Starting phenix.real_space_refine
on Thu Feb  5 19:59:19 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9pnt_71771/02_2026/9pnt_71771.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9pnt_71771/02_2026/9pnt_71771.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9pnt_71771/02_2026/9pnt_71771.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9pnt_71771/02_2026/9pnt_71771.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9pnt_71771/02_2026/9pnt_71771.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9pnt_71771/02_2026/9pnt_71771.cif"
  }
  resolution = 4.3
  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=   0.018
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      91      5.16       5
     C   11936      2.51       5
     N    3298      2.21       5
     O    3684      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 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: 19009
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 19009
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2444, 19009
          Classifications: {'peptide': 2444}
          Link IDs: {'PTRANS': 84, 'TRANS': 2359}
          Chain breaks: 3
  Time building chain proxies: 4.06, per 1000 atoms: 0.21
  Number of scatterers: 19009
  At special positions: 0
  Unit cell: (171.597, 133.87, 119.266, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      91     16.00
     O    3684      8.00
     N    3298      7.00
     C   11936      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.40
  Conformation dependent library (CDL) restraints added in 982.5 milliseconds
  

  4872 Ramachandran restraints generated.
    2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4586

  Finding SS restraints...
    Secondary structure from input PDB file:
      124 helices and 21 sheets defined
      65.9% alpha, 5.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.89
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1050 through 1059
      removed outlier: 3.844A  pdb=" N   ALA A1056 " --> pdb=" O   LEU A1052 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1061 through 1070
    Processing helix  chain 'A' and resid 1079 through 1110
      removed outlier: 3.697A  pdb=" N   GLU A1088 " --> pdb=" O   LYS A1084 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   GLY A1095 " --> pdb=" O   GLU A1091 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   ALA A1105 " --> pdb=" O   ARG A1101 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1112 through 1118
    Processing helix  chain 'A' and resid 1122 through 1126
      removed outlier: 3.659A  pdb=" N   ARG A1125 " --> pdb=" O   GLU A1122 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   TRP A1126 " --> pdb=" O   ALA A1123 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1122 through 1126'
    Processing helix  chain 'A' and resid 1129 through 1133
      removed outlier: 3.862A  pdb=" N   ASN A1133 " --> pdb=" O   LYS A1130 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1145 through 1163
      removed outlier: 3.520A  pdb=" N   LEU A1161 " --> pdb=" O   LEU A1157 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1164 through 1167
      removed outlier: 3.656A  pdb=" N   THR A1167 " --> pdb=" O   THR A1164 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1164 through 1167'
    Processing helix  chain 'A' and resid 1171 through 1180
    Processing helix  chain 'A' and resid 1182 through 1186
    Processing helix  chain 'A' and resid 1189 through 1195
    Processing helix  chain 'A' and resid 1200 through 1216
      removed outlier: 3.548A  pdb=" N   LYS A1210 " --> pdb=" O   SER A1206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1224 through 1229
    Processing helix  chain 'A' and resid 1229 through 1246
      removed outlier: 3.625A  pdb=" N   THR A1233 " --> pdb=" O   LYS A1229 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1256 through 1260
    Processing helix  chain 'A' and resid 1279 through 1284
    Processing helix  chain 'A' and resid 1286 through 1293
    Processing helix  chain 'A' and resid 1322 through 1333
    Processing helix  chain 'A' and resid 1340 through 1351
    Processing helix  chain 'A' and resid 1351 through 1360
    Processing helix  chain 'A' and resid 1365 through 1369
      removed outlier: 3.712A  pdb=" N   LEU A1369 " --> pdb=" O   LYS A1366 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1370 through 1400
      removed outlier: 3.501A  pdb=" N   LYS A1375 " --> pdb=" O   ASP A1371 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   SER A1376 " --> pdb=" O   ASN A1372 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   VAL A1384 " --> pdb=" O   LYS A1380 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   GLN A1397 " --> pdb=" O   SER A1393 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   ALA A1400 " --> pdb=" O   GLU A1396 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1404 through 1408
      removed outlier: 3.903A  pdb=" N   VAL A1408 " --> pdb=" O   ILE A1405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1433 through 1438
      removed outlier: 3.531A  pdb=" N   GLU A1438 " --> pdb=" O   LYS A1434 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1454 through 1468
      removed outlier: 3.511A  pdb=" N   ALA A1459 " --> pdb=" O   GLU A1455 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1471 through 1475
      removed outlier: 3.884A  pdb=" N   MET A1475 " --> pdb=" O   VAL A1472 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1476 through 1490
      removed outlier: 3.504A  pdb=" N   LEU A1487 " --> pdb=" O   GLU A1483 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1492 through 1506
      removed outlier: 3.582A  pdb=" N   THR A1504 " --> pdb=" O   VAL A1500 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1511 through 1521
    Processing helix  chain 'A' and resid 1522 through 1524
      No H-bonds generated for 'chain 'A' and resid 1522 through 1524'
    Processing helix  chain 'A' and resid 1525 through 1540
      removed outlier: 3.642A  pdb=" N   LEU A1529 " --> pdb=" O   SER A1525 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   MET A1530 " --> pdb=" O   PHE A1526 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   ALA A1531 " --> pdb=" O   VAL A1527 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   VAL A1540 " --> pdb=" O   SER A1536 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1543 through 1546
      removed outlier: 3.749A  pdb=" N   ALA A1546 " --> pdb=" O   ASP A1543 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1543 through 1546'
    Processing helix  chain 'A' and resid 1559 through 1569
    Processing helix  chain 'A' and resid 1575 through 1584
      removed outlier: 3.957A  pdb=" N   LYS A1584 " --> pdb=" O   ARG A1580 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1595 through 1603
    Processing helix  chain 'A' and resid 1607 through 1627
    Processing helix  chain 'A' and resid 1630 through 1648
      removed outlier: 3.703A  pdb=" N   PHE A1647 " --> pdb=" O   LEU A1643 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1663 through 1665
      No H-bonds generated for 'chain 'A' and resid 1663 through 1665'
    Processing helix  chain 'A' and resid 1666 through 1675
      removed outlier: 3.524A  pdb=" N   ILE A1674 " --> pdb=" O   LEU A1670 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1678 through 1708
      removed outlier: 3.590A  pdb=" N   VAL A1690 " --> pdb=" O   LEU A1686 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ASP A1700 " --> pdb=" O   GLU A1696 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1712 through 1719
    Processing helix  chain 'A' and resid 1724 through 1744
    Processing helix  chain 'A' and resid 1776 through 1790
    Processing helix  chain 'A' and resid 1790 through 1803
    Processing helix  chain 'A' and resid 1803 through 1840
      removed outlier: 3.758A  pdb=" N   VAL A1807 " --> pdb=" O   GLY A1803 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   GLN A1833 " --> pdb=" O   LYS A1829 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   GLU A1834 " --> pdb=" O   GLN A1830 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   LYS A1835 " --> pdb=" O   ARG A1831 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1852 through 1862
    Processing helix  chain 'A' and resid 1863 through 1867
    Processing helix  chain 'A' and resid 1915 through 1924
    Processing helix  chain 'A' and resid 1925 through 1936
      removed outlier: 3.530A  pdb=" N   THR A1935 " --> pdb=" O   GLN A1931 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1956 through 1972
    Processing helix  chain 'A' and resid 1975 through 1991
      removed outlier: 3.605A  pdb=" N   LYS A1986 " --> pdb=" O   GLU A1982 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ASN A1990 " --> pdb=" O   LYS A1986 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1992 through 1996
      removed outlier: 3.545A  pdb=" N   LYS A1995 " --> pdb=" O   ASP A1992 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1997 through 2009
      removed outlier: 3.808A  pdb=" N   SER A2007 " --> pdb=" O   ALA A2003 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2011 through 2015
      removed outlier: 3.585A  pdb=" N   ARG A2014 " --> pdb=" O   TYR A2011 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   GLU A2015 " --> pdb=" O   ASP A2012 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 2011 through 2015'
    Processing helix  chain 'A' and resid 2018 through 2048
      removed outlier: 3.801A  pdb=" N   ILE A2029 " --> pdb=" O   ALA A2025 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   GLU A2030 " --> pdb=" O   ALA A2026 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   ARG A2031 " --> pdb=" O   SER A2027 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2076 through 2101
      removed outlier: 3.544A  pdb=" N   ASP A2082 " --> pdb=" O   GLU A2078 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2143 through 2148
      removed outlier: 3.660A  pdb=" N   ILE A2147 " --> pdb=" O   ASN A2143 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2151 through 2168
      removed outlier: 3.714A  pdb=" N   ALA A2156 " --> pdb=" O   SER A2152 " (cutoff:3.500A)
      removed outlier: 4.871A  pdb=" N   THR A2157 " --> pdb=" O   THR A2153 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   LEU A2158 " --> pdb=" O   GLN A2154 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   ALA A2159 " --> pdb=" O   ALA A2155 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   LYS A2163 " --> pdb=" O   ALA A2159 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   LYS A2168 " --> pdb=" O   SER A2164 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2176 through 2188
      removed outlier: 3.638A  pdb=" N   ALA A2184 " --> pdb=" O   VAL A2180 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   ARG A2185 " --> pdb=" O   ALA A2181 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   GLN A2186 " --> pdb=" O   GLU A2182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2196 through 2203
    Processing helix  chain 'A' and resid 2222 through 2244
      removed outlier: 3.542A  pdb=" N   LEU A2230 " --> pdb=" O   LEU A2226 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   VAL A2231 " --> pdb=" O   ILE A2227 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   THR A2235 " --> pdb=" O   VAL A2231 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   GLU A2238 " --> pdb=" O   SER A2234 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   VAL A2239 " --> pdb=" O   THR A2235 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2249 through 2267
      removed outlier: 3.554A  pdb=" N   GLU A2264 " --> pdb=" O   GLU A2260 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   GLN A2265 " --> pdb=" O   GLY A2261 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ARG A2267 " --> pdb=" O   MET A2263 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2275 through 2294
      removed outlier: 3.643A  pdb=" N   GLU A2280 " --> pdb=" O   PRO A2276 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   ALA A2281 " --> pdb=" O   GLU A2277 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   HIS A2292 " --> pdb=" O   THR A2288 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2299 through 2318
    Processing helix  chain 'A' and resid 2318 through 2324
      removed outlier: 3.804A  pdb=" N   LYS A2324 " --> pdb=" O   ALA A2320 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2329 through 2348
    Processing helix  chain 'A' and resid 2376 through 2382
      removed outlier: 3.739A  pdb=" N   VAL A2380 " --> pdb=" O   THR A2376 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2395 through 2409
      removed outlier: 3.729A  pdb=" N   SER A2399 " --> pdb=" O   ASN A2395 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2410 through 2413
    Processing helix  chain 'A' and resid 2426 through 2443
      removed outlier: 3.568A  pdb=" N   ALA A2430 " --> pdb=" O   ASN A2426 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   GLN A2442 " --> pdb=" O   VAL A2438 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2449 through 2468
      removed outlier: 3.543A  pdb=" N   SER A2454 " --> pdb=" O   ALA A2450 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   VAL A2455 " --> pdb=" O   GLN A2451 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   GLU A2466 " --> pdb=" O   ALA A2462 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2474 through 2485
      removed outlier: 3.912A  pdb=" N   GLU A2479 " --> pdb=" O   ALA A2475 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   LEU A2480 " --> pdb=" O   ARG A2476 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2489 through 2494
    Processing helix  chain 'A' and resid 2501 through 2517
      removed outlier: 4.040A  pdb=" N   ARG A2505 " --> pdb=" O   ASN A2501 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   THR A2514 " --> pdb=" O   GLN A2510 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2530 through 2542
      removed outlier: 3.952A  pdb=" N   THR A2534 " --> pdb=" O   SER A2530 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   MET A2540 " --> pdb=" O   LEU A2536 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   VAL A2541 " --> pdb=" O   GLY A2537 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2542 through 2551
      removed outlier: 3.866A  pdb=" N   ARG A2546 " --> pdb=" O   ASN A2542 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   SER A2547 " --> pdb=" O   GLU A2543 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   ILE A2548 " --> pdb=" O   GLU A2544 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   GLU A2551 " --> pdb=" O   SER A2547 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2555 through 2559
    Processing helix  chain 'A' and resid 2564 through 2585
      removed outlier: 3.649A  pdb=" N   THR A2574 " --> pdb=" O   THR A2570 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   GLN A2575 " --> pdb=" O   ASN A2571 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2587 through 2592
    Processing helix  chain 'A' and resid 2593 through 2615
      removed outlier: 3.564A  pdb=" N   GLU A2602 " --> pdb=" O   ASP A2598 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   THR A2603 " --> pdb=" O   ALA A2599 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   ARG A2611 " --> pdb=" O   ALA A2607 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   SER A2613 " --> pdb=" O   LEU A2609 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2624 through 2641
      removed outlier: 3.613A  pdb=" N   ARG A2639 " --> pdb=" O   ASP A2635 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   LEU A2640 " --> pdb=" O   SER A2636 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2665 through 2674
      removed outlier: 3.695A  pdb=" N   LEU A2669 " --> pdb=" O   HIS A2665 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   ALA A2671 " --> pdb=" O   ALA A2667 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2681 through 2684
    Processing helix  chain 'A' and resid 2685 through 2693
      removed outlier: 4.039A  pdb=" N   ALA A2689 " --> pdb=" O   GLY A2685 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2695 through 2708
      removed outlier: 3.955A  pdb=" N   PHE A2699 " --> pdb=" O   VAL A2695 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ASP A2701 " --> pdb=" O   GLN A2697 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   LEU A2702 " --> pdb=" O   PRO A2698 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   ASP A2705 " --> pdb=" O   ASP A2701 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2715 through 2736
      removed outlier: 3.508A  pdb=" N   LEU A2719 " --> pdb=" O   ASN A2715 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   LEU A2722 " --> pdb=" O   ASP A2718 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   SER A2725 " --> pdb=" O   LYS A2721 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ILE A2727 " --> pdb=" O   VAL A2723 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   SER A2728 " --> pdb=" O   LYS A2724 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   GLN A2729 " --> pdb=" O   SER A2725 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   GLU A2736 " --> pdb=" O   GLN A2732 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2737 through 2744
    Processing helix  chain 'A' and resid 2751 through 2763
    Processing helix  chain 'A' and resid 2766 through 2773
      removed outlier: 3.731A  pdb=" N   GLU A2772 " --> pdb=" O   VAL A2769 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2775 through 2784
      removed outlier: 3.534A  pdb=" N   ARG A2780 " --> pdb=" O   MET A2776 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   SER A2784 " --> pdb=" O   ARG A2780 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2785 through 2805
      removed outlier: 3.734A  pdb=" N   VAL A2789 " --> pdb=" O   SER A2785 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   GLN A2803 " --> pdb=" O   GLU A2799 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2807 through 2825
      removed outlier: 3.649A  pdb=" N   ILE A2823 " --> pdb=" O   ALA A2819 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2834 through 2841
      removed outlier: 3.631A  pdb=" N   ARG A2840 " --> pdb=" O   HIS A2836 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2853 through 2867
      removed outlier: 3.727A  pdb=" N   GLU A2867 " --> pdb=" O   LEU A2863 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2870 through 2884
      removed outlier: 3.511A  pdb=" N   GLU A2879 " --> pdb=" O   ASP A2875 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   GLN A2882 " --> pdb=" O   SER A2878 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2884 through 2907
      removed outlier: 3.563A  pdb=" N   MET A2895 " --> pdb=" O   SER A2891 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   GLU A2901 " --> pdb=" O   GLY A2897 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   GLU A2902 " --> pdb=" O   GLN A2898 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2909 through 2914
      removed outlier: 3.686A  pdb=" N   LEU A2914 " --> pdb=" O   ASN A2910 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2936 through 2941
      removed outlier: 3.810A  pdb=" N   LYS A2941 " --> pdb=" O   LYS A2937 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3010 through 3021
      removed outlier: 3.578A  pdb=" N   ARG A3016 " --> pdb=" O   PRO A3012 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   LYS A3019 " --> pdb=" O   GLU A3015 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   ALA A3020 " --> pdb=" O   ARG A3016 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3049 through 3057
      removed outlier: 3.792A  pdb=" N   HIS A3055 " --> pdb=" O   MET A3052 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3061 through 3101
      removed outlier: 3.585A  pdb=" N   GLY A3067 " --> pdb=" O   ALA A3063 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   GLU A3075 " --> pdb=" O   GLY A3071 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   ASN A3083 " --> pdb=" O   ALA A3079 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ASP A3084 " --> pdb=" O   GLN A3080 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3102 through 3106
      removed outlier: 3.893A  pdb=" N   LYS A3105 " --> pdb=" O   SER A3102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3117 through 3126
    Processing helix  chain 'A' and resid 3128 through 3139
      removed outlier: 3.569A  pdb=" N   LYS A3134 " --> pdb=" O   GLU A3130 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   LEU A3138 " --> pdb=" O   LYS A3134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3148 through 3155
      removed outlier: 3.659A  pdb=" N   ASP A3153 " --> pdb=" O   ASP A3149 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   ALA A3154 " --> pdb=" O   MET A3150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3173 through 3188
      removed outlier: 3.903A  pdb=" N   LYS A3182 " --> pdb=" O   ASP A3178 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   MET A3183 " --> pdb=" O   THR A3179 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   LEU A3185 " --> pdb=" O   LYS A3181 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   GLY A3186 " --> pdb=" O   LYS A3182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3189 through 3197
      removed outlier: 3.561A  pdb=" N   VAL A3195 " --> pdb=" O   LYS A3191 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3203 through 3207
      removed outlier: 3.919A  pdb=" N   VAL A3207 " --> pdb=" O   GLN A3204 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3209 through 3236
      removed outlier: 3.643A  pdb=" N   VAL A3213 " --> pdb=" O   ASP A3209 " (cutoff:3.500A)
      removed outlier: 4.373A  pdb=" N   ILE A3214 " --> pdb=" O   ALA A3210 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   VAL A3215 " --> pdb=" O   LYS A3211 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   VAL A3220 " --> pdb=" O   VAL A3216 " (cutoff:3.500A)
      removed outlier: 4.720A  pdb=" N   VAL A3221 " --> pdb=" O   LYS A3217 " (cutoff:3.500A)
      Proline residue:  A3222  - end of helix
      removed outlier: 3.629A  pdb=" N   ILE A3230 " --> pdb=" O   PHE A3226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3239 through 3273
      removed outlier: 3.830A  pdb=" N   ILE A3243 " --> pdb=" O   PRO A3239 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   VAL A3245 " --> pdb=" O   LYS A3241 " (cutoff:3.500A)
      Proline residue:  A3248  - end of helix
      removed outlier: 3.625A  pdb=" N   TYR A3257 " --> pdb=" O   GLU A3253 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   ILE A3258 " --> pdb=" O   ILE A3254 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   LYS A3259 " --> pdb=" O   ASN A3255 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   ARG A3263 " --> pdb=" O   LYS A3259 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   GLN A3264 " --> pdb=" O   SER A3260 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   ASP A3266 " --> pdb=" O   LEU A3262 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   GLU A3268 " --> pdb=" O   GLN A3264 " (cutoff:3.500A)
      removed outlier: 5.605A  pdb=" N   ALA A3269 " --> pdb=" O   ILE A3265 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   GLU A3270 " --> pdb=" O   ASP A3266 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3277 through 3297
      removed outlier: 3.931A  pdb=" N   VAL A3281 " --> pdb=" O   ASN A3277 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   ARG A3297 " --> pdb=" O   ASP A3293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3300 through 3307
      removed outlier: 3.533A  pdb=" N   ILE A3304 " --> pdb=" O   ILE A3300 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   GLY A3307 " --> pdb=" O   LEU A3303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3308 through 3311
      removed outlier: 3.908A  pdb=" N   SER A3311 " --> pdb=" O   GLU A3308 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 3308 through 3311'
    Processing helix  chain 'A' and resid 3321 through 3327
      removed outlier: 3.603A  pdb=" N   ALA A3325 " --> pdb=" O   ASP A3321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3328 through 3338
      removed outlier: 3.601A  pdb=" N   LEU A3336 " --> pdb=" O   TYR A3332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3341 through 3346
    Processing helix  chain 'A' and resid 3347 through 3351
    Processing helix  chain 'A' and resid 3357 through 3385
      removed outlier: 3.633A  pdb=" N   GLN A3361 " --> pdb=" O   THR A3357 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   GLN A3364 " --> pdb=" O   PHE A3360 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   ILE A3373 " --> pdb=" O   TYR A3369 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   ALA A3376 " --> pdb=" O   PHE A3372 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   ARG A3385 " --> pdb=" O   ASP A3381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3389 through 3398
      removed outlier: 3.879A  pdb=" N   LEU A3394 " --> pdb=" O   SER A3390 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   THR A3398 " --> pdb=" O   LEU A3394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3403 through 3407
      removed outlier: 3.680A  pdb=" N   ARG A3406 " --> pdb=" O   ASN A3403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3417 through 3441
      removed outlier: 3.788A  pdb=" N   TRP A3422 " --> pdb=" O   MET A3418 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   ARG A3429 " --> pdb=" O   ASN A3425 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   ARG A3439 " --> pdb=" O   MET A3435 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3441 through 3449
      removed outlier: 3.539A  pdb=" N   SER A3445 " --> pdb=" O   ASN A3441 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   THR A3449 " --> pdb=" O   SER A3445 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3467 through 3475
      removed outlier: 3.804A  pdb=" N   MET A3471 " --> pdb=" O   ASN A3467 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   LEU A3472 " --> pdb=" O   MET A3468 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   ALA A3473 " --> pdb=" O   LEU A3469 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3493 through 3500
    Processing sheet with id=AA1, first strand: chain 'A' and resid 1035 through 1036
    Processing sheet with id=AA2, first strand: chain 'A' and resid 1135 through 1138
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1198 through 1199
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1301 through 1302
      removed outlier: 4.531A  pdb=" N   PHE A1301 " --> pdb=" O   HIS A1411 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   HIS A1411 " --> pdb=" O   PHE A1301 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1312 through 1313
      removed outlier: 6.687A  pdb=" N   VAL A1319 " --> pdb=" O   GLN A1313 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1338 through 1339
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1414 through 1416
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1445 through 1447
    Processing sheet with id=AA9, first strand: chain 'A' and resid 1552 through 1554
    Processing sheet with id=AB1, first strand: chain 'A' and resid 1587 through 1589
    Processing sheet with id=AB2, first strand: chain 'A' and resid 1651 through 1653
    Processing sheet with id=AB3, first strand: chain 'A' and resid 1745 through 1750
    Processing sheet with id=AB4, first strand: chain 'A' and resid 1870 through 1871
    Processing sheet with id=AB5, first strand: chain 'A' and resid 1881 through 1884
      removed outlier: 3.532A  pdb=" N   SER A1882 " --> pdb=" O   ALA A1908 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 1891 through 1893
      removed outlier: 6.866A  pdb=" N   VAL A1902 " --> pdb=" O   LEU A1892 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 2126 through 2127
      removed outlier: 6.459A  pdb=" N   LYS A2171 " --> pdb=" O   ILE A2216 " (cutoff:3.500A)
      removed outlier: 7.819A  pdb=" N   LEU A2218 " --> pdb=" O   LYS A2171 " (cutoff:3.500A)
      removed outlier: 6.391A  pdb=" N   ILE A2173 " --> pdb=" O   LEU A2218 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'A' and resid 2930 through 2935
      removed outlier: 7.426A  pdb=" N   LYS A2964 " --> pdb=" O   THR A2952 " (cutoff:3.500A)
      removed outlier: 5.179A  pdb=" N   THR A2952 " --> pdb=" O   LYS A2964 " (cutoff:3.500A)
      removed outlier: 6.457A  pdb=" N   TYR A2966 " --> pdb=" O   ILE A2950 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'A' and resid 2988 through 2989
      removed outlier: 3.574A  pdb=" N   VAL A2992 " --> pdb=" O   ALA A2989 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'A' and resid 3006 through 3008
      removed outlier: 4.176A  pdb=" N   GLY A3006 " --> pdb=" O   GLN A3046 " (cutoff:3.500A)
      removed outlier: 6.820A  pdb=" N   ILE A3034 " --> pdb=" O   VAL A3042 " (cutoff:3.500A)
      removed outlier: 4.564A  pdb=" N   TYR A3044 " --> pdb=" O   MET A3032 " (cutoff:3.500A)
      removed outlier: 6.454A  pdb=" N   MET A3032 " --> pdb=" O   TYR A3044 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'A' and resid 3108 through 3110
    Processing sheet with id=AC3, first strand: chain 'A' and resid 3161 through 3162

    1022 hydrogen bonds defined for protein.
    2916 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 4.40

  Time building geometry restraints manager: 1.94 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: 6416
        1.34 -     1.46: 4019
        1.46 -     1.58: 8694
        1.58 -     1.70: 0
        1.70 -     1.82: 182
  Bond restraints: 19311
  Sorted by residual:
  bond pdb=" CB  LYS A1766 "
       pdb=" CG  LYS A1766 "
    ideal  model  delta    sigma   weight residual
    1.520  1.560 -0.040 3.00e-02 1.11e+03 1.75e+00
  bond pdb=" CB  ASN A3255 "
       pdb=" CG  ASN A3255 "
    ideal  model  delta    sigma   weight residual
    1.516  1.548 -0.032 2.50e-02 1.60e+03 1.65e+00
  bond pdb=" CG  LYS A1766 "
       pdb=" CD  LYS A1766 "
    ideal  model  delta    sigma   weight residual
    1.520  1.554 -0.034 3.00e-02 1.11e+03 1.31e+00
  bond pdb=" CB  LYS A2589 "
       pdb=" CG  LYS A2589 "
    ideal  model  delta    sigma   weight residual
    1.520  1.554 -0.034 3.00e-02 1.11e+03 1.29e+00
  bond pdb=" CB  MET A2223 "
       pdb=" CG  MET A2223 "
    ideal  model  delta    sigma   weight residual
    1.520  1.548 -0.028 3.00e-02 1.11e+03 8.60e-01
  ... (remaining 19306 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.31: 25965
        2.31 -     4.62: 117
        4.62 -     6.93: 14
        6.93 -     9.24: 1
        9.24 -    11.55: 2
  Bond angle restraints: 26099
  Sorted by residual:
  angle pdb=" CB  MET A1256 "
        pdb=" CG  MET A1256 "
        pdb=" SD  MET A1256 "
      ideal   model   delta    sigma   weight residual
     112.70  124.25  -11.55 3.00e+00 1.11e-01 1.48e+01
  angle pdb=" CB  LYS A1766 "
        pdb=" CG  LYS A1766 "
        pdb=" CD  LYS A1766 "
      ideal   model   delta    sigma   weight residual
     111.30  119.98   -8.68 2.30e+00 1.89e-01 1.43e+01
  angle pdb=" CB  MET A2223 "
        pdb=" CG  MET A2223 "
        pdb=" SD  MET A2223 "
      ideal   model   delta    sigma   weight residual
     112.70  123.52  -10.82 3.00e+00 1.11e-01 1.30e+01
  angle pdb=" CB  LYS A2589 "
        pdb=" CG  LYS A2589 "
        pdb=" CD  LYS A2589 "
      ideal   model   delta    sigma   weight residual
     111.30  117.07   -5.77 2.30e+00 1.89e-01 6.30e+00
  angle pdb=" N   VAL A3450 "
        pdb=" CA  VAL A3450 "
        pdb=" C   VAL A3450 "
      ideal   model   delta    sigma   weight residual
     111.62  109.67    1.95 7.90e-01 1.60e+00 6.08e+00
  ... (remaining 26094 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.44: 10275
       17.44 -    34.88: 1166
       34.88 -    52.33: 324
       52.33 -    69.77: 76
       69.77 -    87.21: 18
  Dihedral angle restraints: 11859
    sinusoidal: 4761
      harmonic: 7098
  Sorted by residual:
  dihedral pdb=" CA  PHE A2614 "
           pdb=" C   PHE A2614 "
           pdb=" N   TYR A2615 "
           pdb=" CA  TYR A2615 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.42   17.58     0      5.00e+00 4.00e-02 1.24e+01
  dihedral pdb=" CA  ASP A3122 "
           pdb=" CB  ASP A3122 "
           pdb=" CG  ASP A3122 "
           pdb=" OD1 ASP A3122 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -87.01   57.01     1      2.00e+01 2.50e-03 1.09e+01
  dihedral pdb=" CA  ASP A2616 "
           pdb=" CB  ASP A2616 "
           pdb=" CG  ASP A2616 "
           pdb=" OD1 ASP A2616 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -86.28   56.28     1      2.00e+01 2.50e-03 1.07e+01
  ... (remaining 11856 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 1843
       0.026 -    0.051: 713
       0.051 -    0.077: 270
       0.077 -    0.102: 93
       0.102 -    0.128: 55
  Chirality restraints: 2974
  Sorted by residual:
  chirality pdb=" CA  ILE A2933 "
            pdb=" N   ILE A2933 "
            pdb=" C   ILE A2933 "
            pdb=" CB  ILE A2933 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.10e-01
  chirality pdb=" CA  ASN A2067 "
            pdb=" N   ASN A2067 "
            pdb=" C   ASN A2067 "
            pdb=" CB  ASN A2067 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.07e-01
  chirality pdb=" CA  ILE A1306 "
            pdb=" N   ILE A1306 "
            pdb=" C   ILE A1306 "
            pdb=" CB  ILE A1306 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.03e-01
  ... (remaining 2971 not shown)

  Planarity restraints: 3402
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A1429 "    0.029 5.00e-02 4.00e+02   4.32e-02 2.99e+00
        pdb=" N   PRO A1430 "   -0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO A1430 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A1430 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A1315 "    0.122 9.50e-02 1.11e+02   5.49e-02 2.35e+00
        pdb=" NE  ARG A1315 "   -0.012 2.00e-02 2.50e+03
        pdb=" CZ  ARG A1315 "    0.011 2.00e-02 2.50e+03
        pdb=" NH1 ARG A1315 "   -0.005 2.00e-02 2.50e+03
        pdb=" NH2 ARG A1315 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A2616 "   -0.007 2.00e-02 2.50e+03   1.36e-02 1.86e+00
        pdb=" C   ASP A2616 "    0.024 2.00e-02 2.50e+03
        pdb=" O   ASP A2616 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   ALA A2617 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 3399 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1426
        2.74 -     3.28: 18516
        3.28 -     3.82: 28698
        3.82 -     4.36: 35247
        4.36 -     4.90: 61460
  Nonbonded interactions: 145347
  Sorted by model distance:
  nonbonded pdb=" O   MET A1920 "
            pdb=" OG1 THR A1924 "
     model   vdw
     2.202 3.040
  nonbonded pdb=" O   PRO A3030 "
            pdb=" OG  SER A3047 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" N   GLU A1403 "
            pdb=" OE1 GLU A1403 "
     model   vdw
     2.236 3.120
  nonbonded pdb=" N   GLU A1039 "
            pdb=" OE1 GLU A1039 "
     model   vdw
     2.236 3.120
  nonbonded pdb=" O   GLY A2761 "
            pdb=" OG1 THR A2765 "
     model   vdw
     2.255 3.040
  ... (remaining 145342 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=1.00 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:             2.940
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     17.850
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.530
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.720
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5559
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      :  0.002   0.040  19311  Z= 0.076
  Angle     :  0.400  11.549  26099  Z= 0.207
  Chirality :  0.036   0.128   2974
  Planarity :  0.003   0.055   3402
  Dihedral  : 16.426  87.209   7273
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 3.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 19.92 %
    Favored  : 78.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.29 (0.16), residues: 2436
  helix: -0.12 (0.13), residues: 1408
  sheet:  1.42 (0.55), residues: 103
  loop : -0.26 (0.20), residues: 925

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG A1315 
 TYR   0.008   0.001   TYR A2339 
 PHE   0.018   0.001   PHE A2297 
 TRP   0.005   0.001   TRP A3166 
 HIS   0.001   0.000   HIS A2492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00162 (19311)
  covalent geometry    : angle       0.40035 (26099)
  hydrogen bonds       : bond        0.31620 ( 1022)
  hydrogen bonds       : angle       6.86316 ( 2916)

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

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

  4872 Ramachandran restraints generated.
    2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4872 Ramachandran restraints generated.
    2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  600 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 573
  time to evaluate  : 0.675 
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: 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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1988 MET cc_start: 0.6154 (mmm) cc_final: 0.5476 (tpt)
REVERT: A 2057 MET cc_start: 0.6304 (mmp) cc_final: 0.5657 (mmt)
REVERT: A 2423 ARG cc_start: 0.6757 (ttm-80) cc_final: 0.5834 (ttp-170)
REVERT: A 2615 TYR cc_start: 0.8494 (t80) cc_final: 0.8293 (t80)
REVERT: A 2769 VAL cc_start: 0.8721 (OUTLIER) cc_final: 0.8042 (m)
REVERT: A 2789 VAL cc_start: 0.8116 (t) cc_final: 0.7622 (p)
REVERT: A 2810 LEU cc_start: 0.8474 (mt) cc_final: 0.8195 (mt)
REVERT: A 2860 LEU cc_start: 0.8296 (tp) cc_final: 0.7451 (tt)
REVERT: A 3129 ILE cc_start: 0.9042 (tp) cc_final: 0.8704 (mm)
REVERT: A 3146 VAL cc_start: 0.8123 (m) cc_final: 0.7776 (m)
REVERT: A 3179 THR cc_start: 0.9058 (m) cc_final: 0.8661 (p)
REVERT: A 3213 VAL cc_start: 0.8497 (t) cc_final: 0.7532 (m)
REVERT: A 3219 VAL cc_start: 0.8119 (t) cc_final: 0.7593 (p)
REVERT: A 3288 ILE cc_start: 0.6823 (pt) cc_final: 0.6489 (pt)
REVERT: A 3426 PHE cc_start: 0.7988 (m-10) cc_final: 0.7162 (m-10)
REVERT: A 3437 MET cc_start: 0.8595 (ttp) cc_final: 0.8044 (mtp)
REVERT: A 3456 MET cc_start: 0.8143 (tpp) cc_final: 0.7939 (mmm)
REVERT: A 3481 LEU cc_start: 0.8844 (mt) cc_final: 0.8111 (mt)
  outliers start: 27
  outliers final: 4
  residues processed: 592
  average time/residue: 0.1431
  time to fit residues: 125.3729
Evaluate side-chains
  328 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 323
  time to evaluate  : 0.682 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 244
   random chunks:
   chunk 216 optimal weight:    0.7980
   chunk 98 optimal weight:    1.9990
   chunk 194 optimal weight:    9.9990
   chunk 227 optimal weight:    5.9990
   chunk 107 optimal weight:    6.9990
   chunk 10 optimal weight:    5.9990
   chunk 66 optimal weight:    8.9990
   chunk 130 optimal weight:    0.6980
   chunk 124 optimal weight:   10.0000
   chunk 103 optimal weight:    6.9990
   chunk 235 optimal weight:    9.9990
   overall best weight:    3.0986

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

Flipped N/Q/H residues before XYZ refinement:
A1333 GLN
** A1340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1560 ASN
A1597 ASN
A1955 ASN
A1979 ASN
A2044 HIS
A2067 ASN
A2292 HIS
A2318 ASN
** A2442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2630 ASN
A2733 GLN
A2910 ASN
** A3104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A3190 ASN
** A3198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A3204 GLN
** A3225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A3232 GLN
A3396 GLN

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.088298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.077113 restraints weight = 174919.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.078080 restraints weight = 134879.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.078784 restraints weight = 109283.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.079345 restraints weight = 92417.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.079625 restraints weight = 80662.079|
|-----------------------------------------------------------------------------|
r_work (final): 0.3629
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6662
moved from start:          0.4337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.081  19311  Z= 0.232
  Angle     :  0.701   9.453  26099  Z= 0.381
  Chirality :  0.043   0.181   2974
  Planarity :  0.005   0.046   3402
  Dihedral  :  3.970  16.994   2626
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  :  2.59 %
    Favored  : 97.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.57 (0.17), residues: 2436
  helix:  0.79 (0.13), residues: 1445
  sheet:  0.96 (0.50), residues: 117
  loop : -0.24 (0.20), residues: 874

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A3028 
 TYR   0.030   0.002   TYR A1347 
 PHE   0.019   0.002   PHE A3401 
 TRP   0.034   0.002   TRP A3422 
 HIS   0.006   0.002   HIS A2492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00450 (19311)
  covalent geometry    : angle       0.70128 (26099)
  hydrogen bonds       : bond        0.06919 ( 1022)
  hydrogen bonds       : angle       4.81366 ( 2916)

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

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

  4872 Ramachandran restraints generated.
    2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4872 Ramachandran restraints generated.
    2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  407 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 400
  time to evaluate  : 0.550 
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: 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 1359 MET cc_start: 0.7622 (mmp) cc_final: 0.7360 (mmp)
REVERT: A 1416 MET cc_start: 0.8085 (tpp) cc_final: 0.7849 (tpp)
REVERT: A 2057 MET cc_start: 0.6779 (mmp) cc_final: 0.5697 (mmt)
REVERT: A 2223 MET cc_start: -0.0572 (ttm) cc_final: -0.0790 (ttp)
REVERT: A 2237 GLU cc_start: 0.9068 (mt-10) cc_final: 0.8647 (tm-30)
REVERT: A 2242 PHE cc_start: 0.9057 (t80) cc_final: 0.8774 (t80)
REVERT: A 2278 MET cc_start: 0.6379 (mmm) cc_final: 0.6176 (mmm)
REVERT: A 2439 ARG cc_start: 0.8503 (ttp80) cc_final: 0.8276 (ttp-110)
REVERT: A 2478 GLN cc_start: 0.8693 (pp30) cc_final: 0.7288 (pp30)
REVERT: A 2540 MET cc_start: 0.7954 (mmp) cc_final: 0.7745 (mmm)
REVERT: A 2544 GLU cc_start: 0.9151 (pm20) cc_final: 0.8948 (pm20)
REVERT: A 2571 ASN cc_start: 0.9177 (m110) cc_final: 0.8708 (m-40)
REVERT: A 2575 GLN cc_start: 0.9012 (mp10) cc_final: 0.8617 (mp10)
REVERT: A 2579 SER cc_start: 0.9384 (p) cc_final: 0.8348 (p)
REVERT: A 2580 LEU cc_start: 0.9688 (tp) cc_final: 0.9129 (tp)
REVERT: A 2583 ARG cc_start: 0.8278 (mtt90) cc_final: 0.7900 (mtt180)
REVERT: A 2860 LEU cc_start: 0.9000 (tp) cc_final: 0.8526 (tt)
REVERT: A 2909 ASP cc_start: 0.7951 (t0) cc_final: 0.7603 (t70)
REVERT: A 2929 VAL cc_start: 0.9492 (p) cc_final: 0.9225 (p)
REVERT: A 2984 ASN cc_start: 0.8730 (m110) cc_final: 0.8520 (m110)
REVERT: A 3065 MET cc_start: 0.8287 (mmt) cc_final: 0.7332 (mmt)
REVERT: A 3146 VAL cc_start: 0.8827 (m) cc_final: 0.8574 (m)
REVERT: A 3179 THR cc_start: 0.9169 (m) cc_final: 0.8811 (p)
REVERT: A 3213 VAL cc_start: 0.8272 (t) cc_final: 0.7950 (m)
REVERT: A 3231 TYR cc_start: 0.9161 (m-10) cc_final: 0.8926 (m-10)
REVERT: A 3240 VAL cc_start: 0.8265 (p) cc_final: 0.8047 (p)
REVERT: A 3246 ASN cc_start: 0.8343 (t0) cc_final: 0.8026 (t0)
REVERT: A 3287 GLU cc_start: 0.8627 (tm-30) cc_final: 0.8426 (tm-30)
REVERT: A 3288 ILE cc_start: 0.6470 (pt) cc_final: 0.6180 (pt)
REVERT: A 3298 MET cc_start: 0.6043 (mtm) cc_final: 0.5613 (mtm)
REVERT: A 3364 GLN cc_start: 0.8940 (tm-30) cc_final: 0.8611 (tm-30)
REVERT: A 3400 GLU cc_start: 0.7520 (mt-10) cc_final: 0.7029 (mp0)
REVERT: A 3404 TYR cc_start: 0.8453 (m-80) cc_final: 0.8221 (m-80)
REVERT: A 3421 MET cc_start: 0.8654 (ppp) cc_final: 0.8283 (ppp)
REVERT: A 3425 ASN cc_start: 0.9347 (m-40) cc_final: 0.9069 (m-40)
REVERT: A 3440 ASN cc_start: 0.8259 (m-40) cc_final: 0.7761 (m-40)
  outliers start: 7
  outliers final: 1
  residues processed: 405
  average time/residue: 0.1322
  time to fit residues: 81.2754
Evaluate side-chains
  310 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 309
  time to evaluate  : 0.708 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 244
   random chunks:
   chunk 239 optimal weight:   20.0000
   chunk 88 optimal weight:    9.9990
   chunk 24 optimal weight:    9.9990
   chunk 215 optimal weight:    0.9990
   chunk 5 optimal weight:   10.0000
   chunk 203 optimal weight:    1.9990
   chunk 31 optimal weight:    9.9990
   chunk 214 optimal weight:    5.9990
   chunk 13 optimal weight:    9.9990
   chunk 66 optimal weight:    0.0370
   chunk 227 optimal weight:    0.8980
   overall best weight:    1.9864

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

Flipped N/Q/H residues before XYZ refinement:
A1390 GLN
** A1423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1853 GLN
A2318 ASN
A2910 ASN
A3073 GLN
** A3198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A3225 ASN
A3440 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.087410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.076438 restraints weight = 177394.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.077408 restraints weight = 134824.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.078128 restraints weight = 108308.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.078672 restraints weight = 90984.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.079126 restraints weight = 78999.754|
|-----------------------------------------------------------------------------|
r_work (final): 0.3630
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6668
moved from start:          0.4989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  19311  Z= 0.149
  Angle     :  0.589   9.994  26099  Z= 0.313
  Chirality :  0.041   0.197   2974
  Planarity :  0.004   0.079   3402
  Dihedral  :  3.927  19.282   2626
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.86 (0.17), residues: 2436
  helix:  1.08 (0.13), residues: 1457
  sheet:  0.89 (0.49), residues: 119
  loop : -0.23 (0.21), residues: 860

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A2709 
 TYR   0.019   0.002   TYR A1347 
 PHE   0.033   0.002   PHE A2890 
 TRP   0.008   0.001   TRP A2808 
 HIS   0.009   0.001   HIS A3444 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 (19311)
  covalent geometry    : angle       0.58925 (26099)
  hydrogen bonds       : bond        0.05556 ( 1022)
  hydrogen bonds       : angle       4.38990 ( 2916)

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

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

  4872 Ramachandran restraints generated.
    2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4872 Ramachandran restraints generated.
    2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  382 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 382
  time to evaluate  : 0.717 
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: 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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1416 MET cc_start: 0.8216 (tpp) cc_final: 0.8005 (tpp)
REVERT: A 1530 MET cc_start: 0.8175 (tpt) cc_final: 0.7912 (tpt)
REVERT: A 1786 MET cc_start: 0.8646 (tpt) cc_final: 0.8420 (tpt)
REVERT: A 2345 LEU cc_start: 0.9643 (tp) cc_final: 0.9197 (pp)
REVERT: A 2370 LEU cc_start: 0.6318 (mt) cc_final: 0.6051 (mt)
REVERT: A 2371 MET cc_start: 0.7200 (mtm) cc_final: 0.6734 (mtm)
REVERT: A 2395 ASN cc_start: 0.9193 (t0) cc_final: 0.8937 (t0)
REVERT: A 2439 ARG cc_start: 0.8597 (ttp80) cc_final: 0.8244 (ttp80)
REVERT: A 2478 GLN cc_start: 0.8306 (pp30) cc_final: 0.7232 (pp30)
REVERT: A 2546 ARG cc_start: 0.8364 (mtp180) cc_final: 0.7890 (mtt180)
REVERT: A 2571 ASN cc_start: 0.9084 (m110) cc_final: 0.8786 (m110)
REVERT: A 2778 GLU cc_start: 0.8163 (mp0) cc_final: 0.7916 (mp0)
REVERT: A 2871 LYS cc_start: 0.9211 (tmtt) cc_final: 0.9010 (tptp)
REVERT: A 2909 ASP cc_start: 0.7907 (t0) cc_final: 0.7490 (t70)
REVERT: A 2929 VAL cc_start: 0.9464 (p) cc_final: 0.9095 (p)
REVERT: A 2930 ASN cc_start: 0.9453 (t0) cc_final: 0.9174 (t0)
REVERT: A 2968 PHE cc_start: 0.9290 (t80) cc_final: 0.9085 (t80)
REVERT: A 2984 ASN cc_start: 0.8601 (m110) cc_final: 0.8365 (m110)
REVERT: A 3146 VAL cc_start: 0.8758 (m) cc_final: 0.8450 (m)
REVERT: A 3179 THR cc_start: 0.9282 (m) cc_final: 0.8929 (p)
REVERT: A 3183 MET cc_start: 0.9196 (ptp) cc_final: 0.8992 (ptt)
REVERT: A 3246 ASN cc_start: 0.8499 (t0) cc_final: 0.8102 (t0)
REVERT: A 3247 ILE cc_start: 0.9154 (mm) cc_final: 0.8954 (mm)
REVERT: A 3287 GLU cc_start: 0.8643 (tm-30) cc_final: 0.8362 (tm-30)
REVERT: A 3288 ILE cc_start: 0.6618 (pt) cc_final: 0.6218 (pt)
REVERT: A 3298 MET cc_start: 0.5789 (mtm) cc_final: 0.5448 (mtm)
REVERT: A 3364 GLN cc_start: 0.8869 (tm-30) cc_final: 0.8615 (tm-30)
REVERT: A 3379 TYR cc_start: 0.8285 (t80) cc_final: 0.7983 (t80)
REVERT: A 3381 ASP cc_start: 0.8289 (m-30) cc_final: 0.7995 (m-30)
REVERT: A 3404 TYR cc_start: 0.8538 (m-80) cc_final: 0.8257 (m-80)
REVERT: A 3421 MET cc_start: 0.8664 (ppp) cc_final: 0.8364 (ppp)
REVERT: A 3425 ASN cc_start: 0.9358 (m-40) cc_final: 0.9079 (m-40)
REVERT: A 3467 ASN cc_start: 0.7779 (p0) cc_final: 0.7572 (p0)
REVERT: A 3468 MET cc_start: 0.8365 (mmp) cc_final: 0.8143 (mmp)
REVERT: A 3471 MET cc_start: 0.7116 (ptp) cc_final: 0.6396 (ptp)
  outliers start: 0
  outliers final: 0
  residues processed: 382
  average time/residue: 0.1254
  time to fit residues: 73.8224
Evaluate side-chains
  312 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 312
  time to evaluate  : 0.677 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 244
   random chunks:
   chunk 198 optimal weight:    0.1980
   chunk 22 optimal weight:    7.9990
   chunk 27 optimal weight:    1.9990
   chunk 209 optimal weight:    0.9990
   chunk 230 optimal weight:    0.9980
   chunk 49 optimal weight:    1.9990
   chunk 74 optimal weight:    8.9990
   chunk 166 optimal weight:    0.7980
   chunk 158 optimal weight:    7.9990
   chunk 181 optimal weight:    0.0470
   chunk 241 optimal weight:    5.9990
   overall best weight:    0.6080

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

Flipped N/Q/H residues before XYZ refinement:
A2378 GLN
A2801 GLN
** A3198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A3225 ASN
A3440 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.088089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.077083 restraints weight = 177187.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.078041 restraints weight = 134958.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.078762 restraints weight = 108608.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.079314 restraints weight = 91188.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.079680 restraints weight = 79261.478|
|-----------------------------------------------------------------------------|
r_work (final): 0.3642
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6646
moved from start:          0.5329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046  19311  Z= 0.118
  Angle     :  0.537   9.598  26099  Z= 0.282
  Chirality :  0.039   0.148   2974
  Planarity :  0.003   0.047   3402
  Dihedral  :  3.790  17.461   2626
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.02 (0.17), residues: 2436
  helix:  1.22 (0.14), residues: 1469
  sheet:  0.85 (0.49), residues: 119
  loop : -0.18 (0.21), residues: 848

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A2771 
 TYR   0.037   0.001   TYR A2864 
 PHE   0.020   0.001   PHE A2890 
 TRP   0.007   0.001   TRP A1578 
 HIS   0.009   0.001   HIS A3061 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 (19311)
  covalent geometry    : angle       0.53725 (26099)
  hydrogen bonds       : bond        0.04562 ( 1022)
  hydrogen bonds       : angle       4.10376 ( 2916)

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

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

  4872 Ramachandran restraints generated.
    2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4872 Ramachandran restraints generated.
    2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  383 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 383
  time to evaluate  : 0.687 
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: 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 1198 MET cc_start: 0.7692 (tmm) cc_final: 0.7438 (tmm)
REVERT: A 1786 MET cc_start: 0.8678 (tpt) cc_final: 0.8396 (tpt)
REVERT: A 2057 MET cc_start: 0.6635 (mmp) cc_final: 0.5772 (mmp)
REVERT: A 2141 ILE cc_start: 0.1566 (mm) cc_final: 0.1259 (mm)
REVERT: A 2345 LEU cc_start: 0.9568 (tp) cc_final: 0.9005 (pp)
REVERT: A 2370 LEU cc_start: 0.6271 (mt) cc_final: 0.6006 (mt)
REVERT: A 2371 MET cc_start: 0.7417 (mtm) cc_final: 0.6940 (mtm)
REVERT: A 2478 GLN cc_start: 0.8371 (pp30) cc_final: 0.6929 (pp30)
REVERT: A 2540 MET cc_start: 0.7960 (mmp) cc_final: 0.7641 (mmp)
REVERT: A 2571 ASN cc_start: 0.9072 (m110) cc_final: 0.8837 (m110)
REVERT: A 2776 MET cc_start: 0.9180 (mpp) cc_final: 0.8950 (mpp)
REVERT: A 2869 MET cc_start: 0.8605 (ptm) cc_final: 0.8344 (ptm)
REVERT: A 2909 ASP cc_start: 0.7834 (t0) cc_final: 0.7470 (t70)
REVERT: A 2925 ASN cc_start: 0.8821 (p0) cc_final: 0.8601 (p0)
REVERT: A 2929 VAL cc_start: 0.9579 (p) cc_final: 0.9179 (m)
REVERT: A 2930 ASN cc_start: 0.9427 (t0) cc_final: 0.9056 (t0)
REVERT: A 2966 TYR cc_start: 0.6067 (m-80) cc_final: 0.5621 (m-10)
REVERT: A 2983 GLN cc_start: 0.8254 (pm20) cc_final: 0.8007 (pm20)
REVERT: A 2984 ASN cc_start: 0.8576 (m110) cc_final: 0.8300 (m110)
REVERT: A 3003 MET cc_start: 0.7783 (tpp) cc_final: 0.7415 (tpp)
REVERT: A 3065 MET cc_start: 0.8597 (mmt) cc_final: 0.7666 (mmt)
REVERT: A 3087 ILE cc_start: 0.8883 (mm) cc_final: 0.8609 (tp)
REVERT: A 3146 VAL cc_start: 0.8753 (m) cc_final: 0.8549 (m)
REVERT: A 3179 THR cc_start: 0.9092 (m) cc_final: 0.8678 (p)
REVERT: A 3183 MET cc_start: 0.9174 (ptp) cc_final: 0.8744 (ptt)
REVERT: A 3217 LYS cc_start: 0.8719 (ptpp) cc_final: 0.8477 (pttp)
REVERT: A 3246 ASN cc_start: 0.8347 (t0) cc_final: 0.8087 (t0)
REVERT: A 3253 GLU cc_start: 0.9174 (mp0) cc_final: 0.8947 (mp0)
REVERT: A 3288 ILE cc_start: 0.6774 (pt) cc_final: 0.6419 (pt)
REVERT: A 3343 LYS cc_start: 0.8670 (tptt) cc_final: 0.8330 (tppt)
REVERT: A 3364 GLN cc_start: 0.8780 (tm-30) cc_final: 0.8462 (tm-30)
REVERT: A 3379 TYR cc_start: 0.8333 (t80) cc_final: 0.8058 (t80)
REVERT: A 3381 ASP cc_start: 0.8270 (m-30) cc_final: 0.8030 (m-30)
REVERT: A 3404 TYR cc_start: 0.8544 (m-80) cc_final: 0.8280 (m-80)
REVERT: A 3415 MET cc_start: 0.9374 (tpt) cc_final: 0.9173 (tpp)
REVERT: A 3421 MET cc_start: 0.8591 (ppp) cc_final: 0.8336 (ppp)
REVERT: A 3465 GLN cc_start: 0.6864 (tp-100) cc_final: 0.6527 (tp-100)
REVERT: A 3471 MET cc_start: 0.7001 (ptp) cc_final: 0.6801 (ptp)
  outliers start: 0
  outliers final: 0
  residues processed: 383
  average time/residue: 0.1269
  time to fit residues: 74.9505
Evaluate side-chains
  308 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 308
  time to evaluate  : 0.874 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 244
   random chunks:
   chunk 171 optimal weight:    2.9990
   chunk 32 optimal weight:   10.0000
   chunk 105 optimal weight:   20.0000
   chunk 87 optimal weight:    8.9990
   chunk 166 optimal weight:    0.8980
   chunk 127 optimal weight:   10.0000
   chunk 8 optimal weight:    5.9990
   chunk 159 optimal weight:    2.9990
   chunk 141 optimal weight:    0.9990
   chunk 131 optimal weight:    3.9990
   chunk 195 optimal weight:    6.9990
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
** A1423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2898 GLN
A2910 ASN
** A2984 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A3198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.085586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.075038 restraints weight = 182701.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.075875 restraints weight = 137974.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.076650 restraints weight = 110903.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.077005 restraints weight = 93153.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.077506 restraints weight = 83262.024|
|-----------------------------------------------------------------------------|
r_work (final): 0.3597
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6734
moved from start:          0.5830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  19311  Z= 0.146
  Angle     :  0.585  10.841  26099  Z= 0.308
  Chirality :  0.040   0.177   2974
  Planarity :  0.004   0.047   3402
  Dihedral  :  3.873  17.107   2626
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.06 (0.17), residues: 2436
  helix:  1.28 (0.14), residues: 1466
  sheet:  0.78 (0.47), residues: 117
  loop : -0.18 (0.21), residues: 853

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A2439 
 TYR   0.022   0.002   TYR A2339 
 PHE   0.019   0.002   PHE A2360 
 TRP   0.009   0.001   TRP A3145 
 HIS   0.004   0.001   HIS A2759 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 (19311)
  covalent geometry    : angle       0.58543 (26099)
  hydrogen bonds       : bond        0.04219 ( 1022)
  hydrogen bonds       : angle       4.15178 ( 2916)

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

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

  4872 Ramachandran restraints generated.
    2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4872 Ramachandran restraints generated.
    2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  363 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 363
  time to evaluate  : 0.616 
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: 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 1198 MET cc_start: 0.7823 (tmm) cc_final: 0.7505 (tmm)
REVERT: A 1929 MET cc_start: 0.7658 (tpt) cc_final: 0.7274 (tpt)
REVERT: A 2141 ILE cc_start: 0.1612 (mm) cc_final: 0.1292 (mm)
REVERT: A 2345 LEU cc_start: 0.9593 (tp) cc_final: 0.9029 (pp)
REVERT: A 2370 LEU cc_start: 0.6253 (mt) cc_final: 0.5959 (mt)
REVERT: A 2371 MET cc_start: 0.7407 (mtm) cc_final: 0.6857 (mtm)
REVERT: A 2412 TYR cc_start: 0.8899 (m-80) cc_final: 0.7772 (t80)
REVERT: A 2439 ARG cc_start: 0.8346 (ttp-110) cc_final: 0.7631 (ttp80)
REVERT: A 2440 ASP cc_start: 0.8681 (m-30) cc_final: 0.8386 (m-30)
REVERT: A 2540 MET cc_start: 0.8195 (mmp) cc_final: 0.7870 (mmp)
REVERT: A 2565 ILE cc_start: 0.8958 (mp) cc_final: 0.8671 (pt)
REVERT: A 2568 LEU cc_start: 0.9608 (mp) cc_final: 0.9351 (mt)
REVERT: A 2571 ASN cc_start: 0.9079 (m110) cc_final: 0.8830 (m-40)
REVERT: A 2624 ASN cc_start: 0.8943 (t0) cc_final: 0.8037 (t0)
REVERT: A 2774 MET cc_start: 0.6779 (mpp) cc_final: 0.6550 (mpp)
REVERT: A 2869 MET cc_start: 0.8632 (ptm) cc_final: 0.8415 (ptm)
REVERT: A 2871 LYS cc_start: 0.9176 (tmtt) cc_final: 0.8957 (tptp)
REVERT: A 2909 ASP cc_start: 0.7953 (t0) cc_final: 0.7562 (t70)
REVERT: A 2925 ASN cc_start: 0.9036 (p0) cc_final: 0.8740 (p0)
REVERT: A 2929 VAL cc_start: 0.9563 (p) cc_final: 0.9072 (m)
REVERT: A 2930 ASN cc_start: 0.9346 (t0) cc_final: 0.8898 (t0)
REVERT: A 2932 ILE cc_start: 0.9511 (mt) cc_final: 0.9214 (mm)
REVERT: A 2933 ILE cc_start: 0.9333 (mm) cc_final: 0.9077 (mm)
REVERT: A 2968 PHE cc_start: 0.9362 (t80) cc_final: 0.9044 (t80)
REVERT: A 2983 GLN cc_start: 0.8324 (pm20) cc_final: 0.8064 (pm20)
REVERT: A 3065 MET cc_start: 0.8701 (mmt) cc_final: 0.7993 (mmt)
REVERT: A 3127 MET cc_start: 0.8687 (ppp) cc_final: 0.8283 (ppp)
REVERT: A 3146 VAL cc_start: 0.8718 (m) cc_final: 0.8478 (m)
REVERT: A 3179 THR cc_start: 0.9200 (m) cc_final: 0.8784 (p)
REVERT: A 3183 MET cc_start: 0.9303 (ptp) cc_final: 0.8801 (ptt)
REVERT: A 3217 LYS cc_start: 0.8677 (ptpp) cc_final: 0.8393 (pttp)
REVERT: A 3246 ASN cc_start: 0.8452 (t0) cc_final: 0.8222 (t0)
REVERT: A 3289 GLN cc_start: 0.8418 (tp-100) cc_final: 0.7717 (mm-40)
REVERT: A 3343 LYS cc_start: 0.8815 (tptt) cc_final: 0.8509 (tppt)
REVERT: A 3364 GLN cc_start: 0.8818 (tm-30) cc_final: 0.8505 (tm-30)
REVERT: A 3371 ASP cc_start: 0.9419 (t0) cc_final: 0.9156 (t0)
REVERT: A 3379 TYR cc_start: 0.8380 (t80) cc_final: 0.8015 (t80)
REVERT: A 3381 ASP cc_start: 0.8370 (m-30) cc_final: 0.8142 (m-30)
REVERT: A 3404 TYR cc_start: 0.8482 (m-80) cc_final: 0.8179 (m-80)
REVERT: A 3415 MET cc_start: 0.9487 (tpt) cc_final: 0.9250 (tpp)
REVERT: A 3421 MET cc_start: 0.8621 (ppp) cc_final: 0.8374 (ppp)
REVERT: A 3465 GLN cc_start: 0.6553 (tp-100) cc_final: 0.6251 (tp-100)
REVERT: A 3467 ASN cc_start: 0.7717 (p0) cc_final: 0.7507 (p0)
REVERT: A 3468 MET cc_start: 0.8534 (mmp) cc_final: 0.8231 (mmp)
REVERT: A 3471 MET cc_start: 0.7226 (ptp) cc_final: 0.6578 (ptp)
  outliers start: 0
  outliers final: 0
  residues processed: 363
  average time/residue: 0.1284
  time to fit residues: 71.8748
Evaluate side-chains
  298 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 298
  time to evaluate  : 0.717 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 244
   random chunks:
   chunk 98 optimal weight:    5.9990
   chunk 182 optimal weight:    5.9990
   chunk 184 optimal weight:    9.9990
   chunk 147 optimal weight:    1.9990
   chunk 23 optimal weight:    7.9990
   chunk 13 optimal weight:    0.8980
   chunk 79 optimal weight:    8.9990
   chunk 130 optimal weight:    0.6980
   chunk 21 optimal weight:   10.0000
   chunk 27 optimal weight:    5.9990
   chunk 91 optimal weight:    9.9990
   overall best weight:    3.1186

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

Flipped N/Q/H residues before XYZ refinement:
A1372 ASN
A2074 ASN
** A2179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2204 ASN
A2246 ASN
** A2442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2678 GLN
** A2729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A3198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A3225 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.082999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.072755 restraints weight = 184016.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.073580 restraints weight = 138581.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.074291 restraints weight = 110730.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.074837 restraints weight = 93451.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.075191 restraints weight = 81301.499|
|-----------------------------------------------------------------------------|
r_work (final): 0.3540
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6829
moved from start:          0.6539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  19311  Z= 0.176
  Angle     :  0.622   9.748  26099  Z= 0.330
  Chirality :  0.041   0.273   2974
  Planarity :  0.004   0.046   3402
  Dihedral  :  4.195  21.758   2626
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 11.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.91 (0.17), residues: 2436
  helix:  1.17 (0.13), residues: 1470
  sheet:  0.45 (0.47), residues: 116
  loop : -0.25 (0.20), residues: 850

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A1418 
 TYR   0.027   0.002   TYR A2864 
 PHE   0.023   0.002   PHE A2365 
 TRP   0.014   0.001   TRP A2755 
 HIS   0.010   0.001   HIS A2444 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 (19311)
  covalent geometry    : angle       0.62152 (26099)
  hydrogen bonds       : bond        0.04130 ( 1022)
  hydrogen bonds       : angle       4.30498 ( 2916)

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

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

  4872 Ramachandran restraints generated.
    2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4872 Ramachandran restraints generated.
    2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  366 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 366
  time to evaluate  : 0.639 
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: 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 1198 MET cc_start: 0.7872 (tmm) cc_final: 0.7596 (tmm)
REVERT: A 1929 MET cc_start: 0.7262 (tpt) cc_final: 0.6900 (tpt)
REVERT: A 2141 ILE cc_start: 0.2157 (mm) cc_final: 0.1791 (mm)
REVERT: A 2370 LEU cc_start: 0.6655 (mt) cc_final: 0.6273 (mt)
REVERT: A 2371 MET cc_start: 0.7788 (mtm) cc_final: 0.7289 (mpp)
REVERT: A 2412 TYR cc_start: 0.9028 (m-80) cc_final: 0.8023 (t80)
REVERT: A 2466 GLU cc_start: 0.8838 (tp30) cc_final: 0.8560 (tp30)
REVERT: A 2478 GLN cc_start: 0.8795 (pp30) cc_final: 0.8112 (pp30)
REVERT: A 2565 ILE cc_start: 0.9127 (mp) cc_final: 0.8867 (pt)
REVERT: A 2568 LEU cc_start: 0.9569 (mp) cc_final: 0.9202 (mt)
REVERT: A 2614 PHE cc_start: 0.9182 (t80) cc_final: 0.8852 (t80)
REVERT: A 2624 ASN cc_start: 0.9115 (t0) cc_final: 0.8004 (t0)
REVERT: A 2690 MET cc_start: 0.8733 (ptp) cc_final: 0.8265 (ptp)
REVERT: A 2822 MET cc_start: 0.8356 (ptp) cc_final: 0.8084 (ptp)
REVERT: A 2869 MET cc_start: 0.8718 (ptm) cc_final: 0.8497 (ptm)
REVERT: A 2909 ASP cc_start: 0.8008 (t0) cc_final: 0.7556 (t70)
REVERT: A 2925 ASN cc_start: 0.9118 (p0) cc_final: 0.8844 (p0)
REVERT: A 2929 VAL cc_start: 0.9481 (p) cc_final: 0.8975 (m)
REVERT: A 2930 ASN cc_start: 0.9288 (t0) cc_final: 0.8649 (t0)
REVERT: A 2932 ILE cc_start: 0.9577 (mt) cc_final: 0.9161 (mm)
REVERT: A 2968 PHE cc_start: 0.9415 (t80) cc_final: 0.9090 (t80)
REVERT: A 3065 MET cc_start: 0.8544 (mmt) cc_final: 0.7913 (mmt)
REVERT: A 3093 MET cc_start: 0.8902 (ptp) cc_final: 0.8677 (ptp)
REVERT: A 3179 THR cc_start: 0.9316 (m) cc_final: 0.9093 (p)
REVERT: A 3214 ILE cc_start: 0.9194 (mm) cc_final: 0.8733 (mm)
REVERT: A 3217 LYS cc_start: 0.8606 (ptpp) cc_final: 0.8191 (pttp)
REVERT: A 3289 GLN cc_start: 0.8626 (tp-100) cc_final: 0.8000 (mm-40)
REVERT: A 3343 LYS cc_start: 0.8714 (tptt) cc_final: 0.8441 (tppt)
REVERT: A 3364 GLN cc_start: 0.8850 (tm-30) cc_final: 0.8560 (tm-30)
REVERT: A 3379 TYR cc_start: 0.8302 (t80) cc_final: 0.7875 (t80)
REVERT: A 3381 ASP cc_start: 0.8508 (m-30) cc_final: 0.8245 (m-30)
REVERT: A 3382 LEU cc_start: 0.8917 (tp) cc_final: 0.8381 (tp)
REVERT: A 3404 TYR cc_start: 0.8627 (m-80) cc_final: 0.8218 (m-80)
REVERT: A 3421 MET cc_start: 0.8626 (ppp) cc_final: 0.8048 (ppp)
REVERT: A 3425 ASN cc_start: 0.9324 (m-40) cc_final: 0.8968 (m-40)
REVERT: A 3465 GLN cc_start: 0.7051 (tp-100) cc_final: 0.6753 (tp-100)
REVERT: A 3471 MET cc_start: 0.7177 (ptp) cc_final: 0.6834 (ptp)
  outliers start: 0
  outliers final: 0
  residues processed: 366
  average time/residue: 0.1216
  time to fit residues: 69.8874
Evaluate side-chains
  308 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 308
  time to evaluate  : 0.689 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 244
   random chunks:
   chunk 11 optimal weight:    7.9990
   chunk 208 optimal weight:    0.8980
   chunk 95 optimal weight:    3.9990
   chunk 78 optimal weight:    0.8980
   chunk 227 optimal weight:    0.9980
   chunk 198 optimal weight:    7.9990
   chunk 71 optimal weight:    8.9990
   chunk 202 optimal weight:    6.9990
   chunk 72 optimal weight:    5.9990
   chunk 30 optimal weight:    0.9990
   chunk 189 optimal weight:    6.9990
   overall best weight:    1.5584

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

Flipped N/Q/H residues before XYZ refinement:
** A2179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2295 ASN
** A2378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2400 GLN
A2444 HIS
** A2510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2984 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A3198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A3225 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.083772 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.073420 restraints weight = 183239.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.074233 restraints weight = 139290.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.074952 restraints weight = 112303.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.075479 restraints weight = 94987.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.075835 restraints weight = 82639.446|
|-----------------------------------------------------------------------------|
r_work (final): 0.3560
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6797
moved from start:          0.6699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  19311  Z= 0.121
  Angle     :  0.577  10.686  26099  Z= 0.302
  Chirality :  0.040   0.247   2974
  Planarity :  0.003   0.045   3402
  Dihedral  :  4.024  20.781   2626
  Min Nonbonded Distance : 2.350

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.05 (0.17), residues: 2436
  helix:  1.29 (0.14), residues: 1468
  sheet:  0.39 (0.48), residues: 114
  loop : -0.17 (0.21), residues: 854

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A2439 
 TYR   0.024   0.001   TYR A3369 
 PHE   0.015   0.001   PHE A2360 
 TRP   0.011   0.001   TRP A2314 
 HIS   0.006   0.001   HIS A2044 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 (19311)
  covalent geometry    : angle       0.57689 (26099)
  hydrogen bonds       : bond        0.03784 ( 1022)
  hydrogen bonds       : angle       4.18522 ( 2916)

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

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

  4872 Ramachandran restraints generated.
    2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4872 Ramachandran restraints generated.
    2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  370 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 370
  time to evaluate  : 0.728 
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: 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 1499 MET cc_start: 0.6422 (ttt) cc_final: 0.6044 (ttt)
REVERT: A 1929 MET cc_start: 0.7593 (tpt) cc_final: 0.7251 (tpt)
REVERT: A 2057 MET cc_start: 0.6587 (mmp) cc_final: 0.6161 (mmp)
REVERT: A 2141 ILE cc_start: 0.2151 (mm) cc_final: 0.1754 (mm)
REVERT: A 2237 GLU cc_start: 0.9393 (tt0) cc_final: 0.9061 (tp30)
REVERT: A 2370 LEU cc_start: 0.6379 (mt) cc_final: 0.6102 (mt)
REVERT: A 2371 MET cc_start: 0.8013 (mtm) cc_final: 0.7607 (mtm)
REVERT: A 2406 ASP cc_start: 0.9305 (m-30) cc_final: 0.9105 (m-30)
REVERT: A 2412 TYR cc_start: 0.9053 (m-80) cc_final: 0.8065 (t80)
REVERT: A 2530 SER cc_start: 0.7660 (t) cc_final: 0.7448 (t)
REVERT: A 2552 MET cc_start: 0.7635 (mmm) cc_final: 0.7196 (mmm)
REVERT: A 2565 ILE cc_start: 0.9142 (mp) cc_final: 0.8911 (pt)
REVERT: A 2571 ASN cc_start: 0.9106 (m-40) cc_final: 0.8816 (m-40)
REVERT: A 2614 PHE cc_start: 0.9150 (t80) cc_final: 0.8712 (t80)
REVERT: A 2624 ASN cc_start: 0.8700 (t0) cc_final: 0.7625 (t0)
REVERT: A 2822 MET cc_start: 0.8168 (ptp) cc_final: 0.7926 (ptp)
REVERT: A 2871 LYS cc_start: 0.9162 (tmtt) cc_final: 0.8962 (tptp)
REVERT: A 2909 ASP cc_start: 0.7989 (t0) cc_final: 0.7548 (t70)
REVERT: A 2925 ASN cc_start: 0.9119 (p0) cc_final: 0.8755 (p0)
REVERT: A 2929 VAL cc_start: 0.9465 (p) cc_final: 0.8854 (m)
REVERT: A 2930 ASN cc_start: 0.9263 (t0) cc_final: 0.8560 (t0)
REVERT: A 2931 LEU cc_start: 0.9313 (pp) cc_final: 0.9080 (pp)
REVERT: A 2968 PHE cc_start: 0.9297 (t80) cc_final: 0.8982 (t80)
REVERT: A 3045 GLU cc_start: 0.6653 (mt-10) cc_final: 0.6282 (mt-10)
REVERT: A 3065 MET cc_start: 0.8757 (mmt) cc_final: 0.7538 (mmt)
REVERT: A 3087 ILE cc_start: 0.8772 (mm) cc_final: 0.8514 (tp)
REVERT: A 3093 MET cc_start: 0.8886 (ptp) cc_final: 0.8680 (ptp)
REVERT: A 3127 MET cc_start: 0.8672 (ppp) cc_final: 0.8257 (ppp)
REVERT: A 3132 ARG cc_start: 0.9235 (ttm170) cc_final: 0.8944 (ttm170)
REVERT: A 3179 THR cc_start: 0.9287 (m) cc_final: 0.9025 (p)
REVERT: A 3214 ILE cc_start: 0.9100 (mm) cc_final: 0.8688 (mm)
REVERT: A 3217 LYS cc_start: 0.8667 (ptpp) cc_final: 0.8299 (pttp)
REVERT: A 3289 GLN cc_start: 0.8584 (tp-100) cc_final: 0.7915 (mm-40)
REVERT: A 3343 LYS cc_start: 0.8800 (tptt) cc_final: 0.8531 (tppt)
REVERT: A 3364 GLN cc_start: 0.8857 (tm-30) cc_final: 0.8534 (tm-30)
REVERT: A 3379 TYR cc_start: 0.8249 (t80) cc_final: 0.7968 (t80)
REVERT: A 3381 ASP cc_start: 0.8531 (m-30) cc_final: 0.8297 (m-30)
REVERT: A 3404 TYR cc_start: 0.8640 (m-80) cc_final: 0.8134 (m-80)
REVERT: A 3405 ASP cc_start: 0.8860 (m-30) cc_final: 0.8493 (p0)
REVERT: A 3415 MET cc_start: 0.9437 (tpt) cc_final: 0.9114 (tpp)
REVERT: A 3421 MET cc_start: 0.8610 (ppp) cc_final: 0.8047 (ppp)
REVERT: A 3425 ASN cc_start: 0.9296 (m-40) cc_final: 0.8948 (m-40)
REVERT: A 3465 GLN cc_start: 0.7041 (tp-100) cc_final: 0.6721 (tp-100)
REVERT: A 3468 MET cc_start: 0.8436 (mmp) cc_final: 0.8219 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 370
  average time/residue: 0.1260
  time to fit residues: 73.0357
Evaluate side-chains
  308 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 308
  time to evaluate  : 0.739 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 244
   random chunks:
   chunk 19 optimal weight:    8.9990
   chunk 0 optimal weight:   20.0000
   chunk 238 optimal weight:    6.9990
   chunk 46 optimal weight:    0.3980
   chunk 65 optimal weight:   20.0000
   chunk 79 optimal weight:    8.9990
   chunk 27 optimal weight:    0.6980
   chunk 2 optimal weight:   10.0000
   chunk 67 optimal weight:    0.9980
   chunk 118 optimal weight:    2.9990
   chunk 24 optimal weight:    4.9990
   overall best weight:    2.0184

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

Flipped N/Q/H residues before XYZ refinement:
** A2179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2295 ASN
A2444 HIS
** A2510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2898 GLN
** A3198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A3225 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.082674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.072639 restraints weight = 187233.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.073526 restraints weight = 140875.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.074158 restraints weight = 113284.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.074615 restraints weight = 95465.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.074997 restraints weight = 83649.987|
|-----------------------------------------------------------------------------|
r_work (final): 0.3543
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6817
moved from start:          0.7011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  19311  Z= 0.133
  Angle     :  0.594   8.955  26099  Z= 0.314
  Chirality :  0.041   0.178   2974
  Planarity :  0.004   0.076   3402
  Dihedral  :  4.069  24.769   2626
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 10.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.59 %
    Favored  : 99.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.01 (0.17), residues: 2436
  helix:  1.22 (0.14), residues: 1468
  sheet:  0.35 (0.49), residues: 114
  loop : -0.10 (0.21), residues: 854

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A2874 
 TYR   0.024   0.002   TYR A3479 
 PHE   0.015   0.001   PHE A2360 
 TRP   0.055   0.002   TRP A3069 
 HIS   0.006   0.001   HIS A2044 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 (19311)
  covalent geometry    : angle       0.59364 (26099)
  hydrogen bonds       : bond        0.03795 ( 1022)
  hydrogen bonds       : angle       4.23225 ( 2916)

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

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

  4872 Ramachandran restraints generated.
    2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4872 Ramachandran restraints generated.
    2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  362 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 362
  time to evaluate  : 0.669 
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: 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 1929 MET cc_start: 0.7650 (tpt) cc_final: 0.7294 (tpt)
REVERT: A 2057 MET cc_start: 0.6631 (mmp) cc_final: 0.6292 (mmt)
REVERT: A 2141 ILE cc_start: 0.2132 (mm) cc_final: 0.1720 (mm)
REVERT: A 2366 ASN cc_start: 0.3031 (t0) cc_final: 0.2830 (t0)
REVERT: A 2370 LEU cc_start: 0.6447 (mt) cc_final: 0.6156 (mt)
REVERT: A 2371 MET cc_start: 0.8056 (mtm) cc_final: 0.7609 (mtm)
REVERT: A 2412 TYR cc_start: 0.9093 (m-80) cc_final: 0.8162 (t80)
REVERT: A 2530 SER cc_start: 0.7718 (t) cc_final: 0.7498 (t)
REVERT: A 2540 MET cc_start: 0.9003 (mmp) cc_final: 0.8224 (mmp)
REVERT: A 2545 LEU cc_start: 0.9268 (mt) cc_final: 0.8994 (mm)
REVERT: A 2552 MET cc_start: 0.7626 (mmm) cc_final: 0.7130 (mmm)
REVERT: A 2565 ILE cc_start: 0.9074 (mp) cc_final: 0.8782 (pt)
REVERT: A 2571 ASN cc_start: 0.9112 (m-40) cc_final: 0.8817 (m-40)
REVERT: A 2614 PHE cc_start: 0.9198 (t80) cc_final: 0.8884 (t80)
REVERT: A 2624 ASN cc_start: 0.8739 (t0) cc_final: 0.7679 (t0)
REVERT: A 2909 ASP cc_start: 0.8024 (t0) cc_final: 0.7638 (t70)
REVERT: A 2925 ASN cc_start: 0.9167 (p0) cc_final: 0.8801 (p0)
REVERT: A 2929 VAL cc_start: 0.9495 (p) cc_final: 0.8929 (m)
REVERT: A 2930 ASN cc_start: 0.9157 (t0) cc_final: 0.8576 (t0)
REVERT: A 2931 LEU cc_start: 0.9307 (pp) cc_final: 0.9079 (pp)
REVERT: A 2968 PHE cc_start: 0.9305 (t80) cc_final: 0.9014 (t80)
REVERT: A 3045 GLU cc_start: 0.6686 (mt-10) cc_final: 0.6354 (mt-10)
REVERT: A 3065 MET cc_start: 0.8626 (mmt) cc_final: 0.7587 (mmt)
REVERT: A 3087 ILE cc_start: 0.8813 (mm) cc_final: 0.8525 (tp)
REVERT: A 3127 MET cc_start: 0.8650 (ppp) cc_final: 0.8325 (ppp)
REVERT: A 3132 ARG cc_start: 0.9215 (ttm170) cc_final: 0.8915 (ttm170)
REVERT: A 3179 THR cc_start: 0.9347 (m) cc_final: 0.9119 (p)
REVERT: A 3214 ILE cc_start: 0.9057 (mm) cc_final: 0.8560 (mm)
REVERT: A 3217 LYS cc_start: 0.8519 (ptpp) cc_final: 0.8271 (pttp)
REVERT: A 3289 GLN cc_start: 0.8597 (tp-100) cc_final: 0.7935 (mm110)
REVERT: A 3343 LYS cc_start: 0.8797 (tptt) cc_final: 0.8520 (tppt)
REVERT: A 3364 GLN cc_start: 0.8864 (tm-30) cc_final: 0.8541 (tm-30)
REVERT: A 3379 TYR cc_start: 0.8326 (t80) cc_final: 0.7976 (t80)
REVERT: A 3381 ASP cc_start: 0.8700 (m-30) cc_final: 0.8474 (m-30)
REVERT: A 3404 TYR cc_start: 0.8615 (m-80) cc_final: 0.8081 (m-80)
REVERT: A 3405 ASP cc_start: 0.8832 (m-30) cc_final: 0.8453 (p0)
REVERT: A 3415 MET cc_start: 0.9460 (tpt) cc_final: 0.9167 (tpp)
REVERT: A 3421 MET cc_start: 0.8591 (ppp) cc_final: 0.8000 (ppp)
REVERT: A 3425 ASN cc_start: 0.9289 (m-40) cc_final: 0.8937 (m-40)
REVERT: A 3435 MET cc_start: 0.7408 (ptp) cc_final: 0.7204 (ptp)
REVERT: A 3479 TYR cc_start: 0.7178 (p90) cc_final: 0.6832 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 362
  average time/residue: 0.1247
  time to fit residues: 70.4863
Evaluate side-chains
  312 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 312
  time to evaluate  : 0.718 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 244
   random chunks:
   chunk 238 optimal weight:    4.9990
   chunk 228 optimal weight:    1.9990
   chunk 147 optimal weight:    5.9990
   chunk 142 optimal weight:    0.8980
   chunk 22 optimal weight:    8.9990
   chunk 136 optimal weight:    3.9990
   chunk 194 optimal weight:    9.9990
   chunk 39 optimal weight:    5.9990
   chunk 150 optimal weight:    1.9990
   chunk 137 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
A2179 GLN
** A2378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2444 HIS
A2510 GLN
A2916 HIS
** A2984 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A3198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A3225 ASN
** A3256 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 = 0.3728 r_free = 0.3728 target = 0.082177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.072346 restraints weight = 187390.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.073224 restraints weight = 140657.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.073819 restraints weight = 112195.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.074345 restraints weight = 95040.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.074692 restraints weight = 82638.273|
|-----------------------------------------------------------------------------|
r_work (final): 0.3536
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6826
moved from start:          0.7249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  19311  Z= 0.130
  Angle     :  0.589   8.719  26099  Z= 0.310
  Chirality :  0.040   0.182   2974
  Planarity :  0.004   0.044   3402
  Dihedral  :  4.044  23.891   2626
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 10.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.04 (0.17), residues: 2436
  helix:  1.26 (0.14), residues: 1471
  sheet:  0.37 (0.49), residues: 112
  loop : -0.12 (0.21), residues: 853

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A2546 
 TYR   0.024   0.002   TYR A3369 
 PHE   0.016   0.001   PHE A2365 
 TRP   0.012   0.001   TRP A2755 
 HIS   0.012   0.001   HIS A2759 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 (19311)
  covalent geometry    : angle       0.58939 (26099)
  hydrogen bonds       : bond        0.03609 ( 1022)
  hydrogen bonds       : angle       4.19416 ( 2916)

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

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

  4872 Ramachandran restraints generated.
    2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4872 Ramachandran restraints generated.
    2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  365 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 365
  time to evaluate  : 0.702 
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: 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 1929 MET cc_start: 0.7486 (tpt) cc_final: 0.7173 (tpt)
REVERT: A 2057 MET cc_start: 0.6901 (mmp) cc_final: 0.6448 (mmt)
REVERT: A 2141 ILE cc_start: 0.2121 (mm) cc_final: 0.1690 (mm)
REVERT: A 2366 ASN cc_start: 0.3979 (t0) cc_final: 0.3712 (t0)
REVERT: A 2370 LEU cc_start: 0.6595 (mt) cc_final: 0.6312 (mt)
REVERT: A 2371 MET cc_start: 0.7852 (mtm) cc_final: 0.7376 (mtm)
REVERT: A 2420 GLU cc_start: 0.5889 (pt0) cc_final: 0.5135 (pm20)
REVERT: A 2466 GLU cc_start: 0.8680 (tp30) cc_final: 0.7739 (tp30)
REVERT: A 2552 MET cc_start: 0.7627 (mmm) cc_final: 0.7011 (mmm)
REVERT: A 2565 ILE cc_start: 0.9019 (mp) cc_final: 0.8713 (pt)
REVERT: A 2571 ASN cc_start: 0.9096 (m-40) cc_final: 0.8810 (m-40)
REVERT: A 2583 ARG cc_start: 0.9311 (mtt180) cc_final: 0.8875 (mtp180)
REVERT: A 2584 MET cc_start: 0.9007 (ppp) cc_final: 0.8771 (ppp)
REVERT: A 2624 ASN cc_start: 0.8721 (t0) cc_final: 0.7740 (t0)
REVERT: A 2909 ASP cc_start: 0.8014 (t0) cc_final: 0.7602 (t70)
REVERT: A 2925 ASN cc_start: 0.9190 (p0) cc_final: 0.8810 (p0)
REVERT: A 2929 VAL cc_start: 0.9503 (p) cc_final: 0.8935 (m)
REVERT: A 2930 ASN cc_start: 0.9185 (t0) cc_final: 0.8626 (t0)
REVERT: A 2931 LEU cc_start: 0.9360 (pp) cc_final: 0.9133 (pp)
REVERT: A 2968 PHE cc_start: 0.9239 (t80) cc_final: 0.8994 (t80)
REVERT: A 3045 GLU cc_start: 0.6700 (mt-10) cc_final: 0.6353 (mt-10)
REVERT: A 3065 MET cc_start: 0.8617 (mmt) cc_final: 0.7709 (mmt)
REVERT: A 3087 ILE cc_start: 0.8920 (mm) cc_final: 0.8571 (tp)
REVERT: A 3179 THR cc_start: 0.9397 (m) cc_final: 0.9190 (p)
REVERT: A 3214 ILE cc_start: 0.9064 (mm) cc_final: 0.8628 (mm)
REVERT: A 3289 GLN cc_start: 0.8638 (tp-100) cc_final: 0.7995 (mm110)
REVERT: A 3340 LEU cc_start: 0.9426 (mm) cc_final: 0.9207 (mm)
REVERT: A 3343 LYS cc_start: 0.8768 (tptt) cc_final: 0.8496 (tppt)
REVERT: A 3364 GLN cc_start: 0.8883 (tm-30) cc_final: 0.8623 (tm-30)
REVERT: A 3379 TYR cc_start: 0.8284 (t80) cc_final: 0.7950 (t80)
REVERT: A 3381 ASP cc_start: 0.8709 (m-30) cc_final: 0.8509 (m-30)
REVERT: A 3415 MET cc_start: 0.9441 (tpt) cc_final: 0.9144 (tpp)
REVERT: A 3421 MET cc_start: 0.8568 (ppp) cc_final: 0.7969 (ppp)
REVERT: A 3425 ASN cc_start: 0.9265 (m-40) cc_final: 0.8906 (m-40)
REVERT: A 3435 MET cc_start: 0.7262 (ptp) cc_final: 0.7060 (ptp)
  outliers start: 0
  outliers final: 0
  residues processed: 365
  average time/residue: 0.1222
  time to fit residues: 69.3946
Evaluate side-chains
  309 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 309
  time to evaluate  : 0.695 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 244
   random chunks:
   chunk 210 optimal weight:    6.9990
   chunk 51 optimal weight:    4.9990
   chunk 87 optimal weight:    5.9990
   chunk 230 optimal weight:    5.9990
   chunk 175 optimal weight:    3.9990
   chunk 235 optimal weight:    0.8980
   chunk 205 optimal weight:    6.9990
   chunk 118 optimal weight:    9.9990
   chunk 216 optimal weight:    0.0980
   chunk 52 optimal weight:    9.9990
   chunk 126 optimal weight:    6.9990
   overall best weight:    3.1986

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

Flipped N/Q/H residues before XYZ refinement:
** A1785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2444 HIS
** A2510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2692 GLN
** A2984 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A3198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A3225 ASN
** A3256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A3396 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 = 0.3683 r_free = 0.3683 target = 0.080247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.070687 restraints weight = 191090.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.071579 restraints weight = 144340.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.072126 restraints weight = 115353.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.072643 restraints weight = 97892.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.072921 restraints weight = 84957.520|
|-----------------------------------------------------------------------------|
r_work (final): 0.3496
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6895
moved from start:          0.7732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  19311  Z= 0.178
  Angle     :  0.678  11.176  26099  Z= 0.358
  Chirality :  0.043   0.408   2974
  Planarity :  0.004   0.045   3402
  Dihedral  :  4.358  23.806   2626
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 12.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.15 %
    Favored  : 99.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.83 (0.17), residues: 2436
  helix:  1.11 (0.13), residues: 1452
  sheet: -0.02 (0.50), residues: 106
  loop : -0.16 (0.21), residues: 878

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A3236 
 TYR   0.023   0.002   TYR A2864 
 PHE   0.019   0.002   PHE A2365 
 TRP   0.033   0.002   TRP A3069 
 HIS   0.008   0.001   HIS A3091 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 (19311)
  covalent geometry    : angle       0.67795 (26099)
  hydrogen bonds       : bond        0.03911 ( 1022)
  hydrogen bonds       : angle       4.42982 ( 2916)

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

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

  4872 Ramachandran restraints generated.
    2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4872 Ramachandran restraints generated.
    2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  362 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 362
  time to evaluate  : 0.545 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1198 MET cc_start: 0.7561 (ppp) cc_final: 0.7159 (tmm)
REVERT: A 1300 MET cc_start: 0.7984 (tpt) cc_final: 0.7391 (tpp)
REVERT: A 1698 MET cc_start: 0.4966 (tmm) cc_final: 0.4648 (ppp)
REVERT: A 2237 GLU cc_start: 0.9402 (tt0) cc_final: 0.8961 (tt0)
REVERT: A 2366 ASN cc_start: 0.5672 (t0) cc_final: 0.5465 (t0)
REVERT: A 2370 LEU cc_start: 0.6566 (mt) cc_final: 0.6270 (mt)
REVERT: A 2371 MET cc_start: 0.7900 (mtm) cc_final: 0.7323 (mtm)
REVERT: A 2405 PHE cc_start: 0.9193 (t80) cc_final: 0.8984 (t80)
REVERT: A 2412 TYR cc_start: 0.9061 (m-80) cc_final: 0.8855 (m-10)
REVERT: A 2420 GLU cc_start: 0.5974 (pt0) cc_final: 0.5290 (pm20)
REVERT: A 2478 GLN cc_start: 0.9162 (pp30) cc_final: 0.8439 (pp30)
REVERT: A 2479 GLU cc_start: 0.9175 (mm-30) cc_final: 0.8951 (mm-30)
REVERT: A 2546 ARG cc_start: 0.8701 (mtm180) cc_final: 0.7949 (mtt180)
REVERT: A 2552 MET cc_start: 0.7648 (mmm) cc_final: 0.6870 (mmm)
REVERT: A 2568 LEU cc_start: 0.9474 (mt) cc_final: 0.9260 (mt)
REVERT: A 2584 MET cc_start: 0.9013 (ppp) cc_final: 0.8740 (ppp)
REVERT: A 2624 ASN cc_start: 0.8866 (t0) cc_final: 0.7854 (t0)
REVERT: A 2909 ASP cc_start: 0.8236 (t0) cc_final: 0.7787 (t70)
REVERT: A 2925 ASN cc_start: 0.9229 (p0) cc_final: 0.8862 (p0)
REVERT: A 2929 VAL cc_start: 0.9412 (p) cc_final: 0.8792 (m)
REVERT: A 2930 ASN cc_start: 0.9127 (t0) cc_final: 0.8575 (t0)
REVERT: A 2931 LEU cc_start: 0.9304 (pp) cc_final: 0.9042 (pt)
REVERT: A 2932 ILE cc_start: 0.9457 (mm) cc_final: 0.9193 (mm)
REVERT: A 2968 PHE cc_start: 0.9363 (t80) cc_final: 0.9154 (t80)
REVERT: A 3065 MET cc_start: 0.8751 (mmt) cc_final: 0.7911 (mmt)
REVERT: A 3087 ILE cc_start: 0.8902 (mm) cc_final: 0.8540 (tp)
REVERT: A 3289 GLN cc_start: 0.8765 (tp-100) cc_final: 0.7987 (mm110)
REVERT: A 3309 PHE cc_start: 0.7383 (t80) cc_final: 0.7028 (t80)
REVERT: A 3343 LYS cc_start: 0.8756 (tptt) cc_final: 0.8467 (tppt)
REVERT: A 3364 GLN cc_start: 0.8941 (tm-30) cc_final: 0.8682 (tm-30)
REVERT: A 3379 TYR cc_start: 0.8343 (t80) cc_final: 0.8067 (t80)
REVERT: A 3415 MET cc_start: 0.9451 (tpt) cc_final: 0.9126 (tpp)
REVERT: A 3421 MET cc_start: 0.8606 (ppp) cc_final: 0.8070 (ppp)
REVERT: A 3425 ASN cc_start: 0.9305 (m-40) cc_final: 0.8992 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 362
  average time/residue: 0.1223
  time to fit residues: 69.2254
Evaluate side-chains
  305 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 305
  time to evaluate  : 0.725 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 244
   random chunks:
   chunk 127 optimal weight:    9.9990
   chunk 243 optimal weight:    2.9990
   chunk 206 optimal weight:    3.9990
   chunk 75 optimal weight:   10.0000
   chunk 162 optimal weight:    0.0570
   chunk 3 optimal weight:   10.0000
   chunk 149 optimal weight:    0.7980
   chunk 117 optimal weight:    0.6980
   chunk 101 optimal weight:    8.9990
   chunk 138 optimal weight:    0.9980
   chunk 156 optimal weight:    3.9990
   overall best weight:    1.1100

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

Flipped N/Q/H residues before XYZ refinement:
A2374 GLN
** A2378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2444 HIS
** A2510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2984 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A3198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A3225 ASN
** A3256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

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ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.081530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.071710 restraints weight = 188238.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.072606 restraints weight = 141683.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.073216 restraints weight = 113038.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.073574 restraints weight = 95089.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.074050 restraints weight = 84268.235|
|-----------------------------------------------------------------------------|
r_work (final): 0.3521
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Occupancy refinement
********************
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Overall statistics
******************
model-to-map fit, CC_mask: 0.6857
moved from start:          0.7789

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  19311  Z= 0.117
  Angle     :  0.604   9.391  26099  Z= 0.314
  Chirality :  0.041   0.250   2974
  Planarity :  0.003   0.044   3402
  Dihedral  :  4.162  24.399   2626
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 9.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.20 %
    Favored  : 99.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.09 (0.17), residues: 2436
  helix:  1.31 (0.14), residues: 1458
  sheet:  0.22 (0.51), residues: 99
  loop : -0.07 (0.21), residues: 879

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A2439 
 TYR   0.023   0.001   TYR A2864 
 PHE   0.033   0.002   PHE A2211 
 TRP   0.033   0.002   TRP A2314 
 HIS   0.006   0.001   HIS A2759 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 (19311)
  covalent geometry    : angle       0.60422 (26099)
  hydrogen bonds       : bond        0.03540 ( 1022)
  hydrogen bonds       : angle       4.21495 ( 2916)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2941.59 seconds
wall clock time: 51 minutes 45.22 seconds (3105.22 seconds total)