2618 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2640 through 2656
    Processing helix  chain 'A' and resid 2657 through 2660
    Processing helix  chain 'A' and resid 2663 through 2681
    Processing helix  chain 'A' and resid 2708 through 2727
    Processing helix  chain 'A' and resid 2735 through 2751
    Processing helix  chain 'A' and resid 2765 through 2777
      removed outlier: 4.203A  pdb=" N   ARG A2771 " --> pdb=" O   THR A2767 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2791 through 2809
      removed outlier: 4.320A  pdb=" N   PHE A2795 " --> pdb=" O   ASN A2791 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   LYS A2809 " --> pdb=" O   ASP A2805 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2825 through 2837
    Processing helix  chain 'A' and resid 2845 through 2863
    Processing helix  chain 'A' and resid 2869 through 2885
    Processing helix  chain 'A' and resid 2896 through 2905
    Processing helix  chain 'A' and resid 2905 through 2912
    Processing helix  chain 'A' and resid 2921 through 2933
    Processing helix  chain 'A' and resid 2960 through 2981
      removed outlier: 4.493A  pdb=" N   ALA A2964 " --> pdb=" O   THR A2960 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2990 through 3026
      removed outlier: 3.555A  pdb=" N   ASP A2994 " --> pdb=" O   GLY A2990 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3297 through 3303
      removed outlier: 4.036A  pdb=" N   THR A3300 " --> pdb=" O   LYS A3297 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   PHE A3301 " --> pdb=" O   SER A3298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3304 through 3309
    Processing helix  chain 'A' and resid 3309 through 3333
      removed outlier: 4.447A  pdb=" N   ILE A3321 " --> pdb=" O   SER A3317 " (cutoff:3.500A)
      removed outlier: 5.656A  pdb=" N   GLY A3322 " --> pdb=" O   GLN A3318 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3334 through 3336
      No H-bonds generated for 'chain 'A' and resid 3334 through 3336'
    Processing helix  chain 'A' and resid 3338 through 3356
    Processing helix  chain 'A' and resid 3366 through 3371
      removed outlier: 3.953A  pdb=" N   VAL A3371 " --> pdb=" O   ILE A3367 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3372 through 3383
    Processing helix  chain 'A' and resid 3387 through 3400
      removed outlier: 3.848A  pdb=" N   SER A3400 " --> pdb=" O   ILE A3396 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3412 through 3423
      removed outlier: 3.793A  pdb=" N   THR A3416 " --> pdb=" O   SER A3412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3434 through 3447
      removed outlier: 4.510A  pdb=" N   LYS A3438 " --> pdb=" O   GLU A3434 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   ARG A3445 " --> pdb=" O   GLU A3441 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   PHE A3446 " --> pdb=" O   ASN A3442 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3462 through 3467
    Processing helix  chain 'A' and resid 3506 through 3513
    Processing helix  chain 'A' and resid 3525 through 3537
    Processing helix  chain 'A' and resid 3539 through 3571
      removed outlier: 3.670A  pdb=" N   GLU A3546 " --> pdb=" O   GLN A3542 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3576 through 3606
      removed outlier: 4.082A  pdb=" N   LEU A3583 " --> pdb=" O   GLU A3579 " (cutoff:3.500A)
      removed outlier: 4.860A  pdb=" N   MET A3584 " --> pdb=" O   ASN A3580 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   VAL A3585 " --> pdb=" O   ASP A3581 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   GLU A3606 " --> pdb=" O   SER A3602 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3607 through 3639
      removed outlier: 3.939A  pdb=" N   GLU A3616 " --> pdb=" O   ASP A3612 " (cutoff:3.500A)
      removed outlier: 4.553A  pdb=" N   GLU A3617 " --> pdb=" O   ASN A3613 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   TYR A3618 " --> pdb=" O   LEU A3614 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   HIS A3624 " --> pdb=" O   ILE A3620 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   LYS A3627 " --> pdb=" O   LYS A3623 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3645 through 3659
      removed outlier: 4.192A  pdb=" N   PHE A3657 " --> pdb=" O   PHE A3653 " (cutoff:3.500A)
      removed outlier: 4.255A  pdb=" N   ILE A3658 " --> pdb=" O   LYS A3654 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3670 through 3688
      removed outlier: 4.323A  pdb=" N   THR A3688 " --> pdb=" O   CYS A3684 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3691 through 3711
      removed outlier: 3.712A  pdb=" N   ASP A3709 " --> pdb=" O   LEU A3705 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3712 through 3727
    Processing helix  chain 'A' and resid 3728 through 3731
    Processing helix  chain 'A' and resid 3741 through 3753
      removed outlier: 3.733A  pdb=" N   ARG A3745 " --> pdb=" O   ASN A3741 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3755 through 3767
      removed outlier: 4.371A  pdb=" N   PHE A3763 " --> pdb=" O   ALA A3759 " (cutoff:3.500A)
      removed outlier: 4.385A  pdb=" N   LYS A3764 " --> pdb=" O   LEU A3760 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   PHE A3767 " --> pdb=" O   PHE A3763 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3773 through 3781
    Processing helix  chain 'A' and resid 3796 through 3807
    Processing helix  chain 'A' and resid 3818 through 3836
      removed outlier: 3.928A  pdb=" N   ILE A3834 " --> pdb=" O   SER A3830 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3847 through 3854
    Processing helix  chain 'A' and resid 3854 through 3862
    Processing helix  chain 'A' and resid 3863 through 3868
      removed outlier: 3.938A  pdb=" N   GLU A3866 " --> pdb=" O   LYS A3863 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3885 through 3892
    Processing helix  chain 'A' and resid 3902 through 3916
    Processing helix  chain 'A' and resid 3922 through 3943
      removed outlier: 3.757A  pdb=" N   VAL A3926 " --> pdb=" O   GLY A3922 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3957 through 3975
      removed outlier: 4.068A  pdb=" N   PHE A3961 " --> pdb=" O   ASN A3957 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3981 through 3992
    Processing helix  chain 'A' and resid 4000 through 4015
    Processing helix  chain 'A' and resid 4037 through 4052
      removed outlier: 3.550A  pdb=" N   GLU A4041 " --> pdb=" O   SER A4037 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   THR A4052 " --> pdb=" O   ILE A4048 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4057 through 4062
    Processing helix  chain 'A' and resid 4066 through 4092
    Processing sheet with id=AA1, first strand: chain 'A' and resid 1569 through 1574
      removed outlier: 3.541A  pdb=" N   SER A1571 " --> pdb=" O   ARG A1583 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   GLY A1581 " --> pdb=" O   ILE A1573 " (cutoff:3.500A)
      removed outlier: 6.175A  pdb=" N   THR A1580 " --> pdb=" O   LEU A1592 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 1733 through 1736
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1817 through 1821
      removed outlier: 6.032A  pdb=" N   GLY A1845 " --> pdb=" O   PHE A1895 " (cutoff:3.500A)
      removed outlier: 7.550A  pdb=" N   THR A1897 " --> pdb=" O   GLY A1845 " (cutoff:3.500A)
      removed outlier: 6.148A  pdb=" N   PHE A1847 " --> pdb=" O   THR A1897 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   ARG A1917 " --> pdb=" O   GLY A1791 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1878 through 1881
      removed outlier: 3.574A  pdb=" N   LEU A1881 " --> pdb=" O   GLU A1884 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 2099 through 2104
      removed outlier: 5.970A  pdb=" N   VAL A2100 " --> pdb=" O   TRP A2151 " (cutoff:3.500A)
      removed outlier: 7.423A  pdb=" N   VAL A2153 " --> pdb=" O   VAL A2100 " (cutoff:3.500A)
      removed outlier: 6.301A  pdb=" N   TYR A2102 " --> pdb=" O   VAL A2153 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   ILE A2150 " --> pdb=" O   ARG A2191 " (cutoff:3.500A)
      removed outlier: 7.670A  pdb=" N   LEU A2193 " --> pdb=" O   ILE A2150 " (cutoff:3.500A)
      removed outlier: 6.347A  pdb=" N   VAL A2152 " --> pdb=" O   LEU A2193 " (cutoff:3.500A)
      removed outlier: 7.748A  pdb=" N   GLU A2195 " --> pdb=" O   VAL A2152 " (cutoff:3.500A)
      removed outlier: 6.297A  pdb=" N   PHE A2154 " --> pdb=" O   GLU A2195 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   GLY A2074 " --> pdb=" O   THR A2196 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   GLY A2211 " --> pdb=" O   ALA A2069 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 2438 through 2444
      removed outlier: 5.533A  pdb=" N   ASP A2439 " --> pdb=" O   VAL A2483 " (cutoff:3.500A)
      removed outlier: 6.608A  pdb=" N   PHE A2485 " --> pdb=" O   ASP A2439 " (cutoff:3.500A)
      removed outlier: 6.562A  pdb=" N   VAL A2441 " --> pdb=" O   PHE A2485 " (cutoff:3.500A)
      removed outlier: 7.224A  pdb=" N   ASP A2487 " --> pdb=" O   VAL A2441 " (cutoff:3.500A)
      removed outlier: 7.442A  pdb=" N   ILE A2443 " --> pdb=" O   ASP A2487 " (cutoff:3.500A)
      removed outlier: 7.049A  pdb=" N   LEU A2482 " --> pdb=" O   HIS A2530 " (cutoff:3.500A)
      removed outlier: 8.081A  pdb=" N   VAL A2532 " --> pdb=" O   LEU A2482 " (cutoff:3.500A)
      removed outlier: 6.030A  pdb=" N   LEU A2484 " --> pdb=" O   VAL A2532 " (cutoff:3.500A)
      removed outlier: 8.077A  pdb=" N   ALA A2534 " --> pdb=" O   LEU A2484 " (cutoff:3.500A)
      removed outlier: 7.507A  pdb=" N   CYS A2486 " --> pdb=" O   ALA A2534 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   ILE A2414 " --> pdb=" O   GLY A2533 " (cutoff:3.500A)
      removed outlier: 8.276A  pdb=" N   CYS A2535 " --> pdb=" O   ILE A2414 " (cutoff:3.500A)
      removed outlier: 5.970A  pdb=" N   LEU A2416 " --> pdb=" O   CYS A2535 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 2465 through 2466
      removed outlier: 4.936A  pdb=" N   THR A2472 " --> pdb=" O   TRP A2523 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   THR A2525 " --> pdb=" O   THR A2472 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   LEU A2474 " --> pdb=" O   THR A2525 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   LYS A2522 " --> pdb=" O   LYS A2517 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 2696 through 2697
      removed outlier: 3.687A  pdb=" N   LYS A2705 " --> pdb=" O   SER A2697 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 2780 through 2782
      removed outlier: 5.900A  pdb=" N   LYS A2780 " --> pdb=" O   CYS A2814 " (cutoff:3.500A)
      removed outlier: 7.250A  pdb=" N   ILE A2816 " --> pdb=" O   LYS A2780 " (cutoff:3.500A)
      removed outlier: 6.685A  pdb=" N   VAL A2782 " --> pdb=" O   ILE A2816 " (cutoff:3.500A)
      removed outlier: 8.432A  pdb=" N   ASP A2818 " --> pdb=" O   VAL A2782 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   THR A2813 " --> pdb=" O   HIS A2886 " (cutoff:3.500A)
      removed outlier: 8.224A  pdb=" N   VAL A2888 " --> pdb=" O   THR A2813 " (cutoff:3.500A)
      removed outlier: 6.239A  pdb=" N   LEU A2815 " --> pdb=" O   VAL A2888 " (cutoff:3.500A)
      removed outlier: 7.231A  pdb=" N   THR A2890 " --> pdb=" O   LEU A2815 " (cutoff:3.500A)
      removed outlier: 6.300A  pdb=" N   ILE A2817 " --> pdb=" O   THR A2890 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 3427 through 3429
      removed outlier: 3.707A  pdb=" N   ILE A3451 " --> pdb=" O   VAL A3427 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   LEU A3429 " --> pdb=" O   ILE A3451 " (cutoff:3.500A)
      removed outlier: 6.789A  pdb=" N   VAL A3450 " --> pdb=" O   PHE A3495 " (cutoff:3.500A)
      removed outlier: 7.794A  pdb=" N   HIS A3497 " --> pdb=" O   VAL A3450 " (cutoff:3.500A)
      removed outlier: 6.306A  pdb=" N   ILE A3452 " --> pdb=" O   HIS A3497 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 3478 through 3481
      removed outlier: 3.900A  pdb=" N   VAL A3479 " --> pdb=" O   VAL A3486 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 3813 through 3814
    Processing sheet with id=AB4, first strand: chain 'A' and resid 4021 through 4024
      removed outlier: 3.798A  pdb=" N   ILE A4023 " --> pdb=" O   VAL A4027 " (cutoff:3.500A)
      removed outlier: 7.051A  pdb=" N   VAL A4027 " --> pdb=" O   ILE A4023 " (cutoff:3.500A)

    1214 hydrogen bonds defined for protein.
    3573 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: 6.01

  Time building geometry restraints manager: 2.79 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 6735
        1.34 -     1.46: 4530
        1.46 -     1.58: 10032
        1.58 -     1.70: 11
        1.70 -     1.82: 158
  Bond restraints: 21466
  Sorted by residual:
  bond pdb=" N   ILE A1386 "
       pdb=" CA  ILE A1386 "
    ideal  model  delta    sigma   weight residual
    1.459  1.496 -0.037 1.25e-02 6.40e+03 8.74e+00
  bond pdb=" N   ILE A1374 "
       pdb=" CA  ILE A1374 "
    ideal  model  delta    sigma   weight residual
    1.462  1.493 -0.031 1.14e-02 7.69e+03 7.56e+00
  bond pdb=" N   LEU A1392 "
       pdb=" CA  LEU A1392 "
    ideal  model  delta    sigma   weight residual
    1.453  1.486 -0.034 1.31e-02 5.83e+03 6.62e+00
  bond pdb=" N   ASP A1408 "
       pdb=" CA  ASP A1408 "
    ideal  model  delta    sigma   weight residual
    1.459  1.490 -0.031 1.21e-02 6.83e+03 6.58e+00
  bond pdb=" N   GLN A1382 "
       pdb=" CA  GLN A1382 "
    ideal  model  delta    sigma   weight residual
    1.453  1.486 -0.034 1.31e-02 5.83e+03 6.56e+00
  ... (remaining 21461 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.21: 28522
        2.21 -     4.43: 426
        4.43 -     6.64: 66
        6.64 -     8.85: 15
        8.85 -    11.06: 2
  Bond angle restraints: 29031
  Sorted by residual:
  angle pdb=" N   LEU A1392 "
        pdb=" CA  LEU A1392 "
        pdb=" CB  LEU A1392 "
      ideal   model   delta    sigma   weight residual
     110.44  103.66    6.78 1.43e+00 4.89e-01 2.25e+01
  angle pdb=" C   TYR A1383 "
        pdb=" CA  TYR A1383 "
        pdb=" CB  TYR A1383 "
      ideal   model   delta    sigma   weight residual
     110.19  116.29   -6.10 1.62e+00 3.81e-01 1.42e+01
  angle pdb=" O   GLU A1380 "
        pdb=" C   GLU A1380 "
        pdb=" N   ALA A1381 "
      ideal   model   delta    sigma   weight residual
     120.58  124.79   -4.21 1.13e+00 7.83e-01 1.39e+01
  angle pdb=" N   GLU A4086 "
        pdb=" CA  GLU A4086 "
        pdb=" CB  GLU A4086 "
      ideal   model   delta    sigma   weight residual
     110.01  115.34   -5.33 1.45e+00 4.76e-01 1.35e+01
  angle pdb=" CA  GLU A1380 "
        pdb=" C   GLU A1380 "
        pdb=" N   ALA A1381 "
      ideal   model   delta    sigma   weight residual
     119.46  117.25    2.21 6.10e-01 2.69e+00 1.31e+01
  ... (remaining 29026 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.59: 12629
       33.59 -    67.18: 274
       67.18 -   100.77: 55
      100.77 -   134.36: 0
      134.36 -   167.95: 1
  Dihedral angle restraints: 12959
    sinusoidal: 5368
      harmonic: 7591
  Sorted by residual:
  dihedral pdb=" CD  ARG A1373 "
           pdb=" NE  ARG A1373 "
           pdb=" CZ  ARG A1373 "
           pdb=" NH1 ARG A1373 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   78.28  -78.28     1      1.00e+01 1.00e-02 7.65e+01
  dihedral pdb=" O1B ADP A4103 "
           pdb=" O3A ADP A4103 "
           pdb=" PB  ADP A4103 "
           pdb=" PA  ADP A4103 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00  107.94 -167.95     1      2.00e+01 2.50e-03 4.75e+01
  dihedral pdb=" CA  SER A1825 "
           pdb=" C   SER A1825 "
           pdb=" N   PHE A1826 "
           pdb=" CA  PHE A1826 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.58  -26.42     0      5.00e+00 4.00e-02 2.79e+01
  ... (remaining 12956 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 2715
       0.055 -    0.110: 504
       0.110 -    0.165: 61
       0.165 -    0.220: 4
       0.220 -    0.275: 3
  Chirality restraints: 3287
  Sorted by residual:
  chirality pdb=" CA  LEU A1371 "
            pdb=" N   LEU A1371 "
            pdb=" C   LEU A1371 "
            pdb=" CB  LEU A1371 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.79   -0.28 2.00e-01 2.50e+01 1.90e+00
  chirality pdb=" CB  ILE A2071 "
            pdb=" CA  ILE A2071 "
            pdb=" CG1 ILE A2071 "
            pdb=" CG2 ILE A2071 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.37    0.27 2.00e-01 2.50e+01 1.87e+00
  chirality pdb=" CA  ILE A1374 "
            pdb=" N   ILE A1374 "
            pdb=" C   ILE A1374 "
            pdb=" CB  ILE A1374 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.67   -0.23 2.00e-01 2.50e+01 1.37e+00
  ... (remaining 3284 not shown)

  Planarity restraints: 3652
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A1373 "    1.083 9.50e-02 1.11e+02   4.85e-01 1.42e+02
        pdb=" NE  ARG A1373 "   -0.065 2.00e-02 2.50e+03
        pdb=" CZ  ARG A1373 "   -0.013 2.00e-02 2.50e+03
        pdb=" NH1 ARG A1373 "    0.010 2.00e-02 2.50e+03
        pdb=" NH2 ARG A1373 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A2943 "   -0.021 2.00e-02 2.50e+03   4.11e-02 1.69e+01
        pdb=" C   PHE A2943 "    0.071 2.00e-02 2.50e+03
        pdb=" O   PHE A2943 "   -0.027 2.00e-02 2.50e+03
        pdb=" N   ILE A2944 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A3658 "   -0.018 2.00e-02 2.50e+03   3.56e-02 1.27e+01
        pdb=" C   ILE A3658 "    0.062 2.00e-02 2.50e+03
        pdb=" O   ILE A3658 "   -0.023 2.00e-02 2.50e+03
        pdb=" N   LYS A3659 "   -0.021 2.00e-02 2.50e+03
  ... (remaining 3649 not shown)

  Histogram of nonbonded interaction distances:
        0.92 -     1.71: 6
        1.71 -     2.51: 225
        2.51 -     3.31: 27603
        3.31 -     4.10: 54182
        4.10 -     4.90: 95613
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions: 177629
  Sorted by model distance:
  nonbonded pdb=" NE2 HIS A1314 "
            pdb=" OH  TYR A1420 "
     model   vdw
     0.916 3.120
  nonbonded pdb=" CE1 HIS A1314 "
            pdb=" OH  TYR A1420 "
     model   vdw
     1.347 3.260
  nonbonded pdb=" CZ  ARG A1360 "
            pdb=" CE1 TYR A1420 "
     model   vdw
     1.512 2.856
  nonbonded pdb=" NH1 ARG A1360 "
            pdb=" CE1 TYR A1420 "
     model   vdw
     1.625 3.420
  nonbonded pdb=" CD  GLU A1364 "
            pdb=" O   TYR A1420 "
     model   vdw
     1.656 3.270
  ... (remaining 177624 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.580
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.070
  Set scattering table:                    0.060
  Process input model:                     23.460
  Find NCS groups from input model:        0.090
  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:             0.000
  Load rotamer database and sin/cos tables:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8504
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      :  0.003   0.056  21468  Z= 0.182
  Angle     :  0.662  11.065  29031  Z= 0.354
  Chirality :  0.043   0.275   3287
  Planarity :  0.009   0.485   3652
  Dihedral  : 15.240 167.945   8029
  Min Nonbonded Distance : 0.916

Molprobity Statistics.
  All-atom Clashscore : 19.08
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.81 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  0.55 %
    Favored  : 99.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.11 (0.16), residues: 2579
  helix:  0.97 (0.13), residues: 1501
  sheet: -0.32 (0.38), residues: 185
  loop : -1.34 (0.20), residues: 893

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A2962 
 TYR   0.017   0.001   TYR A2674 
 PHE   0.018   0.001   PHE A1249 
 TRP   0.044   0.002   TRP A1445 
 HIS   0.012   0.001   HIS A1965 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 (21466)
  covalent geometry    : angle       0.66180 (29031)
  hydrogen bonds       : bond        0.13728 ( 1214)
  hydrogen bonds       : angle       5.98978 ( 3573)
  Misc. bond           : bond        0.03996 (    2)

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

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

  5158 Ramachandran restraints generated.
    2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5158 Ramachandran restraints generated.
    2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 2358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 210
  time to evaluate  : 0.769 
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: symmetry clash
   revert: symmetry clash
REVERT: A 1284 MET cc_start: 0.3148 (mmp) cc_final: 0.2775 (tmm)
REVERT: A 1380 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.7129 (tp30)
REVERT: A 1565 MET cc_start: 0.9236 (ppp) cc_final: 0.8544 (ppp)
REVERT: A 1655 MET cc_start: 0.8723 (tpt) cc_final: 0.8376 (tpp)
REVERT: A 1659 LEU cc_start: 0.9413 (mt) cc_final: 0.8729 (mt)
REVERT: A 2345 TYR cc_start: 0.8870 (m-80) cc_final: 0.8548 (m-80)
REVERT: A 2385 VAL cc_start: 0.8883 (t) cc_final: 0.8501 (t)
REVERT: A 2426 MET cc_start: 0.8411 (pmm) cc_final: 0.7445 (pmm)
REVERT: A 2908 LEU cc_start: 0.9469 (mt) cc_final: 0.9263 (mt)
REVERT: A 2925 MET cc_start: 0.9219 (mpp) cc_final: 0.8951 (mpp)
REVERT: A 2963 ASP cc_start: 0.7584 (m-30) cc_final: 0.7355 (m-30)
REVERT: A 2975 ASN cc_start: 0.9371 (t0) cc_final: 0.9148 (t0)
REVERT: A 3398 MET cc_start: 0.8448 (mmp) cc_final: 0.8228 (mmp)
REVERT: A 3458 PHE cc_start: 0.8724 (t80) cc_final: 0.8494 (t80)
REVERT: A 3633 GLU cc_start: 0.8809 (mp0) cc_final: 0.8319 (pm20)
REVERT: A 3700 MET cc_start: 0.9378 (ppp) cc_final: 0.9104 (ppp)
REVERT: A 3722 MET cc_start: 0.8780 (mmp) cc_final: 0.8437 (mmp)
REVERT: A 3931 LEU cc_start: 0.9662 (mt) cc_final: 0.9443 (mt)
  outliers start: 6
  outliers final: 2
  residues processed: 215
  average time/residue: 0.1418
  time to fit residues: 48.9040
Evaluate side-chains
  146 residues out of total 2358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 143
  time to evaluate  : 0.878 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 258
   random chunks:
   chunk 197 optimal weight:    3.9990
   chunk 215 optimal weight:    4.9990
   chunk 20 optimal weight:    7.9990
   chunk 132 optimal weight:    3.9990
   chunk 248 optimal weight:    0.9980
   chunk 207 optimal weight:   10.0000
   chunk 155 optimal weight:    2.9990
   chunk 244 optimal weight:    0.9980
   chunk 183 optimal weight:    0.8980
   chunk 111 optimal weight:    9.9990
   chunk 71 optimal weight:    0.9980
   overall best weight:    1.3782

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

Flipped N/Q/H residues before XYZ refinement:
A1554 HIS
A1646 GLN
A1757 GLN
** A1811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2777 ASN
A2832 ASN
A2915 ASN
A2931 ASN
A3323 ASN
A3336 HIS
A3484 HIS
A3780 ASN
** A4035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.073539 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.052034 restraints weight = 117145.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.053264 restraints weight = 73026.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.054047 restraints weight = 53148.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.054589 restraints weight = 43032.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 65)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.054969 restraints weight = 37399.343|
|-----------------------------------------------------------------------------|
r_work (final): 0.3167
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8486
moved from start:          0.0973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  21468  Z= 0.135
  Angle     :  0.597   9.402  29031  Z= 0.304
  Chirality :  0.041   0.182   3287
  Planarity :  0.004   0.077   3652
  Dihedral  :  7.290 154.891   2838
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 13.36
  Ramachandran Plot:
    Outliers :  0.04 %
    Allowed  :  4.07 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  5.77 %
    Favored  : 93.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.26 (0.16), residues: 2579
  helix:  1.06 (0.13), residues: 1533
  sheet: -0.44 (0.38), residues: 185
  loop : -1.25 (0.20), residues: 861

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG A1360 
 TYR   0.024   0.001   TYR A1420 
 PHE   0.019   0.001   PHE A2940 
 TRP   0.023   0.001   TRP A2084 
 HIS   0.009   0.001   HIS A1965 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 (21466)
  covalent geometry    : angle       0.59709 (29031)
  hydrogen bonds       : bond        0.04138 ( 1214)
  hydrogen bonds       : angle       4.83533 ( 3573)
  Misc. bond           : bond        0.00830 (    2)

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

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

  5158 Ramachandran restraints generated.
    2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5158 Ramachandran restraints generated.
    2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 2358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 214
  time to evaluate  : 0.671 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1284 MET cc_start: 0.3448 (mmp) cc_final: 0.3005 (tmm)
REVERT: A 1317 MET cc_start: 0.0391 (ptp) cc_final: 0.0119 (ptp)
REVERT: A 1407 GLU cc_start: 0.9279 (pt0) cc_final: 0.9054 (tp30)
REVERT: A 1453 LEU cc_start: 0.9476 (tp) cc_final: 0.9186 (pp)
REVERT: A 1565 MET cc_start: 0.9280 (ppp) cc_final: 0.8704 (ppp)
REVERT: A 1655 MET cc_start: 0.8748 (tpt) cc_final: 0.8454 (tpp)
REVERT: A 1659 LEU cc_start: 0.9363 (mt) cc_final: 0.8522 (mt)
REVERT: A 1714 GLN cc_start: 0.9105 (pp30) cc_final: 0.8902 (pp30)
REVERT: A 2085 LYS cc_start: 0.9446 (mmtt) cc_final: 0.9205 (mmmm)
REVERT: A 2345 TYR cc_start: 0.8925 (m-80) cc_final: 0.8371 (m-80)
REVERT: A 2426 MET cc_start: 0.8715 (pmm) cc_final: 0.7738 (pmm)
REVERT: A 2427 ILE cc_start: 0.9168 (pt) cc_final: 0.8698 (pt)
REVERT: A 2432 LEU cc_start: 0.9447 (tp) cc_final: 0.9234 (tp)
REVERT: A 2902 MET cc_start: 0.8717 (mmp) cc_final: 0.8481 (mmm)
REVERT: A 2908 LEU cc_start: 0.9437 (mt) cc_final: 0.9197 (mt)
REVERT: A 2913 ILE cc_start: 0.9397 (mt) cc_final: 0.9176 (mt)
REVERT: A 2938 MET cc_start: 0.7301 (tpt) cc_final: 0.6926 (tmm)
REVERT: A 2963 ASP cc_start: 0.7680 (m-30) cc_final: 0.7395 (m-30)
REVERT: A 3633 GLU cc_start: 0.8623 (mp0) cc_final: 0.8135 (mp0)
REVERT: A 3722 MET cc_start: 0.8731 (mmp) cc_final: 0.8371 (mmp)
REVERT: A 3788 MET cc_start: 0.8756 (tpt) cc_final: 0.8458 (tpt)
REVERT: A 3875 MET cc_start: 0.9313 (mpp) cc_final: 0.8949 (mpp)
REVERT: A 3931 LEU cc_start: 0.9653 (mt) cc_final: 0.9441 (mt)
  outliers start: 6
  outliers final: 0
  residues processed: 215
  average time/residue: 0.1273
  time to fit residues: 44.2799
Evaluate side-chains
  153 residues out of total 2358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 0.657 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 258
   random chunks:
   chunk 149 optimal weight:    7.9990
   chunk 40 optimal weight:    0.9980
   chunk 139 optimal weight:    6.9990
   chunk 26 optimal weight:    4.9990
   chunk 123 optimal weight:    6.9990
   chunk 190 optimal weight:   10.0000
   chunk 7 optimal weight:    2.9990
   chunk 192 optimal weight:    2.9990
   chunk 227 optimal weight:    0.9980
   chunk 107 optimal weight:    7.9990
   chunk 185 optimal weight:    1.9990
   overall best weight:    1.9986

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

Flipped N/Q/H residues before XYZ refinement:
A1382 GLN
A1717 ASN
** A1811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1967 HIS
** A2293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2777 ASN
A2931 ASN
A3323 ASN
A3484 HIS
** A3639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A3780 ASN
** A4035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A4090 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.072869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.051459 restraints weight = 117732.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.052733 restraints weight = 71325.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 59)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.053560 restraints weight = 51563.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.054110 restraints weight = 41354.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.054468 restraints weight = 35818.295|
|-----------------------------------------------------------------------------|
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8508
moved from start:          0.1332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  21468  Z= 0.152
  Angle     :  0.592   9.628  29031  Z= 0.302
  Chirality :  0.041   0.180   3287
  Planarity :  0.004   0.070   3652
  Dihedral  :  7.175 153.821   2838
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 13.93
  Ramachandran Plot:
    Outliers :  0.04 %
    Allowed  :  4.27 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  4.03 %
    Favored  : 95.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.26 (0.16), residues: 2579
  helix:  1.09 (0.13), residues: 1537
  sheet: -0.53 (0.37), residues: 195
  loop : -1.30 (0.20), residues: 847

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A2627 
 TYR   0.022   0.001   TYR A2571 
 PHE   0.012   0.001   PHE A2940 
 TRP   0.022   0.001   TRP A2084 
 HIS   0.009   0.001   HIS A1965 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 (21466)
  covalent geometry    : angle       0.59170 (29031)
  hydrogen bonds       : bond        0.03799 ( 1214)
  hydrogen bonds       : angle       4.69013 ( 3573)
  Misc. bond           : bond        0.00448 (    2)

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

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

  5158 Ramachandran restraints generated.
    2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5158 Ramachandran restraints generated.
    2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 2358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 212
  time to evaluate  : 0.620 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1284 MET cc_start: 0.3444 (mmp) cc_final: 0.3029 (tmm)
REVERT: A 1317 MET cc_start: 0.0302 (ptp) cc_final: 0.0045 (ptp)
REVERT: A 1453 LEU cc_start: 0.9507 (tp) cc_final: 0.9198 (pp)
REVERT: A 1518 MET cc_start: 0.9381 (tmm) cc_final: 0.9026 (tmm)
REVERT: A 1565 MET cc_start: 0.9350 (ppp) cc_final: 0.8615 (ppp)
REVERT: A 1655 MET cc_start: 0.8866 (tpt) cc_final: 0.8521 (tpp)
REVERT: A 1659 LEU cc_start: 0.9409 (mt) cc_final: 0.8610 (mt)
REVERT: A 1697 LYS cc_start: 0.9121 (mttt) cc_final: 0.8746 (mttm)
REVERT: A 1714 GLN cc_start: 0.9233 (pp30) cc_final: 0.9018 (pp30)
REVERT: A 2085 LYS cc_start: 0.9456 (mmtt) cc_final: 0.9213 (mmmm)
REVERT: A 2345 TYR cc_start: 0.9042 (m-80) cc_final: 0.8521 (m-80)
REVERT: A 2385 VAL cc_start: 0.8998 (t) cc_final: 0.8785 (t)
REVERT: A 2432 LEU cc_start: 0.9520 (tp) cc_final: 0.9150 (tp)
REVERT: A 2902 MET cc_start: 0.8701 (mmp) cc_final: 0.8418 (mmm)
REVERT: A 2908 LEU cc_start: 0.9409 (mt) cc_final: 0.9164 (mt)
REVERT: A 2913 ILE cc_start: 0.9356 (mt) cc_final: 0.9091 (mm)
REVERT: A 2925 MET cc_start: 0.9315 (mpp) cc_final: 0.9068 (mpp)
REVERT: A 2937 PRO cc_start: 0.6994 (Cg_endo) cc_final: 0.6407 (Cg_exo)
REVERT: A 3593 GLU cc_start: 0.7480 (tp30) cc_final: 0.6650 (pp20)
REVERT: A 3722 MET cc_start: 0.8805 (mmp) cc_final: 0.8443 (mmp)
REVERT: A 3788 MET cc_start: 0.8857 (tpt) cc_final: 0.8526 (tpt)
REVERT: A 3873 MET cc_start: 0.9075 (mmp) cc_final: 0.8869 (mmm)
REVERT: A 3875 MET cc_start: 0.9254 (mpp) cc_final: 0.8858 (mpp)
REVERT: A 3931 LEU cc_start: 0.9682 (mt) cc_final: 0.9457 (mt)
  outliers start: 4
  outliers final: 0
  residues processed: 213
  average time/residue: 0.1395
  time to fit residues: 47.4209
Evaluate side-chains
  146 residues out of total 2358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 0.663 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 258
   random chunks:
   chunk 231 optimal weight:    9.9990
   chunk 48 optimal weight:    0.9980
   chunk 120 optimal weight:    8.9990
   chunk 169 optimal weight:    5.9990
   chunk 128 optimal weight:    0.0000
   chunk 88 optimal weight:    0.0470
   chunk 232 optimal weight:    2.9990
   chunk 116 optimal weight:    1.9990
   chunk 249 optimal weight:    6.9990
   chunk 34 optimal weight:    0.9990
   chunk 91 optimal weight:    7.9990
   overall best weight:    0.8086

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

Flipped N/Q/H residues before XYZ refinement:
** A1811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2777 ASN
A2931 ASN
A3323 ASN
A3484 HIS
A3574 GLN
A3639 HIS
A3780 ASN
A3858 HIS
** A4035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.074717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.052959 restraints weight = 119156.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 73)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.054120 restraints weight = 76335.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.054880 restraints weight = 56318.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.055433 restraints weight = 46172.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.055809 restraints weight = 40371.839|
|-----------------------------------------------------------------------------|
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8473
moved from start:          0.1587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043  21468  Z= 0.117
  Angle     :  0.580   8.787  29031  Z= 0.291
  Chirality :  0.040   0.166   3287
  Planarity :  0.004   0.079   3652
  Dihedral  :  6.936 147.727   2838
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 12.25
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.15 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  3.73 %
    Favored  : 96.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.33 (0.16), residues: 2579
  helix:  1.16 (0.13), residues: 1532
  sheet: -0.42 (0.37), residues: 194
  loop : -1.30 (0.20), residues: 853

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A3565 
 TYR   0.013   0.001   TYR A1420 
 PHE   0.014   0.001   PHE A2827 
 TRP   0.021   0.001   TRP A2084 
 HIS   0.005   0.001   HIS A2293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 (21466)
  covalent geometry    : angle       0.58024 (29031)
  hydrogen bonds       : bond        0.03541 ( 1214)
  hydrogen bonds       : angle       4.52262 ( 3573)
  Misc. bond           : bond        0.00407 (    2)

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

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

  5158 Ramachandran restraints generated.
    2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5158 Ramachandran restraints generated.
    2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 2358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 222
  time to evaluate  : 0.997 
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: symmetry clash
   revert: symmetry clash
REVERT: A 1284 MET cc_start: 0.3306 (mmp) cc_final: 0.2866 (tmm)
REVERT: A 1317 MET cc_start: 0.0421 (ptp) cc_final: 0.0147 (ptp)
REVERT: A 1453 LEU cc_start: 0.9430 (tp) cc_final: 0.9108 (pp)
REVERT: A 1565 MET cc_start: 0.9246 (ppp) cc_final: 0.8548 (ppp)
REVERT: A 1655 MET cc_start: 0.8694 (tpt) cc_final: 0.8385 (tpp)
REVERT: A 1659 LEU cc_start: 0.9316 (mt) cc_final: 0.8462 (mt)
REVERT: A 1697 LYS cc_start: 0.9118 (mttt) cc_final: 0.8830 (mttm)
REVERT: A 1714 GLN cc_start: 0.8985 (pp30) cc_final: 0.8784 (pp30)
REVERT: A 1782 LEU cc_start: 0.9544 (tp) cc_final: 0.9321 (tp)
REVERT: A 2085 LYS cc_start: 0.9410 (mmtt) cc_final: 0.9164 (mmmm)
REVERT: A 2345 TYR cc_start: 0.8942 (m-80) cc_final: 0.8497 (m-80)
REVERT: A 2385 VAL cc_start: 0.8931 (t) cc_final: 0.8729 (t)
REVERT: A 2432 LEU cc_start: 0.9475 (tp) cc_final: 0.9106 (tp)
REVERT: A 2902 MET cc_start: 0.8667 (mmp) cc_final: 0.8410 (mmm)
REVERT: A 2908 LEU cc_start: 0.9396 (mt) cc_final: 0.9169 (mt)
REVERT: A 2913 ILE cc_start: 0.9361 (mt) cc_final: 0.9083 (mm)
REVERT: A 2925 MET cc_start: 0.9318 (mpp) cc_final: 0.9087 (mpp)
REVERT: A 3541 MET cc_start: 0.7389 (pmm) cc_final: 0.7180 (pmm)
REVERT: A 3633 GLU cc_start: 0.8575 (mp0) cc_final: 0.8180 (mp0)
REVERT: A 3722 MET cc_start: 0.8873 (mmp) cc_final: 0.8422 (mmp)
REVERT: A 3873 MET cc_start: 0.8682 (mmp) cc_final: 0.8312 (mmm)
REVERT: A 3875 MET cc_start: 0.9279 (mpp) cc_final: 0.8875 (mpp)
REVERT: A 3931 LEU cc_start: 0.9635 (mt) cc_final: 0.9404 (mt)
  outliers start: 4
  outliers final: 0
  residues processed: 223
  average time/residue: 0.1230
  time to fit residues: 44.7707
Evaluate side-chains
  144 residues out of total 2358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 0.919 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 258
   random chunks:
   chunk 226 optimal weight:    4.9990
   chunk 140 optimal weight:    3.9990
   chunk 111 optimal weight:    3.9990
   chunk 52 optimal weight:    5.9990
   chunk 27 optimal weight:    3.9990
   chunk 146 optimal weight:    9.9990
   chunk 31 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9990
   chunk 239 optimal weight:    1.9990
   chunk 164 optimal weight:   10.0000
   chunk 91 optimal weight:    4.9990
   overall best weight:    2.3588

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

Flipped N/Q/H residues before XYZ refinement:
** A1811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2741 HIS
** A2777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2931 ASN
A3323 ASN
A3780 ASN
** A4035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.072584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.051593 restraints weight = 117335.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 76)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.052719 restraints weight = 72511.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.053524 restraints weight = 52221.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.054100 restraints weight = 41995.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.054421 restraints weight = 36317.783|
|-----------------------------------------------------------------------------|
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8506
moved from start:          0.1750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  21468  Z= 0.161
  Angle     :  0.596   9.012  29031  Z= 0.302
  Chirality :  0.041   0.177   3287
  Planarity :  0.004   0.076   3652
  Dihedral  :  6.930 145.792   2838
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 13.96
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.03 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  3.01 %
    Favored  : 96.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.30 (0.16), residues: 2579
  helix:  1.15 (0.13), residues: 1536
  sheet: -0.63 (0.36), residues: 201
  loop : -1.32 (0.20), residues: 842

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A3745 
 TYR   0.017   0.001   TYR A3679 
 PHE   0.020   0.001   PHE A3334 
 TRP   0.020   0.001   TRP A2084 
 HIS   0.008   0.001   HIS A1965 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 (21466)
  covalent geometry    : angle       0.59595 (29031)
  hydrogen bonds       : bond        0.03559 ( 1214)
  hydrogen bonds       : angle       4.53925 ( 3573)
  Misc. bond           : bond        0.00409 (    2)

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

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

  5158 Ramachandran restraints generated.
    2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5158 Ramachandran restraints generated.
    2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 2358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 200
  time to evaluate  : 0.672 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1284 MET cc_start: 0.3471 (mmp) cc_final: 0.3036 (tmm)
REVERT: A 1317 MET cc_start: 0.0084 (ptp) cc_final: -0.0131 (ptp)
REVERT: A 1453 LEU cc_start: 0.9471 (tp) cc_final: 0.9193 (pp)
REVERT: A 1518 MET cc_start: 0.9310 (tmm) cc_final: 0.8932 (tmm)
REVERT: A 1565 MET cc_start: 0.9299 (ppp) cc_final: 0.8591 (ppp)
REVERT: A 1655 MET cc_start: 0.8841 (tpt) cc_final: 0.8470 (tpp)
REVERT: A 1659 LEU cc_start: 0.9383 (mt) cc_final: 0.8512 (mt)
REVERT: A 1697 LYS cc_start: 0.9161 (mttt) cc_final: 0.8734 (mttm)
REVERT: A 1714 GLN cc_start: 0.9227 (pp30) cc_final: 0.8937 (pp30)
REVERT: A 1717 ASN cc_start: 0.9046 (m-40) cc_final: 0.8610 (m-40)
REVERT: A 2345 TYR cc_start: 0.9057 (m-80) cc_final: 0.8524 (m-80)
REVERT: A 2385 VAL cc_start: 0.8936 (t) cc_final: 0.7932 (t)
REVERT: A 2432 LEU cc_start: 0.9495 (tp) cc_final: 0.9183 (tp)
REVERT: A 2902 MET cc_start: 0.8649 (mmp) cc_final: 0.8289 (mmm)
REVERT: A 2913 ILE cc_start: 0.9391 (mt) cc_final: 0.9109 (mm)
REVERT: A 2925 MET cc_start: 0.9295 (mpp) cc_final: 0.9075 (mpp)
REVERT: A 2980 MET cc_start: 0.8199 (tmm) cc_final: 0.7658 (tmm)
REVERT: A 3541 MET cc_start: 0.7383 (pmm) cc_final: 0.7169 (pmm)
REVERT: A 3722 MET cc_start: 0.8772 (mmp) cc_final: 0.8375 (mmp)
REVERT: A 3875 MET cc_start: 0.9256 (mpp) cc_final: 0.8944 (mpp)
REVERT: A 3931 LEU cc_start: 0.9659 (mt) cc_final: 0.9436 (mt)
REVERT: A 3938 LEU cc_start: 0.9555 (mm) cc_final: 0.9315 (mm)
  outliers start: 2
  outliers final: 0
  residues processed: 200
  average time/residue: 0.1317
  time to fit residues: 42.2783
Evaluate side-chains
  141 residues out of total 2358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 0.599 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 258
   random chunks:
   chunk 94 optimal weight:    0.0670
   chunk 91 optimal weight:    3.9990
   chunk 75 optimal weight:    3.9990
   chunk 246 optimal weight:    0.9990
   chunk 151 optimal weight:    8.9990
   chunk 42 optimal weight:    0.9990
   chunk 222 optimal weight:    7.9990
   chunk 249 optimal weight:    0.4980
   chunk 160 optimal weight:    1.9990
   chunk 218 optimal weight:    1.9990
   chunk 96 optimal weight:    5.9990
   overall best weight:    0.9124

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

Flipped N/Q/H residues before XYZ refinement:
** A1811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2931 ASN
A3323 ASN
A3780 ASN
** A4035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.074668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.053270 restraints weight = 117512.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 68)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.054312 restraints weight = 75645.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.055086 restraints weight = 55747.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.055634 restraints weight = 45513.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.056013 restraints weight = 39696.599|
|-----------------------------------------------------------------------------|
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8474
moved from start:          0.1896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.054  21468  Z= 0.114
  Angle     :  0.592  10.681  29031  Z= 0.293
  Chirality :  0.041   0.221   3287
  Planarity :  0.004   0.082   3652
  Dihedral  :  6.736 142.610   2838
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 12.56
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.80 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.35 (0.16), residues: 2579
  helix:  1.19 (0.13), residues: 1540
  sheet: -0.62 (0.36), residues: 201
  loop : -1.32 (0.20), residues: 838

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A1373 
 TYR   0.019   0.001   TYR A3679 
 PHE   0.013   0.001   PHE A2827 
 TRP   0.026   0.001   TRP A2084 
 HIS   0.010   0.001   HIS A1965 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 (21466)
  covalent geometry    : angle       0.59196 (29031)
  hydrogen bonds       : bond        0.03424 ( 1214)
  hydrogen bonds       : angle       4.44538 ( 3573)
  Misc. bond           : bond        0.00353 (    2)

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

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

  5158 Ramachandran restraints generated.
    2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5158 Ramachandran restraints generated.
    2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 2358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 223
  time to evaluate  : 0.855 
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 1284 MET cc_start: 0.3431 (mmp) cc_final: 0.3009 (tmm)
REVERT: A 1317 MET cc_start: 0.0214 (ptp) cc_final: -0.0013 (ptp)
REVERT: A 1453 LEU cc_start: 0.9439 (tp) cc_final: 0.9123 (pp)
REVERT: A 1565 MET cc_start: 0.9298 (ppp) cc_final: 0.8542 (ppp)
REVERT: A 1655 MET cc_start: 0.8711 (tpt) cc_final: 0.8387 (tpp)
REVERT: A 1659 LEU cc_start: 0.9315 (mt) cc_final: 0.8460 (mt)
REVERT: A 1697 LYS cc_start: 0.9127 (mttt) cc_final: 0.8810 (mttm)
REVERT: A 1714 GLN cc_start: 0.9152 (pp30) cc_final: 0.8846 (pp30)
REVERT: A 1717 ASN cc_start: 0.8960 (m-40) cc_final: 0.8547 (m-40)
REVERT: A 1782 LEU cc_start: 0.9549 (tp) cc_final: 0.9332 (tp)
REVERT: A 2345 TYR cc_start: 0.9031 (m-80) cc_final: 0.8550 (m-80)
REVERT: A 2432 LEU cc_start: 0.9507 (tp) cc_final: 0.9168 (tp)
REVERT: A 2797 MET cc_start: 0.9378 (ppp) cc_final: 0.9044 (ppp)
REVERT: A 2902 MET cc_start: 0.8618 (mmp) cc_final: 0.8385 (mmm)
REVERT: A 2908 LEU cc_start: 0.9407 (mt) cc_final: 0.9165 (mt)
REVERT: A 2913 ILE cc_start: 0.9359 (mt) cc_final: 0.9095 (mm)
REVERT: A 2925 MET cc_start: 0.9278 (mpp) cc_final: 0.9069 (mpp)
REVERT: A 2980 MET cc_start: 0.8097 (tmm) cc_final: 0.7816 (tmm)
REVERT: A 3633 GLU cc_start: 0.8601 (mp0) cc_final: 0.8132 (mp0)
REVERT: A 3722 MET cc_start: 0.8925 (mmp) cc_final: 0.8503 (mmp)
REVERT: A 3875 MET cc_start: 0.9313 (mpp) cc_final: 0.9049 (mpp)
REVERT: A 3931 LEU cc_start: 0.9641 (mt) cc_final: 0.9438 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 223
  average time/residue: 0.1316
  time to fit residues: 47.4800
Evaluate side-chains
  158 residues out of total 2358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 158
  time to evaluate  : 0.635 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 258
   random chunks:
   chunk 116 optimal weight:    0.4980
   chunk 255 optimal weight:    0.8980
   chunk 81 optimal weight:    5.9990
   chunk 156 optimal weight:    5.9990
   chunk 215 optimal weight:    4.9990
   chunk 248 optimal weight:    2.9990
   chunk 176 optimal weight:    3.9990
   chunk 147 optimal weight:    5.9990
   chunk 51 optimal weight:    1.9990
   chunk 138 optimal weight:    2.9990
   chunk 196 optimal weight:    0.0010
   overall best weight:    1.2790

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

Flipped N/Q/H residues before XYZ refinement:
** A1811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2777 ASN
A2931 ASN
A3323 ASN
A3780 ASN
** A4035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.073727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.052712 restraints weight = 116371.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 65)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.053849 restraints weight = 72135.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.054715 restraints weight = 52071.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.055237 restraints weight = 41626.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.055597 restraints weight = 36093.294|
|-----------------------------------------------------------------------------|
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8483
moved from start:          0.2033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  21468  Z= 0.123
  Angle     :  0.596   9.587  29031  Z= 0.299
  Chirality :  0.041   0.198   3287
  Planarity :  0.004   0.072   3652
  Dihedral  :  6.655 139.686   2838
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 12.58
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.03 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.36 (0.16), residues: 2579
  helix:  1.18 (0.13), residues: 1540
  sheet: -0.62 (0.36), residues: 200
  loop : -1.26 (0.20), residues: 839

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A2627 
 TYR   0.021   0.001   TYR A2571 
 PHE   0.014   0.001   PHE A3518 
 TRP   0.022   0.001   TRP A2084 
 HIS   0.009   0.001   HIS A1965 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 (21466)
  covalent geometry    : angle       0.59637 (29031)
  hydrogen bonds       : bond        0.03444 ( 1214)
  hydrogen bonds       : angle       4.48266 ( 3573)
  Misc. bond           : bond        0.00244 (    2)

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

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

  5158 Ramachandran restraints generated.
    2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5158 Ramachandran restraints generated.
    2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 2358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 208
  time to evaluate  : 0.707 
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 1284 MET cc_start: 0.3735 (mmp) cc_final: 0.3347 (tmm)
REVERT: A 1317 MET cc_start: 0.0016 (ptp) cc_final: -0.0217 (ptp)
REVERT: A 1453 LEU cc_start: 0.9459 (tp) cc_final: 0.9132 (pp)
REVERT: A 1565 MET cc_start: 0.9336 (ppp) cc_final: 0.8532 (ppp)
REVERT: A 1655 MET cc_start: 0.8807 (tpt) cc_final: 0.8448 (tpp)
REVERT: A 1659 LEU cc_start: 0.9340 (mt) cc_final: 0.8418 (mt)
REVERT: A 1697 LYS cc_start: 0.9154 (mttt) cc_final: 0.8912 (mttt)
REVERT: A 1714 GLN cc_start: 0.9187 (pp30) cc_final: 0.8884 (pp30)
REVERT: A 1717 ASN cc_start: 0.9025 (m-40) cc_final: 0.8584 (m-40)
REVERT: A 1782 LEU cc_start: 0.9603 (tp) cc_final: 0.9379 (tp)
REVERT: A 2345 TYR cc_start: 0.9094 (m-80) cc_final: 0.8545 (m-80)
REVERT: A 2426 MET cc_start: 0.8843 (pmm) cc_final: 0.7543 (pmm)
REVERT: A 2432 LEU cc_start: 0.9494 (tp) cc_final: 0.9162 (tp)
REVERT: A 2797 MET cc_start: 0.9367 (ppp) cc_final: 0.9058 (ppp)
REVERT: A 2902 MET cc_start: 0.8662 (mmp) cc_final: 0.8438 (mmm)
REVERT: A 2908 LEU cc_start: 0.9415 (mt) cc_final: 0.9177 (mt)
REVERT: A 2913 ILE cc_start: 0.9428 (mt) cc_final: 0.9194 (mm)
REVERT: A 2925 MET cc_start: 0.9319 (mpp) cc_final: 0.9102 (mpp)
REVERT: A 2980 MET cc_start: 0.8113 (tmm) cc_final: 0.7887 (tmm)
REVERT: A 3633 GLU cc_start: 0.8664 (mp0) cc_final: 0.8237 (mp0)
REVERT: A 3722 MET cc_start: 0.8956 (mmp) cc_final: 0.8529 (mmp)
REVERT: A 3875 MET cc_start: 0.9304 (mpp) cc_final: 0.8903 (mpp)
REVERT: A 3931 LEU cc_start: 0.9668 (mt) cc_final: 0.9453 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 208
  average time/residue: 0.1355
  time to fit residues: 46.1559
Evaluate side-chains
  152 residues out of total 2358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 0.846 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 258
   random chunks:
   chunk 113 optimal weight:   10.0000
   chunk 223 optimal weight:    3.9990
   chunk 160 optimal weight:    0.0030
   chunk 75 optimal weight:    0.8980
   chunk 190 optimal weight:    6.9990
   chunk 177 optimal weight:    3.9990
   chunk 173 optimal weight:    4.9990
   chunk 125 optimal weight:    1.9990
   chunk 201 optimal weight:    7.9990
   chunk 87 optimal weight:    6.9990
   chunk 132 optimal weight:    7.9990
   overall best weight:    2.1796

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

Flipped N/Q/H residues before XYZ refinement:
** A1811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1967 HIS
** A2293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2931 ASN
A3323 ASN
A3453 GLN
A3780 ASN
** A4035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.073142 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.051813 restraints weight = 121079.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 76)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.052789 restraints weight = 76890.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.053602 restraints weight = 56543.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.054066 restraints weight = 46061.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.054410 restraints weight = 40590.919|
|-----------------------------------------------------------------------------|
r_work (final): 0.3174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8517
moved from start:          0.2099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  21468  Z= 0.155
  Angle     :  0.616   9.290  29031  Z= 0.310
  Chirality :  0.041   0.178   3287
  Planarity :  0.004   0.073   3652
  Dihedral  :  6.649 138.957   2838
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 13.81
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.07 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.36 (0.16), residues: 2579
  helix:  1.18 (0.13), residues: 1538
  sheet: -0.73 (0.36), residues: 201
  loop : -1.23 (0.20), residues: 840

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1373 
 TYR   0.015   0.001   TYR A3679 
 PHE   0.019   0.001   PHE A2795 
 TRP   0.022   0.001   TRP A1445 
 HIS   0.009   0.001   HIS A1965 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 (21466)
  covalent geometry    : angle       0.61575 (29031)
  hydrogen bonds       : bond        0.03535 ( 1214)
  hydrogen bonds       : angle       4.52219 ( 3573)
  Misc. bond           : bond        0.00320 (    2)

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

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

  5158 Ramachandran restraints generated.
    2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5158 Ramachandran restraints generated.
    2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 2358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 200
  time to evaluate  : 0.854 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1284 MET cc_start: 0.3941 (mmp) cc_final: 0.3562 (tmm)
REVERT: A 1317 MET cc_start: 0.0518 (ptp) cc_final: 0.0246 (ptp)
REVERT: A 1437 LYS cc_start: 0.8310 (mptt) cc_final: 0.8026 (mttp)
REVERT: A 1453 LEU cc_start: 0.9418 (tp) cc_final: 0.9113 (pp)
REVERT: A 1518 MET cc_start: 0.9210 (tmm) cc_final: 0.8789 (tmm)
REVERT: A 1565 MET cc_start: 0.9319 (ppp) cc_final: 0.8636 (ppp)
REVERT: A 1655 MET cc_start: 0.8787 (tpt) cc_final: 0.8409 (tpp)
REVERT: A 1659 LEU cc_start: 0.9333 (mt) cc_final: 0.8424 (mt)
REVERT: A 1697 LYS cc_start: 0.9155 (mttt) cc_final: 0.8810 (mttm)
REVERT: A 1714 GLN cc_start: 0.9211 (pp30) cc_final: 0.8913 (pp30)
REVERT: A 1717 ASN cc_start: 0.8954 (m-40) cc_final: 0.8524 (m-40)
REVERT: A 1782 LEU cc_start: 0.9547 (tp) cc_final: 0.9314 (tp)
REVERT: A 2345 TYR cc_start: 0.9022 (m-80) cc_final: 0.8647 (m-80)
REVERT: A 2432 LEU cc_start: 0.9461 (tp) cc_final: 0.9111 (tp)
REVERT: A 2738 MET cc_start: 0.8925 (ppp) cc_final: 0.8695 (ppp)
REVERT: A 2797 MET cc_start: 0.9366 (ppp) cc_final: 0.9047 (ppp)
REVERT: A 2908 LEU cc_start: 0.9413 (mt) cc_final: 0.9162 (mt)
REVERT: A 2913 ILE cc_start: 0.9471 (mt) cc_final: 0.9259 (mm)
REVERT: A 2925 MET cc_start: 0.9260 (mpp) cc_final: 0.9060 (mpp)
REVERT: A 3633 GLU cc_start: 0.8567 (mp0) cc_final: 0.8181 (mp0)
REVERT: A 3722 MET cc_start: 0.8940 (mmp) cc_final: 0.8522 (mmp)
REVERT: A 3875 MET cc_start: 0.9333 (mpp) cc_final: 0.8954 (mpp)
REVERT: A 3938 LEU cc_start: 0.9523 (mm) cc_final: 0.9322 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 200
  average time/residue: 0.1350
  time to fit residues: 44.1238
Evaluate side-chains
  141 residues out of total 2358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 0.821 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 258
   random chunks:
   chunk 44 optimal weight:    3.9990
   chunk 240 optimal weight:    0.3980
   chunk 15 optimal weight:    5.9990
   chunk 32 optimal weight:    0.7980
   chunk 257 optimal weight:    2.9990
   chunk 85 optimal weight:    0.9990
   chunk 65 optimal weight:    4.9990
   chunk 241 optimal weight:    5.9990
   chunk 184 optimal weight:    0.7980
   chunk 155 optimal weight:    1.9990
   chunk 121 optimal weight:    0.8980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** A1811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2931 ASN
A3323 ASN
** A3336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A3780 ASN
** A4035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.074044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 86)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.052844 restraints weight = 115750.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 74)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.054047 restraints weight = 72502.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.054899 restraints weight = 52471.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.055425 restraints weight = 42209.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.055819 restraints weight = 36689.838|
|-----------------------------------------------------------------------------|
r_work (final): 0.3200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8476
moved from start:          0.2217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  21468  Z= 0.118
  Angle     :  0.613   9.444  29031  Z= 0.305
  Chirality :  0.041   0.180   3287
  Planarity :  0.004   0.071   3652
  Dihedral  :  6.515 135.487   2838
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 12.25
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.11 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.40 (0.16), residues: 2579
  helix:  1.20 (0.13), residues: 1536
  sheet: -0.59 (0.36), residues: 201
  loop : -1.22 (0.20), residues: 842

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A3745 
 TYR   0.015   0.001   TYR A3679 
 PHE   0.022   0.001   PHE A2827 
 TRP   0.021   0.001   TRP A2084 
 HIS   0.011   0.001   HIS A1965 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 (21466)
  covalent geometry    : angle       0.61346 (29031)
  hydrogen bonds       : bond        0.03396 ( 1214)
  hydrogen bonds       : angle       4.47193 ( 3573)
  Misc. bond           : bond        0.00355 (    2)

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

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

  5158 Ramachandran restraints generated.
    2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5158 Ramachandran restraints generated.
    2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 2358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 215
  time to evaluate  : 0.865 
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: symmetry clash
   revert: symmetry clash
REVERT: A 1284 MET cc_start: 0.4229 (mmp) cc_final: 0.3857 (tmm)
REVERT: A 1317 MET cc_start: 0.0188 (ptp) cc_final: -0.0043 (ptp)
REVERT: A 1415 MET cc_start: 0.4417 (ppp) cc_final: 0.4019 (ptp)
REVERT: A 1453 LEU cc_start: 0.9445 (tp) cc_final: 0.9119 (pp)
REVERT: A 1518 MET cc_start: 0.9250 (tmm) cc_final: 0.8774 (tmm)
REVERT: A 1565 MET cc_start: 0.8963 (ppp) cc_final: 0.8520 (ppp)
REVERT: A 1655 MET cc_start: 0.8774 (tpt) cc_final: 0.8438 (tpp)
REVERT: A 1659 LEU cc_start: 0.9322 (mt) cc_final: 0.8396 (mt)
REVERT: A 1697 LYS cc_start: 0.9120 (mttt) cc_final: 0.8872 (mttt)
REVERT: A 1714 GLN cc_start: 0.9196 (pp30) cc_final: 0.8887 (pp30)
REVERT: A 1717 ASN cc_start: 0.8999 (m-40) cc_final: 0.8552 (m-40)
REVERT: A 1765 ILE cc_start: 0.8778 (mt) cc_final: 0.8572 (mt)
REVERT: A 1782 LEU cc_start: 0.9611 (tp) cc_final: 0.9398 (tp)
REVERT: A 2345 TYR cc_start: 0.9107 (m-80) cc_final: 0.8722 (m-80)
REVERT: A 2432 LEU cc_start: 0.9551 (tp) cc_final: 0.9204 (tp)
REVERT: A 2738 MET cc_start: 0.8923 (ppp) cc_final: 0.8677 (ppp)
REVERT: A 2797 MET cc_start: 0.9363 (ppp) cc_final: 0.9050 (ppp)
REVERT: A 2908 LEU cc_start: 0.9418 (mt) cc_final: 0.9166 (mt)
REVERT: A 3633 GLU cc_start: 0.8732 (mp0) cc_final: 0.8244 (mp0)
REVERT: A 3635 PHE cc_start: 0.9155 (m-80) cc_final: 0.8553 (m-80)
REVERT: A 3722 MET cc_start: 0.8966 (mmp) cc_final: 0.8543 (mmp)
REVERT: A 3875 MET cc_start: 0.9320 (mpp) cc_final: 0.8955 (mpp)
REVERT: A 3931 LEU cc_start: 0.9665 (mt) cc_final: 0.9465 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 215
  average time/residue: 0.1361
  time to fit residues: 48.1674
Evaluate side-chains
  155 residues out of total 2358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 0.825 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 258
   random chunks:
   chunk 44 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9980
   chunk 69 optimal weight:    0.5980
   chunk 49 optimal weight:    2.9990
   chunk 16 optimal weight:    5.9990
   chunk 178 optimal weight:    8.9990
   chunk 63 optimal weight:    8.9990
   chunk 36 optimal weight:    0.2980
   chunk 111 optimal weight:    0.4980
   chunk 187 optimal weight:    6.9990
   chunk 33 optimal weight:    9.9990
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
** A1811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2931 ASN
A3323 ASN
A3780 ASN
** A4035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.075017 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.053404 restraints weight = 117880.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.054633 restraints weight = 75595.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 67)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.055432 restraints weight = 55913.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.055946 restraints weight = 45411.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.056352 restraints weight = 39720.872|
|-----------------------------------------------------------------------------|
r_work (final): 0.3225
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8467
moved from start:          0.2351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.050  21468  Z= 0.114
  Angle     :  0.624  14.064  29031  Z= 0.306
  Chirality :  0.041   0.184   3287
  Planarity :  0.004   0.070   3652
  Dihedral  :  6.329 131.119   2838
  Min Nonbonded Distance : 2.372

Molprobity Statistics.
  All-atom Clashscore : 11.80
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.15 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.55 %
    Favored  : 99.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.45 (0.16), residues: 2579
  helix:  1.24 (0.13), residues: 1527
  sheet: -0.54 (0.36), residues: 201
  loop : -1.16 (0.20), residues: 851

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A3305 
 TYR   0.018   0.001   TYR A3679 
 PHE   0.024   0.001   PHE A2669 
 TRP   0.021   0.001   TRP A2084 
 HIS   0.011   0.001   HIS A1965 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 (21466)
  covalent geometry    : angle       0.62366 (29031)
  hydrogen bonds       : bond        0.03372 ( 1214)
  hydrogen bonds       : angle       4.43479 ( 3573)
  Misc. bond           : bond        0.00357 (    2)

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

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

  5158 Ramachandran restraints generated.
    2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5158 Ramachandran restraints generated.
    2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 2358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 209
  time to evaluate  : 0.884 
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: symmetry clash
   revert: symmetry clash
REVERT: A 1284 MET cc_start: 0.4233 (mmp) cc_final: 0.3858 (tmm)
REVERT: A 1317 MET cc_start: 0.0469 (ptp) cc_final: 0.0202 (ptp)
REVERT: A 1415 MET cc_start: 0.4141 (ppp) cc_final: 0.3840 (ptp)
REVERT: A 1453 LEU cc_start: 0.9408 (tp) cc_final: 0.9105 (pp)
REVERT: A 1518 MET cc_start: 0.9201 (tmm) cc_final: 0.8755 (tmm)
REVERT: A 1565 MET cc_start: 0.8945 (ppp) cc_final: 0.8456 (ppp)
REVERT: A 1655 MET cc_start: 0.8722 (tpt) cc_final: 0.8392 (tpp)
REVERT: A 1659 LEU cc_start: 0.9297 (mt) cc_final: 0.8450 (mt)
REVERT: A 1697 LYS cc_start: 0.9097 (mttt) cc_final: 0.8796 (mtpt)
REVERT: A 1714 GLN cc_start: 0.9176 (pp30) cc_final: 0.8872 (pp30)
REVERT: A 1717 ASN cc_start: 0.8932 (m-40) cc_final: 0.8483 (m-40)
REVERT: A 2345 TYR cc_start: 0.9023 (m-80) cc_final: 0.8648 (m-80)
REVERT: A 2432 LEU cc_start: 0.9506 (tp) cc_final: 0.9160 (tp)
REVERT: A 2738 MET cc_start: 0.8934 (ppp) cc_final: 0.8730 (ppp)
REVERT: A 2797 MET cc_start: 0.9362 (ppp) cc_final: 0.9038 (ppp)
REVERT: A 2908 LEU cc_start: 0.9406 (mt) cc_final: 0.9153 (mt)
REVERT: A 3633 GLU cc_start: 0.8727 (mp0) cc_final: 0.8250 (mp0)
REVERT: A 3635 PHE cc_start: 0.9081 (m-80) cc_final: 0.8501 (m-80)
REVERT: A 3696 MET cc_start: 0.8499 (mmm) cc_final: 0.8043 (tpt)
REVERT: A 3722 MET cc_start: 0.8933 (mmp) cc_final: 0.8525 (mmp)
REVERT: A 3875 MET cc_start: 0.9360 (mpp) cc_final: 0.8919 (mpp)
REVERT: A 3908 LYS cc_start: 0.9133 (mmtt) cc_final: 0.8919 (mmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 209
  average time/residue: 0.1372
  time to fit residues: 47.1844
Evaluate side-chains
  164 residues out of total 2358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 164
  time to evaluate  : 0.827 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 258
   random chunks:
   chunk 56 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 210 optimal weight:   10.0000
   chunk 156 optimal weight:    0.9990
   chunk 189 optimal weight:    9.9990
   chunk 131 optimal weight:    0.4980
   chunk 219 optimal weight:   10.0000
   chunk 199 optimal weight:    8.9990
   chunk 144 optimal weight:    8.9990
   chunk 209 optimal weight:    7.9990
   chunk 84 optimal weight:    0.7980
   overall best weight:    1.2586

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

Flipped N/Q/H residues before XYZ refinement:
** A1811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2931 ASN
A3323 ASN
A3780 ASN
** A4035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.074180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.053083 restraints weight = 116730.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 62)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.054244 restraints weight = 72941.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.055073 restraints weight = 52596.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.055665 restraints weight = 42349.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.056003 restraints weight = 36526.447|
|-----------------------------------------------------------------------------|
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8478
moved from start:          0.2434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  21468  Z= 0.123
  Angle     :  0.618  10.573  29031  Z= 0.307
  Chirality :  0.041   0.220   3287
  Planarity :  0.004   0.086   3652
  Dihedral  :  6.302 131.047   2838
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 12.56
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.03 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.47 %
    Favored  : 99.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.47 (0.16), residues: 2579
  helix:  1.26 (0.13), residues: 1535
  sheet: -0.52 (0.37), residues: 201
  loop : -1.20 (0.20), residues: 843

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.000   ARG A3565 
 TYR   0.015   0.001   TYR A3679 
 PHE   0.016   0.001   PHE A2669 
 TRP   0.020   0.001   TRP A2084 
 HIS   0.010   0.001   HIS A1965 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 (21466)
  covalent geometry    : angle       0.61824 (29031)
  hydrogen bonds       : bond        0.03376 ( 1214)
  hydrogen bonds       : angle       4.41814 ( 3573)
  Misc. bond           : bond        0.00402 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3974.89 seconds
wall clock time: 69 minutes 35.64 seconds (4175.64 seconds total)