Starting phenix.real_space_refine
on Fri Mar  6 03:50:24 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7bc4_12138/03_2026/7bc4_12138.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7bc4_12138/03_2026/7bc4_12138.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7bc4_12138/03_2026/7bc4_12138.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7bc4_12138/03_2026/7bc4_12138.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7bc4_12138/03_2026/7bc4_12138.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7bc4_12138/03_2026/7bc4_12138.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.014
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       1      5.49       5
     S      95      5.16       5
     C   17595      2.51       5
     N    4640      2.21       5
     O    5279      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 243 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 27610
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 11486
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1460, 11486
          Classifications: {'peptide': 1460}
          Link IDs: {'PTRANS': 61, 'TRANS': 1398}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 16093
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2054, 16093
          Classifications: {'peptide': 2054}
          Link IDs: {'PTRANS': 102, 'TRANS': 1951}
    Chain: "B"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'FMN': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.24, per 1000 atoms: 0.19
  Number of scatterers: 27610
  At special positions: 0
  Unit cell: (204.48, 129.93, 178.92, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      95     16.00
     P       1     15.00
     O    5279      8.00
     N    4640      7.00
     C   17595      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.99
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  7012 Ramachandran restraints generated.
    3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  6524

  Finding SS restraints...
    Secondary structure from input PDB file:
      155 helices and 31 sheets defined
      44.9% alpha, 13.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 20
      removed outlier: 4.218A  pdb=" N   GLN A   7 " --> pdb=" O   PRO A   3 " (cutoff:3.500A)
      removed outlier: 4.719A  pdb=" N   GLU A   8 " --> pdb=" O   GLU A   4 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   LEU A   9 " --> pdb=" O   VAL A   5 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   GLU A  16 " --> pdb=" O   VAL A  12 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   TYR A  20 " --> pdb=" O   GLU A  16 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 28 through 33
    Processing helix  chain 'A' and resid 54 through 62
      removed outlier: 3.697A  pdb=" N   SER A  58 " --> pdb=" O   ALA A  54 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 65 through 72
    Processing helix  chain 'A' and resid 84 through 89
      removed outlier: 3.585A  pdb=" N   TYR A  89 " --> pdb=" O   THR A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 323 through 326
      removed outlier: 3.792A  pdb=" N   LEU A 326 " --> pdb=" O   PHE A 323 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 323 through 326'
    Processing helix  chain 'A' and resid 327 through 346
      removed outlier: 3.755A  pdb=" N   ARG A 331 " --> pdb=" O   THR A 327 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   VAL A 340 " --> pdb=" O   GLN A 336 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 350 through 357
      removed outlier: 3.847A  pdb=" N   VAL A 357 " --> pdb=" O   GLU A 353 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 377
      removed outlier: 3.712A  pdb=" N   LEU A 372 " --> pdb=" O   GLN A 368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 378 through 385
    Processing helix  chain 'A' and resid 399 through 417
      removed outlier: 3.539A  pdb=" N   TRP A 403 " --> pdb=" O   SER A 399 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   ARG A 405 " --> pdb=" O   TRP A 401 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   ILE A 416 " --> pdb=" O   TYR A 412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 424 through 437
      removed outlier: 3.740A  pdb=" N   VAL A 428 " --> pdb=" O   ASP A 424 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   GLN A 433 " --> pdb=" O   SER A 429 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 439 through 452
      removed outlier: 3.541A  pdb=" N   ILE A 443 " --> pdb=" O   ASN A 439 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   HIS A 449 " --> pdb=" O   PHE A 445 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   ILE A 450 " --> pdb=" O   MET A 446 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 454 through 457
    Processing helix  chain 'A' and resid 458 through 478
      removed outlier: 3.706A  pdb=" N   GLN A 470 " --> pdb=" O   SER A 466 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 517 through 527
      removed outlier: 3.767A  pdb=" N   GLY A 527 " --> pdb=" O   GLU A 523 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 642 through 657
      removed outlier: 3.580A  pdb=" N   LEU A 646 " --> pdb=" O   ASP A 642 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   GLN A 652 " --> pdb=" O   LEU A 648 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 676 through 688
      removed outlier: 3.503A  pdb=" N   GLN A 682 " --> pdb=" O   ALA A 678 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 699 through 714
    Processing helix  chain 'A' and resid 729 through 742
      removed outlier: 3.565A  pdb=" N   VAL A 733 " --> pdb=" O   SER A 729 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   ILE A 737 " --> pdb=" O   VAL A 733 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 773 through 784
    Processing helix  chain 'A' and resid 784 through 801
      removed outlier: 3.524A  pdb=" N   ARG A 801 " --> pdb=" O   GLN A 797 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 826 through 832
    Processing helix  chain 'A' and resid 833 through 835
      No H-bonds generated for 'chain 'A' and resid 833 through 835'
    Processing helix  chain 'A' and resid 836 through 844
      removed outlier: 4.638A  pdb=" N   TYR A 842 " --> pdb=" O   PHE A 838 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 867 through 872
      removed outlier: 4.149A  pdb=" N   ILE A 872 " --> pdb=" O   GLY A 868 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 872 through 877
    Processing helix  chain 'A' and resid 878 through 880
      No H-bonds generated for 'chain 'A' and resid 878 through 880'
    Processing helix  chain 'A' and resid 885 through 895
    Processing helix  chain 'A' and resid 896 through 898
      No H-bonds generated for 'chain 'A' and resid 896 through 898'
    Processing helix  chain 'A' and resid 917 through 921
      removed outlier: 3.645A  pdb=" N   ILE A 921 " --> pdb=" O   LEU A 918 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 923 through 957
      removed outlier: 3.552A  pdb=" N   THR A 938 " --> pdb=" O   GLU A 934 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   ARG A 943 " --> pdb=" O   SER A 939 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   VAL A 945 " --> pdb=" O   VAL A 941 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   THR A 953 " --> pdb=" O   THR A 949 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   ARG A 954 " --> pdb=" O   GLY A 950 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   VAL A 956 " --> pdb=" O   GLU A 952 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 958 through 962
      removed outlier: 3.810A  pdb=" N   ALA A 961 " --> pdb=" O   GLY A 958 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   ASP A 962 " --> pdb=" O   GLU A 959 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 958 through 962'
    Processing helix  chain 'A' and resid 985 through 993
    Processing helix  chain 'A' and resid 1001 through 1004
    Processing helix  chain 'A' and resid 1023 through 1028
    Processing helix  chain 'A' and resid 1033 through 1044
    Processing helix  chain 'A' and resid 1072 through 1074
      No H-bonds generated for 'chain 'A' and resid 1072 through 1074'
    Processing helix  chain 'A' and resid 1075 through 1080
    Processing helix  chain 'A' and resid 1080 through 1087
    Processing helix  chain 'A' and resid 1094 through 1098
    Processing helix  chain 'A' and resid 1124 through 1135
    Processing helix  chain 'A' and resid 1181 through 1186
    Processing helix  chain 'A' and resid 1188 through 1193
    Processing helix  chain 'A' and resid 1196 through 1212
      removed outlier: 3.611A  pdb=" N   LEU A1200 " --> pdb=" O   ASP A1196 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   TYR A1201 " --> pdb=" O   PRO A1197 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   GLU A1208 " --> pdb=" O   VAL A1204 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1217 through 1224
    Processing helix  chain 'A' and resid 1240 through 1249
      removed outlier: 3.714A  pdb=" N   GLY A1246 " --> pdb=" O   SER A1242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1266 through 1268
      No H-bonds generated for 'chain 'A' and resid 1266 through 1268'
    Processing helix  chain 'A' and resid 1269 through 1278
      removed outlier: 3.588A  pdb=" N   ASN A1275 " --> pdb=" O   SER A1271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1295 through 1308
    Processing helix  chain 'A' and resid 1323 through 1333
      removed outlier: 3.511A  pdb=" N   ALA A1331 " --> pdb=" O   SER A1327 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1340 through 1345
    Processing helix  chain 'A' and resid 1348 through 1352
    Processing helix  chain 'A' and resid 1377 through 1384
    Processing helix  chain 'A' and resid 1410 through 1416
      removed outlier: 3.569A  pdb=" N   LEU A1413 " --> pdb=" O   LYS A1410 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   THR A1414 " --> pdb=" O   GLY A1411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1427 through 1430
    Processing helix  chain 'A' and resid 1431 through 1462
      removed outlier: 3.620A  pdb=" N   ARG A1435 " --> pdb=" O   ASP A1431 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   GLN A1445 " --> pdb=" O   LYS A1441 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   LYS A1447 " --> pdb=" O   LYS A1443 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   GLU A1451 " --> pdb=" O   LYS A1447 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   GLU A1455 " --> pdb=" O   GLU A1451 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   TYR A1456 " --> pdb=" O   ASP A1452 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1475 through 1480
      removed outlier: 3.809A  pdb=" N   GLU A1479 " --> pdb=" O   SER A1475 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1481 through 1499
      removed outlier: 3.727A  pdb=" N   GLN A1497 " --> pdb=" O   LYS A1493 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1511 through 1519
      removed outlier: 3.898A  pdb=" N   LEU A1517 " --> pdb=" O   LEU A1513 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1523 through 1527
    Processing helix  chain 'A' and resid 1537 through 1555
      removed outlier: 4.043A  pdb=" N   LYS A1542 " --> pdb=" O   LYS A1538 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   SER A1545 " --> pdb=" O   ASP A1541 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1567 through 1571
      removed outlier: 3.648A  pdb=" N   TYR A1570 " --> pdb=" O   PHE A1567 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1578 through 1594
      removed outlier: 3.561A  pdb=" N   LEU A1591 " --> pdb=" O   ALA A1587 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1606 through 1611
      removed outlier: 3.585A  pdb=" N   GLU A1610 " --> pdb=" O   LYS A1607 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1649 through 1654
      removed outlier: 3.589A  pdb=" N   PHE A1653 " --> pdb=" O   PRO A1649 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1657 through 1686
      removed outlier: 3.503A  pdb=" N   LYS A1667 " --> pdb=" O   GLU A1663 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   LYS A1673 " --> pdb=" O   GLU A1669 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   SER A1674 " --> pdb=" O   ALA A1670 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   ILE A1684 " --> pdb=" O   HIS A1680 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1698 through 1700
      No H-bonds generated for 'chain 'A' and resid 1698 through 1700'
    Processing helix  chain 'A' and resid 1701 through 1707
    Processing helix  chain 'A' and resid 1726 through 1730
    Processing helix  chain 'B' and resid 30 through 44
      removed outlier: 4.526A  pdb=" N   GLY B  39 " --> pdb=" O   THR B  35 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   PHE B  40 " --> pdb=" O   LEU B  36 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   LYS B  42 " --> pdb=" O   GLU B  38 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   LEU B  44 " --> pdb=" O   PHE B  40 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 59 through 74
      removed outlier: 3.578A  pdb=" N   LEU B  63 " --> pdb=" O   SER B  59 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   LEU B  64 " --> pdb=" O   LYS B  60 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   LYS B  66 " --> pdb=" O   GLU B  62 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 78 through 97
      removed outlier: 3.591A  pdb=" N   ALA B  84 " --> pdb=" O   GLN B  80 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 102 through 112
      removed outlier: 3.653A  pdb=" N   ILE B 109 " --> pdb=" O   SER B 105 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   LYS B 112 " --> pdb=" O   ALA B 108 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 119 through 126
    Processing helix  chain 'B' and resid 127 through 138
      removed outlier: 3.639A  pdb=" N   TYR B 132 " --> pdb=" O   ILE B 128 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   VAL B 138 " --> pdb=" O   GLY B 134 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 151 through 159
    Processing helix  chain 'B' and resid 177 through 188
      removed outlier: 3.643A  pdb=" N   LEU B 181 " --> pdb=" O   TYR B 177 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 195 through 207
      removed outlier: 4.164A  pdb=" N   GLU B 205 " --> pdb=" O   LEU B 201 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 229
      removed outlier: 3.535A  pdb=" N   GLU B 228 " --> pdb=" O   ILE B 224 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 241 through 244
    Processing helix  chain 'B' and resid 245 through 264
      removed outlier: 3.623A  pdb=" N   CYS B 250 " --> pdb=" O   CYS B 246 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   LEU B 264 " --> pdb=" O   THR B 260 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 267 through 273
      removed outlier: 3.862A  pdb=" N   ASP B 273 " --> pdb=" O   GLY B 269 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 284 through 294
      removed outlier: 3.545A  pdb=" N   VAL B 290 " --> pdb=" O   VAL B 286 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 296 through 321
      removed outlier: 3.854A  pdb=" N   GLU B 301 " --> pdb=" O   TRP B 297 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   GLN B 306 " --> pdb=" O   LYS B 302 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   TYR B 313 " --> pdb=" O   GLU B 309 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 328 through 338
      removed outlier: 3.602A  pdb=" N   ASP B 334 " --> pdb=" O   SER B 330 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 356 through 366
      removed outlier: 3.534A  pdb=" N   VAL B 361 " --> pdb=" O   LEU B 357 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   THR B 364 " --> pdb=" O   PHE B 360 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 390 through 403
      removed outlier: 3.786A  pdb=" N   LEU B 397 " --> pdb=" O   SER B 393 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   LYS B 403 " --> pdb=" O   LEU B 399 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 444 through 452
    Processing helix  chain 'B' and resid 482 through 493
      removed outlier: 3.643A  pdb=" N   GLU B 489 " --> pdb=" O   ALA B 485 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 498 through 502
    Processing helix  chain 'B' and resid 519 through 524
    Processing helix  chain 'B' and resid 525 through 529
      removed outlier: 3.868A  pdb=" N   GLU B 529 " --> pdb=" O   ARG B 526 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 552 through 556
    Processing helix  chain 'B' and resid 560 through 564
      removed outlier: 3.656A  pdb=" N   ALA B 563 " --> pdb=" O   ASN B 560 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   ILE B 564 " --> pdb=" O   GLU B 561 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 560 through 564'
    Processing helix  chain 'B' and resid 569 through 574
    Processing helix  chain 'B' and resid 590 through 597
      removed outlier: 3.629A  pdb=" N   LEU B 595 " --> pdb=" O   LYS B 591 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 612 through 622
      removed outlier: 3.626A  pdb=" N   ALA B 618 " --> pdb=" O   ASP B 614 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 635 through 649
      removed outlier: 4.091A  pdb=" N   GLN B 649 " --> pdb=" O   ARG B 645 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 664 through 682
      removed outlier: 3.865A  pdb=" N   LEU B 668 " --> pdb=" O   ASN B 664 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   TRP B 670 " --> pdb=" O   ARG B 666 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   ILE B 672 " --> pdb=" O   LEU B 668 " (cutoff:3.500A)
      Proline residue:  B 673  - end of helix
      removed outlier: 3.627A  pdb=" N   GLN B 681 " --> pdb=" O   GLU B 677 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 696 through 705
      removed outlier: 3.822A  pdb=" N   GLU B 702 " --> pdb=" O   GLU B 698 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   TYR B 703 " --> pdb=" O   VAL B 699 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 719 through 730
      removed outlier: 3.568A  pdb=" N   ASN B 723 " --> pdb=" O   ILE B 719 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 757 through 769
      removed outlier: 3.561A  pdb=" N   GLN B 761 " --> pdb=" O   GLN B 757 " (cutoff:3.500A)
      removed outlier: 6.158A  pdb=" N   SER B 764 " --> pdb=" O   LEU B 760 " (cutoff:3.500A)
      removed outlier: 5.210A  pdb=" N   LYS B 765 " --> pdb=" O   GLN B 761 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   LYS B 768 " --> pdb=" O   SER B 764 " (cutoff:3.500A)
      removed outlier: 4.035A  pdb=" N   CYS B 769 " --> pdb=" O   LYS B 765 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 782 through 792
      Proline residue:  B 788  - end of helix
    Processing helix  chain 'B' and resid 794 through 799
      removed outlier: 4.110A  pdb=" N   GLN B 797 " --> pdb=" O   TRP B 794 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   SER B 799 " --> pdb=" O   HIS B 796 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 823 through 832
      removed outlier: 3.576A  pdb=" N   GLN B 828 " --> pdb=" O   PRO B 824 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ALA B 829 " --> pdb=" O   ALA B 825 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 841 through 845
      removed outlier: 3.737A  pdb=" N   THR B 844 " --> pdb=" O   TRP B 841 " (cutoff:3.500A)
      removed outlier: 4.382A  pdb=" N   TYR B 845 " --> pdb=" O   GLU B 842 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 841 through 845'
    Processing helix  chain 'B' and resid 868 through 879
    Processing helix  chain 'B' and resid 885 through 896
      removed outlier: 4.383A  pdb=" N   LEU B 890 " --> pdb=" O   LYS B 886 " (cutoff:3.500A)
      removed outlier: 4.391A  pdb=" N   GLU B 891 " --> pdb=" O   ASN B 887 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   ALA B 892 " --> pdb=" O   LYS B 888 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 896 through 908
      removed outlier: 3.730A  pdb=" N   LYS B 902 " --> pdb=" O   ASP B 898 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   TYR B 908 " --> pdb=" O   LEU B 904 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 922 through 926
      removed outlier: 3.551A  pdb=" N   MET B 926 " --> pdb=" O   LEU B 923 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 927 through 939
      removed outlier: 3.859A  pdb=" N   VAL B 936 " --> pdb=" O   ALA B 932 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 949 through 967
    Processing helix  chain 'B' and resid 979 through 984
      removed outlier: 3.532A  pdb=" N   GLN B 982 " --> pdb=" O   ASN B 979 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   GLU B 984 " --> pdb=" O   SER B 981 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 985 through 997
      removed outlier: 3.607A  pdb=" N   ALA B 989 " --> pdb=" O   GLU B 985 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   SER B 992 " --> pdb=" O   LYS B 988 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   ALA B 996 " --> pdb=" O   SER B 992 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 998 through 1002
    Processing helix  chain 'B' and resid 1006 through 1018
      removed outlier: 3.596A  pdb=" N   GLN B1018 " --> pdb=" O   LEU B1014 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1034 through 1040
    Processing helix  chain 'B' and resid 1044 through 1048
      removed outlier: 3.895A  pdb=" N   SER B1047 " --> pdb=" O   LEU B1044 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1053 through 1061
      removed outlier: 3.630A  pdb=" N   ASP B1057 " --> pdb=" O   VAL B1054 " (cutoff:3.500A)
      removed outlier: 6.341A  pdb=" N   VAL B1058 " --> pdb=" O   GLY B1055 " (cutoff:3.500A)
      removed outlier: 6.052A  pdb=" N   GLN B1059 " --> pdb=" O   GLU B1056 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   ARG B1060 " --> pdb=" O   ASP B1057 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1079 through 1084
    Processing helix  chain 'B' and resid 1084 through 1100
      removed outlier: 3.860A  pdb=" N   LYS B1097 " --> pdb=" O   LYS B1093 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   GLU B1098 " --> pdb=" O   SER B1094 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1103 through 1107
      removed outlier: 3.799A  pdb=" N   LYS B1106 " --> pdb=" O   ASP B1103 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1146 through 1155
      removed outlier: 3.634A  pdb=" N   ASP B1152 " --> pdb=" O   GLN B1148 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1160 through 1167
    Processing helix  chain 'B' and resid 1181 through 1186
    Processing helix  chain 'B' and resid 1269 through 1283
      removed outlier: 3.546A  pdb=" N   SER B1273 " --> pdb=" O   GLY B1269 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   LYS B1280 " --> pdb=" O   ASN B1276 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1307 through 1319
    Processing helix  chain 'B' and resid 1322 through 1326
      removed outlier: 3.607A  pdb=" N   PHE B1325 " --> pdb=" O   CYS B1322 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1336 through 1338
      No H-bonds generated for 'chain 'B' and resid 1336 through 1338'
    Processing helix  chain 'B' and resid 1339 through 1344
    Processing helix  chain 'B' and resid 1344 through 1349
    Processing helix  chain 'B' and resid 1350 through 1352
      No H-bonds generated for 'chain 'B' and resid 1350 through 1352'
    Processing helix  chain 'B' and resid 1360 through 1362
      No H-bonds generated for 'chain 'B' and resid 1360 through 1362'
    Processing helix  chain 'B' and resid 1451 through 1460
      removed outlier: 3.949A  pdb=" N   ILE B1455 " --> pdb=" O   SER B1451 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   ALA B1456 " --> pdb=" O   ALA B1452 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1527 through 1537
      removed outlier: 3.536A  pdb=" N   ARG B1535 " --> pdb=" O   ASP B1531 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1568 through 1574
    Processing helix  chain 'B' and resid 1582 through 1589
    Processing helix  chain 'B' and resid 1597 through 1613
      removed outlier: 3.670A  pdb=" N   SER B1601 " --> pdb=" O   HIS B1597 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   ALA B1607 " --> pdb=" O   ALA B1603 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   LEU B1608 " --> pdb=" O   ALA B1604 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1617 through 1619
      No H-bonds generated for 'chain 'B' and resid 1617 through 1619'
    Processing helix  chain 'B' and resid 1694 through 1701
    Processing helix  chain 'B' and resid 1704 through 1720
      removed outlier: 3.795A  pdb=" N   TRP B1708 " --> pdb=" O   ALA B1704 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   ARG B1710 " --> pdb=" O   SER B1706 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   HIS B1714 " --> pdb=" O   ARG B1710 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1722 through 1729
    Processing helix  chain 'B' and resid 1740 through 1752
      removed outlier: 3.581A  pdb=" N   SER B1745 " --> pdb=" O   ALA B1741 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   ILE B1746 " --> pdb=" O   LYS B1742 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   ASN B1749 " --> pdb=" O   SER B1745 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   TYR B1750 " --> pdb=" O   ILE B1746 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1787 through 1790
    Processing helix  chain 'B' and resid 1791 through 1813
      Proline residue:  B1797  - end of helix
      removed outlier: 3.664A  pdb=" N   LEU B1801 " --> pdb=" O   PRO B1797 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1827 through 1834
      removed outlier: 3.655A  pdb=" N   SER B1831 " --> pdb=" O   LEU B1827 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   LEU B1833 " --> pdb=" O   GLU B1829 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1841 through 1856
    Processing helix  chain 'B' and resid 1885 through 1899
      removed outlier: 4.231A  pdb=" N   VAL B1892 " --> pdb=" O   ALA B1888 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1924 through 1929
      removed outlier: 3.673A  pdb=" N   LEU B1928 " --> pdb=" O   GLY B1924 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1953 through 1958
      removed outlier: 4.038A  pdb=" N   LEU B1958 " --> pdb=" O   VAL B1954 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1958 through 1972
      removed outlier: 3.539A  pdb=" N   VAL B1965 " --> pdb=" O   ILE B1961 " (cutoff:3.500A)
      removed outlier: 4.369A  pdb=" N   LYS B1968 " --> pdb=" O   GLU B1964 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   SER B1970 " --> pdb=" O   SER B1966 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2002 through 2011
      removed outlier: 3.826A  pdb=" N   PHE B2006 " --> pdb=" O   GLY B2002 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   THR B2008 " --> pdb=" O   LYS B2004 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2042 through 2052
      removed outlier: 3.899A  pdb=" N   ASP B2046 " --> pdb=" O   GLU B2042 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   VAL B2047 " --> pdb=" O   TYR B2043 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2053 through 2061
      removed outlier: 3.516A  pdb=" N   HIS B2058 " --> pdb=" O   GLU B2054 " (cutoff:3.500A)
      removed outlier: 4.309A  pdb=" N   ILE B2059 " --> pdb=" O   LYS B2055 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   ASP B2061 " --> pdb=" O   LYS B2057 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 80
    Processing sheet with id=AA2, first strand: chain 'A' and resid 395 through 397
      removed outlier: 6.636A  pdb=" N   ASN A 665 " --> pdb=" O   ALA A 755 " (cutoff:3.500A)
      removed outlier: 8.065A  pdb=" N   ILE A 757 " --> pdb=" O   ASN A 665 " (cutoff:3.500A)
      removed outlier: 6.903A  pdb=" N   LEU A 667 " --> pdb=" O   ILE A 757 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 492 through 498
    Processing sheet with id=AA4, first strand: chain 'A' and resid 637 through 640
      removed outlier: 4.759A  pdb=" N   LEU A 628 " --> pdb=" O   ASP A 640 " (cutoff:3.500A)
      removed outlier: 4.515A  pdb=" N   VAL A 911 " --> pdb=" O   LYS A 629 " (cutoff:3.500A)
      removed outlier: 6.879A  pdb=" N   LEU A 814 " --> pdb=" O   ILE A 857 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1230 through 1232
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1230 through 1232
      removed outlier: 6.574A  pdb=" N   SER A1369 " --> pdb=" O   GLU A1013 " (cutoff:3.500A)
      removed outlier: 4.873A  pdb=" N   GLU A1013 " --> pdb=" O   SER A1369 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   THR A1371 " --> pdb=" O   PHE A1011 " (cutoff:3.500A)
      removed outlier: 4.481A  pdb=" N   PHE A1011 " --> pdb=" O   THR A1371 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   VAL A1373 " --> pdb=" O   THR A1009 " (cutoff:3.500A)
      removed outlier: 4.735A  pdb=" N   ILE A1006 " --> pdb=" O   VAL A1391 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ALA A1389 " --> pdb=" O   VAL A1008 " (cutoff:3.500A)
      removed outlier: 6.652A  pdb=" N   ILE A1645 " --> pdb=" O   ALA A1392 " (cutoff:3.500A)
      removed outlier: 4.361A  pdb=" N   THR A1394 " --> pdb=" O   GLN A1643 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   GLN A1643 " --> pdb=" O   THR A1394 " (cutoff:3.500A)
      removed outlier: 4.529A  pdb=" N   THR A1396 " --> pdb=" O   GLY A1641 " (cutoff:3.500A)
      removed outlier: 6.979A  pdb=" N   GLY A1641 " --> pdb=" O   THR A1396 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1047 through 1049
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1052 through 1053
    Processing sheet with id=AA9, first strand: chain 'A' and resid 1106 through 1113
    Processing sheet with id=AB1, first strand: chain 'A' and resid 1121 through 1123
    Processing sheet with id=AB2, first strand: chain 'A' and resid 1529 through 1531
      removed outlier: 5.997A  pdb=" N   VAL A1563 " --> pdb=" O   LEU A1616 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 1595 through 1596
    Processing sheet with id=AB4, first strand: chain 'A' and resid 1714 through 1715
      removed outlier: 3.598A  pdb=" N   ASN A1714 " --> pdb=" O   VAL A1724 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 12 through 13
    Processing sheet with id=AB6, first strand: chain 'B' and resid 276 through 280
      removed outlier: 6.140A  pdb=" N   ILE B 164 " --> pdb=" O   LYS B 276 " (cutoff:3.500A)
      removed outlier: 6.108A  pdb=" N   THR B 278 " --> pdb=" O   ILE B 164 " (cutoff:3.500A)
      removed outlier: 6.510A  pdb=" N   ALA B 166 " --> pdb=" O   THR B 278 " (cutoff:3.500A)
      removed outlier: 5.601A  pdb=" N   GLY B 280 " --> pdb=" O   ALA B 166 " (cutoff:3.500A)
      removed outlier: 6.064A  pdb=" N   PHE B 168 " --> pdb=" O   GLY B 280 " (cutoff:3.500A)
      removed outlier: 6.448A  pdb=" N   TYR B 165 " --> pdb=" O   LEU B 510 " (cutoff:3.500A)
      removed outlier: 6.277A  pdb=" N   VAL B 509 " --> pdb=" O   ILE B 536 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB6
    Processing sheet with id=AB7, first strand: chain 'B' and resid 425 through 428
      removed outlier: 7.282A  pdb=" N   ASN B 384 " --> pdb=" O   ILE B 379 " (cutoff:3.500A)
      removed outlier: 5.096A  pdb=" N   ILE B 379 " --> pdb=" O   ASN B 384 " (cutoff:3.500A)
      removed outlier: 7.062A  pdb=" N   VAL B 386 " --> pdb=" O   SER B 377 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 577 through 580
    Processing sheet with id=AB9, first strand: chain 'B' and resid 601 through 602
    Processing sheet with id=AC1, first strand: chain 'B' and resid 628 through 629
      removed outlier: 6.685A  pdb=" N   ILE B 628 " --> pdb=" O   ASN B 659 " (cutoff:3.500A)
      removed outlier: 8.563A  pdb=" N   ILE B 661 " --> pdb=" O   ILE B 628 " (cutoff:3.500A)
      removed outlier: 6.250A  pdb=" N   ILE B 658 " --> pdb=" O   SER B 689 " (cutoff:3.500A)
      removed outlier: 7.039A  pdb=" N   GLY B 691 " --> pdb=" O   ILE B 658 " (cutoff:3.500A)
      removed outlier: 6.544A  pdb=" N   LEU B 660 " --> pdb=" O   GLY B 691 " (cutoff:3.500A)
      removed outlier: 6.314A  pdb=" N   LEU B 688 " --> pdb=" O   GLY B 713 " (cutoff:3.500A)
      removed outlier: 6.239A  pdb=" N   LEU B 712 " --> pdb=" O   VAL B 738 " (cutoff:3.500A)
      removed outlier: 7.102A  pdb=" N   GLN B 740 " --> pdb=" O   LEU B 712 " (cutoff:3.500A)
      removed outlier: 6.275A  pdb=" N   LEU B 714 " --> pdb=" O   GLN B 740 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'B' and resid 852 through 855
    Processing sheet with id=AC3, first strand: chain 'B' and resid 940 through 941
    Processing sheet with id=AC4, first strand: chain 'B' and resid 1129 through 1131
      removed outlier: 4.232A  pdb=" N   VAL B1194 " --> pdb=" O   PHE B1138 " (cutoff:3.500A)
      removed outlier: 6.815A  pdb=" N   LEU B1207 " --> pdb=" O   SER B1222 " (cutoff:3.500A)
      removed outlier: 4.612A  pdb=" N   SER B1222 " --> pdb=" O   LEU B1207 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   ALA B1209 " --> pdb=" O   ALA B1220 " (cutoff:3.500A)
      removed outlier: 4.915A  pdb=" N   ALA B1220 " --> pdb=" O   ILE B1236 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'B' and resid 1171 through 1172
    Processing sheet with id=AC6, first strand: chain 'B' and resid 1299 through 1305
      removed outlier: 5.582A  pdb=" N   THR B1388 " --> pdb=" O   GLY B1301 " (cutoff:3.500A)
      removed outlier: 4.700A  pdb=" N   GLU B1303 " --> pdb=" O   VAL B1386 " (cutoff:3.500A)
      removed outlier: 6.667A  pdb=" N   VAL B1386 " --> pdb=" O   GLU B1303 " (cutoff:3.500A)
      removed outlier: 6.611A  pdb=" N   GLU B1405 " --> pdb=" O   ARG B1393 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   VAL B1395 " --> pdb=" O   THR B1403 " (cutoff:3.500A)
      removed outlier: 5.324A  pdb=" N   THR B1403 " --> pdb=" O   VAL B1395 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   LEU B1418 " --> pdb=" O   ILE B1410 " (cutoff:3.500A)
      removed outlier: 5.807A  pdb=" N   ARG B1412 " --> pdb=" O   PRO B1416 " (cutoff:3.500A)
      removed outlier: 6.878A  pdb=" N   PHE B1425 " --> pdb=" O   HIS B1366 " (cutoff:3.500A)
      removed outlier: 5.700A  pdb=" N   HIS B1366 " --> pdb=" O   PHE B1425 " (cutoff:3.500A)
      removed outlier: 5.695A  pdb=" N   LEU B1367 " --> pdb=" O   PHE B1628 " (cutoff:3.500A)
      removed outlier: 7.091A  pdb=" N   ARG B1622 " --> pdb=" O   MET B1373 " (cutoff:3.500A)
      removed outlier: 6.315A  pdb=" N   VAL B1621 " --> pdb=" O   GLU B1675 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   GLU B1675 " --> pdb=" O   VAL B1621 " (cutoff:3.500A)
      removed outlier: 4.151A  pdb=" N   ALA B1623 " --> pdb=" O   GLU B1673 " (cutoff:3.500A)
      removed outlier: 6.483A  pdb=" N   VAL B1666 " --> pdb=" O   LYS B1660 " (cutoff:3.500A)
      removed outlier: 6.452A  pdb=" N   LYS B1660 " --> pdb=" O   VAL B1666 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   GLY B1646 " --> pdb=" O   ILE B1653 " (cutoff:3.500A)
      removed outlier: 6.542A  pdb=" N   LYS B1655 " --> pdb=" O   HIS B1644 " (cutoff:3.500A)
      removed outlier: 5.383A  pdb=" N   HIS B1644 " --> pdb=" O   LYS B1655 " (cutoff:3.500A)
      removed outlier: 7.062A  pdb=" N   GLY B1646 " --> pdb=" O   ASN B1548 " (cutoff:3.500A)
      removed outlier: 10.461A  pdb=" N   ASN B1548 " --> pdb=" O   GLY B1646 " (cutoff:3.500A)
      removed outlier: 11.465A  pdb=" N   ILE B1648 " --> pdb=" O   PHE B1546 " (cutoff:3.500A)
      removed outlier: 11.597A  pdb=" N   PHE B1546 " --> pdb=" O   ILE B1648 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'B' and resid 1299 through 1305
      removed outlier: 5.582A  pdb=" N   THR B1388 " --> pdb=" O   GLY B1301 " (cutoff:3.500A)
      removed outlier: 4.700A  pdb=" N   GLU B1303 " --> pdb=" O   VAL B1386 " (cutoff:3.500A)
      removed outlier: 6.667A  pdb=" N   VAL B1386 " --> pdb=" O   GLU B1303 " (cutoff:3.500A)
      removed outlier: 6.611A  pdb=" N   GLU B1405 " --> pdb=" O   ARG B1393 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   VAL B1395 " --> pdb=" O   THR B1403 " (cutoff:3.500A)
      removed outlier: 5.324A  pdb=" N   THR B1403 " --> pdb=" O   VAL B1395 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   LEU B1418 " --> pdb=" O   ILE B1410 " (cutoff:3.500A)
      removed outlier: 5.807A  pdb=" N   ARG B1412 " --> pdb=" O   PRO B1416 " (cutoff:3.500A)
      removed outlier: 6.878A  pdb=" N   PHE B1425 " --> pdb=" O   HIS B1366 " (cutoff:3.500A)
      removed outlier: 5.700A  pdb=" N   HIS B1366 " --> pdb=" O   PHE B1425 " (cutoff:3.500A)
      removed outlier: 5.695A  pdb=" N   LEU B1367 " --> pdb=" O   PHE B1628 " (cutoff:3.500A)
      removed outlier: 7.091A  pdb=" N   ARG B1622 " --> pdb=" O   MET B1373 " (cutoff:3.500A)
      removed outlier: 6.315A  pdb=" N   VAL B1621 " --> pdb=" O   GLU B1675 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   GLU B1675 " --> pdb=" O   VAL B1621 " (cutoff:3.500A)
      removed outlier: 4.151A  pdb=" N   ALA B1623 " --> pdb=" O   GLU B1673 " (cutoff:3.500A)
      removed outlier: 6.483A  pdb=" N   VAL B1666 " --> pdb=" O   LYS B1660 " (cutoff:3.500A)
      removed outlier: 6.452A  pdb=" N   LYS B1660 " --> pdb=" O   VAL B1666 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'B' and resid 1334 through 1335
      removed outlier: 4.228A  pdb=" N   LEU B1380 " --> pdb=" O   ALA B1335 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'B' and resid 1437 through 1439
      removed outlier: 6.759A  pdb=" N   TYR B1484 " --> pdb=" O   VAL B1496 " (cutoff:3.500A)
      removed outlier: 4.635A  pdb=" N   VAL B1496 " --> pdb=" O   TYR B1484 " (cutoff:3.500A)
      removed outlier: 6.415A  pdb=" N   LYS B1486 " --> pdb=" O   ALA B1494 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'B' and resid 1464 through 1466
      removed outlier: 6.979A  pdb=" N   ALA B1502 " --> pdb=" O   VAL B1514 " (cutoff:3.500A)
      removed outlier: 4.432A  pdb=" N   GLU B1505 " --> pdb=" O   THR B1476 " (cutoff:3.500A)
      removed outlier: 6.513A  pdb=" N   THR B1476 " --> pdb=" O   GLU B1505 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   GLN B1475 " --> pdb=" O   PHE B1449 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   VAL B1445 " --> pdb=" O   PHE B1479 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'B' and resid 1733 through 1737
    Processing sheet with id=AD3, first strand: chain 'B' and resid 1754 through 1755
    Processing sheet with id=AD4, first strand: chain 'B' and resid 1870 through 1875
      removed outlier: 7.458A  pdb=" N   VAL B1917 " --> pdb=" O   TYR B1909 " (cutoff:3.500A)
      removed outlier: 5.791A  pdb=" N   TYR B1909 " --> pdb=" O   VAL B1917 " (cutoff:3.500A)
      removed outlier: 7.462A  pdb=" N   ALA B1919 " --> pdb=" O   VAL B1907 " (cutoff:3.500A)
      removed outlier: 5.948A  pdb=" N   VAL B1907 " --> pdb=" O   ALA B1919 " (cutoff:3.500A)
      removed outlier: 7.786A  pdb=" N   ASP B1921 " --> pdb=" O   GLU B1905 " (cutoff:3.500A)
      removed outlier: 8.247A  pdb=" N   GLU B1905 " --> pdb=" O   ASP B1921 " (cutoff:3.500A)

    1099 hydrogen bonds defined for protein.
    3081 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: 8.27

  Time building geometry restraints manager: 2.78 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 8395
        1.33 -     1.45: 4418
        1.45 -     1.57: 15221
        1.57 -     1.69: 2
        1.69 -     1.81: 163
  Bond restraints: 28199
  Sorted by residual:
  bond pdb=" C4  FMN B2101 "
       pdb=" C4A FMN B2101 "
    ideal  model  delta    sigma   weight residual
    1.485  1.386  0.099 2.00e-02 2.50e+03 2.47e+01
  bond pdb=" C4A FMN B2101 "
       pdb=" N5  FMN B2101 "
    ideal  model  delta    sigma   weight residual
    1.300  1.374 -0.074 2.00e-02 2.50e+03 1.37e+01
  bond pdb=" O5' FMN B2101 "
       pdb=" P   FMN B2101 "
    ideal  model  delta    sigma   weight residual
    1.676  1.608  0.068 2.00e-02 2.50e+03 1.17e+01
  bond pdb=" C10 FMN B2101 "
       pdb=" N1  FMN B2101 "
    ideal  model  delta    sigma   weight residual
    1.317  1.378 -0.061 2.00e-02 2.50e+03 9.41e+00
  bond pdb=" C10 FMN B2101 "
       pdb=" C4A FMN B2101 "
    ideal  model  delta    sigma   weight residual
    1.443  1.386  0.057 2.00e-02 2.50e+03 8.13e+00
  ... (remaining 28194 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.82: 37571
        2.82 -     5.64: 549
        5.64 -     8.46: 65
        8.46 -    11.27: 8
       11.27 -    14.09: 6
  Bond angle restraints: 38199
  Sorted by residual:
  angle pdb=" C   SER B 241 "
        pdb=" N   ILE B 242 "
        pdb=" CA  ILE B 242 "
      ideal   model   delta    sigma   weight residual
     120.24  125.35   -5.11 6.30e-01 2.52e+00 6.59e+01
  angle pdb=" N   PHE B1353 "
        pdb=" CA  PHE B1353 "
        pdb=" C   PHE B1353 "
      ideal   model   delta    sigma   weight residual
     109.81  122.50  -12.69 2.21e+00 2.05e-01 3.30e+01
  angle pdb=" C   GLN B1899 "
        pdb=" N   THR B1900 "
        pdb=" CA  THR B1900 "
      ideal   model   delta    sigma   weight residual
     121.54  132.16  -10.62 1.91e+00 2.74e-01 3.09e+01
  angle pdb=" CA  ASN A 439 "
        pdb=" C   ASN A 439 "
        pdb=" N   PRO A 440 "
      ideal   model   delta    sigma   weight residual
     117.68  121.09   -3.41 7.10e-01 1.98e+00 2.31e+01
  angle pdb=" C   SER B 751 "
        pdb=" N   PHE B 752 "
        pdb=" CA  PHE B 752 "
      ideal   model   delta    sigma   weight residual
     121.54  129.57   -8.03 1.91e+00 2.74e-01 1.77e+01
  ... (remaining 38194 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.79: 15103
       17.79 -    35.58: 1498
       35.58 -    53.37: 284
       53.37 -    71.16: 58
       71.16 -    88.95: 50
  Dihedral angle restraints: 16993
    sinusoidal: 6835
      harmonic: 10158
  Sorted by residual:
  dihedral pdb=" CA  ASP B 235 "
           pdb=" C   ASP B 235 "
           pdb=" N   GLN B 236 "
           pdb=" CA  GLN B 236 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  145.69   34.31     0      5.00e+00 4.00e-02 4.71e+01
  dihedral pdb=" CA  LEU A  53 "
           pdb=" C   LEU A  53 "
           pdb=" N   ALA A  54 "
           pdb=" CA  ALA A  54 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.08   29.92     0      5.00e+00 4.00e-02 3.58e+01
  dihedral pdb=" CA  PHE B1935 "
           pdb=" C   PHE B1935 "
           pdb=" N   LYS B1936 "
           pdb=" CA  LYS B1936 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.55   26.45     0      5.00e+00 4.00e-02 2.80e+01
  ... (remaining 16990 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 3238
       0.062 -    0.125: 889
       0.125 -    0.187: 119
       0.187 -    0.249: 14
       0.249 -    0.311: 6
  Chirality restraints: 4266
  Sorted by residual:
  chirality pdb=" CB  VAL B 386 "
            pdb=" CA  VAL B 386 "
            pdb=" CG1 VAL B 386 "
            pdb=" CG2 VAL B 386 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.32   -0.31 2.00e-01 2.50e+01 2.42e+00
  chirality pdb=" CA  PHE B1353 "
            pdb=" N   PHE B1353 "
            pdb=" C   PHE B1353 "
            pdb=" CB  PHE B1353 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.20e+00
  chirality pdb=" CB  ILE B 628 "
            pdb=" CA  ILE B 628 "
            pdb=" CG1 ILE B 628 "
            pdb=" CG2 ILE B 628 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.37    0.27 2.00e-01 2.50e+01 1.83e+00
  ... (remaining 4263 not shown)

  Planarity restraints: 4927
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 963 "    0.049 5.00e-02 4.00e+02   7.29e-02 8.51e+00
        pdb=" N   PRO A 964 "   -0.126 5.00e-02 4.00e+02
        pdb=" CA  PRO A 964 "    0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO A 964 "    0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B 441 "    0.049 5.00e-02 4.00e+02   7.29e-02 8.50e+00
        pdb=" N   PRO B 442 "   -0.126 5.00e-02 4.00e+02
        pdb=" CA  PRO B 442 "    0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO B 442 "    0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A1015 "   -0.048 5.00e-02 4.00e+02   7.19e-02 8.27e+00
        pdb=" N   PRO A1016 "    0.124 5.00e-02 4.00e+02
        pdb=" CA  PRO A1016 "   -0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO A1016 "   -0.040 5.00e-02 4.00e+02
  ... (remaining 4924 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.81: 8383
        2.81 -     3.33: 23916
        3.33 -     3.85: 45932
        3.85 -     4.38: 55630
        4.38 -     4.90: 94994
  Nonbonded interactions: 228855
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A1064 "
            pdb=" OH  TYR A1080 "
     model   vdw
     2.285 3.040
  nonbonded pdb=" O   VAL B1962 "
            pdb=" OG  SER B1966 "
     model   vdw
     2.289 3.040
  nonbonded pdb=" O   GLU B 702 "
            pdb=" OG1 THR B 706 "
     model   vdw
     2.295 3.040
  nonbonded pdb=" O   SER B 506 "
            pdb=" OG  SER B 533 "
     model   vdw
     2.297 3.040
  nonbonded pdb=" O   SER A  73 "
            pdb=" OG  SER A  73 "
     model   vdw
     2.297 3.040
  ... (remaining 228850 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.010
  Normalize map: mean=0, sd=1:             6.880
  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:             0.020
  Extract box with map and model:          0.400
  Check model and map are aligned:         0.080
  Set scattering table:                    0.080
  Process input model:                     27.030
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8268
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      :  0.008   0.099  28200  Z= 0.340
  Angle     :  0.883  14.093  38199  Z= 0.476
  Chirality :  0.057   0.311   4266
  Planarity :  0.007   0.073   4927
  Dihedral  : 15.462  88.949  10469
  Min Nonbonded Distance : 2.285

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.39 %
    Favored  : 93.61 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  :  8.22 %
    Favored  : 90.59 %
  Cbeta Deviations :  0.03 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.03 %

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: -5.07 (0.10), residues: 3506
  helix: -4.39 (0.05), residues: 1458
  sheet: -2.27 (0.21), residues: 474
  loop : -2.49 (0.13), residues: 1574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 932 
 TYR   0.025   0.002   TYR B  30 
 PHE   0.040   0.003   PHE A1363 
 TRP   0.019   0.002   TRP A  28 
 HIS   0.019   0.002   HIS A1135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00796 (28199)
  covalent geometry    : angle       0.88258 (38199)
  hydrogen bonds       : bond        0.29898 ( 1055)
  hydrogen bonds       : angle      10.45329 ( 3081)
  Misc. bond           : bond        0.00293 (    1)

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

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

  7012 Ramachandran restraints generated.
    3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7012 Ramachandran restraints generated.
    3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  384 residues out of total 3017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 348
  time to evaluate  : 1.017 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  336 GLN cc_start: 0.8840 (tt0) cc_final: 0.8509 (mt0)
REVERT: A  411 MET cc_start: 0.8771 (ttp) cc_final: 0.8555 (ttp)
REVERT: A 1069 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7710 (mm-30)
REVERT: A 1096 GLU cc_start: 0.8056 (pm20) cc_final: 0.7692 (pm20)
REVERT: A 1198 VAL cc_start: 0.8871 (OUTLIER) cc_final: 0.8538 (p)
REVERT: A 1247 MET cc_start: 0.8279 (ptm) cc_final: 0.8001 (ptm)
REVERT: B  213 THR cc_start: 0.7481 (OUTLIER) cc_final: 0.7271 (m)
REVERT: B  674 MET cc_start: 0.8219 (ttp) cc_final: 0.7970 (ttp)
  outliers start: 36
  outliers final: 14
  residues processed: 375
  average time/residue: 0.1970
  time to fit residues: 111.9866
Evaluate side-chains
  231 residues out of total 3017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 215
  time to evaluate  : 0.975 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue 1198 VAL
Chi-restraints excluded: chain A residue 1747 VAL
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain B residue  105 SER
Chi-restraints excluded: chain B residue  118 THR
Chi-restraints excluded: chain B residue  213 THR
Chi-restraints excluded: chain B residue  386 VAL
Chi-restraints excluded: chain B residue  419 GLU
Chi-restraints excluded: chain B residue  488 VAL
Chi-restraints excluded: chain B residue 1132 SER
Chi-restraints excluded: chain B residue 1140 VAL
Chi-restraints excluded: chain B residue 1193 VAL
Chi-restraints excluded: chain B residue 1357 VAL
Chi-restraints excluded: chain B residue 1617 VAL
Chi-restraints excluded: chain B residue 1999 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 351
   random chunks:
   chunk 197 optimal weight:    0.9990
   chunk 215 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9990
   chunk 132 optimal weight:    3.9990
   chunk 261 optimal weight:    2.9990
   chunk 248 optimal weight:    3.9990
   chunk 207 optimal weight:    2.9990
   chunk 155 optimal weight:    3.9990
   chunk 244 optimal weight:    4.9990
   chunk 183 optimal weight:    3.9990
   chunk 298 optimal weight:    5.9990
   overall best weight:    1.7990

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

Flipped N/Q/H residues before XYZ refinement:
A  32 GLN
** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 436 ASN
A 449 HIS
A 452 HIS
A 780 HIS
A 975 ASN
A1175 GLN
A1226 HIS
A1491 GLN
A1501 ASN
A1727 ASN
B  80 GLN
B  91 ASN
B 102 ASN
B 236 GLN
B 508 HIS
B 525 HIS
B 796 HIS
B1006 ASN
B1018 GLN
B1180 ASN
B1518 ASN
B1548 ASN
B1611 GLN
B1644 HIS
B1676 GLN
B1717 ASN
B1729 ASN
B1730 ASN
** B1933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1995 HIS
B2031 ASN
B2038 GLN
B2062 HIS

Total number of N/Q/H flips: 33

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.119804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.083467 restraints weight = 45097.050|
|-----------------------------------------------------------------------------|
r_work (start): 0.2968 rms_B_bonded: 1.74
r_work: 0.2836 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.2717 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.2717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8564
moved from start:          0.1546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  28200  Z= 0.169
  Angle     :  0.622  11.742  38199  Z= 0.330
  Chirality :  0.046   0.183   4266
  Planarity :  0.006   0.058   4927
  Dihedral  :  5.934  65.053   3799
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 10.67 %
    Favored  : 87.44 %
  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: -3.28 (0.12), residues: 3506
  helix: -2.36 (0.11), residues: 1471
  sheet: -1.78 (0.22), residues: 479
  loop : -1.95 (0.15), residues: 1556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  59 
 TYR   0.019   0.001   TYR A 347 
 PHE   0.023   0.002   PHE B1935 
 TRP   0.020   0.001   TRP A1017 
 HIS   0.015   0.001   HIS A1135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 (28199)
  covalent geometry    : angle       0.62154 (38199)
  hydrogen bonds       : bond        0.05287 ( 1055)
  hydrogen bonds       : angle       5.54970 ( 3081)
  Misc. bond           : bond        0.00028 (    1)

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

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

  7012 Ramachandran restraints generated.
    3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7012 Ramachandran restraints generated.
    3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  316 residues out of total 3017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 259
  time to evaluate  : 1.180 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.6734 (mmt) cc_final: 0.6416 (mmt)
REVERT: A  375 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8298 (tt0)
REVERT: A  419 LYS cc_start: 0.8457 (mmtt) cc_final: 0.8251 (ttpt)
REVERT: A  866 MET cc_start: 0.4203 (mmt) cc_final: 0.3367 (mmt)
REVERT: A  951 ILE cc_start: 0.9124 (mm) cc_final: 0.8851 (mt)
REVERT: A  954 ARG cc_start: 0.8319 (mtm-85) cc_final: 0.7994 (mtm-85)
REVERT: A 1247 MET cc_start: 0.8448 (ptm) cc_final: 0.8224 (ptm)
REVERT: B   14 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7784 (pp)
REVERT: B  674 MET cc_start: 0.8914 (ttp) cc_final: 0.8675 (ttp)
REVERT: B  704 ILE cc_start: 0.9356 (OUTLIER) cc_final: 0.9086 (mp)
REVERT: B 1268 GLU cc_start: 0.8650 (pp20) cc_final: 0.8251 (pp20)
REVERT: B 1423 GLN cc_start: 0.9102 (tt0) cc_final: 0.8815 (tt0)
REVERT: B 1638 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8664 (pp)
REVERT: B 1754 MET cc_start: 0.7606 (mmt) cc_final: 0.7382 (mmt)
  outliers start: 57
  outliers final: 38
  residues processed: 309
  average time/residue: 0.1924
  time to fit residues: 91.8477
Evaluate side-chains
  263 residues out of total 3017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 222
  time to evaluate  : 1.007 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue 1190 ASP
Chi-restraints excluded: chain A residue 1254 ASP
Chi-restraints excluded: chain A residue 1341 ASP
Chi-restraints excluded: chain A residue 1357 THR
Chi-restraints excluded: chain A residue 1400 LYS
Chi-restraints excluded: chain A residue 1420 HIS
Chi-restraints excluded: chain A residue 1478 SER
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   22 THR
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue  105 SER
Chi-restraints excluded: chain B residue  118 THR
Chi-restraints excluded: chain B residue  386 VAL
Chi-restraints excluded: chain B residue  397 LEU
Chi-restraints excluded: chain B residue  419 GLU
Chi-restraints excluded: chain B residue  446 LYS
Chi-restraints excluded: chain B residue  522 VAL
Chi-restraints excluded: chain B residue  601 LEU
Chi-restraints excluded: chain B residue  677 GLU
Chi-restraints excluded: chain B residue  704 ILE
Chi-restraints excluded: chain B residue  732 HIS
Chi-restraints excluded: chain B residue  756 HIS
Chi-restraints excluded: chain B residue 1095 LEU
Chi-restraints excluded: chain B residue 1127 VAL
Chi-restraints excluded: chain B residue 1140 VAL
Chi-restraints excluded: chain B residue 1193 VAL
Chi-restraints excluded: chain B residue 1357 VAL
Chi-restraints excluded: chain B residue 1400 THR
Chi-restraints excluded: chain B residue 1420 VAL
Chi-restraints excluded: chain B residue 1503 LEU
Chi-restraints excluded: chain B residue 1511 ILE
Chi-restraints excluded: chain B residue 1617 VAL
Chi-restraints excluded: chain B residue 1638 LEU
Chi-restraints excluded: chain B residue 1656 VAL
Chi-restraints excluded: chain B residue 1707 VAL
Chi-restraints excluded: chain B residue 1833 LEU
Chi-restraints excluded: chain B residue 1999 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 351
   random chunks:
   chunk 244 optimal weight:    0.9980
   chunk 54 optimal weight:    0.9990
   chunk 330 optimal weight:    4.9990
   chunk 157 optimal weight:    6.9990
   chunk 60 optimal weight:    0.6980
   chunk 78 optimal weight:    5.9990
   chunk 331 optimal weight:    0.0060
   chunk 81 optimal weight:    0.2980
   chunk 302 optimal weight:    3.9990
   chunk 178 optimal weight:    3.9990
   chunk 247 optimal weight:    0.9990
   overall best weight:    0.5998

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

Flipped N/Q/H residues before XYZ refinement:
** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1501 ASN
A1727 ASN
B  16 HIS
B 525 HIS
B 724 GLN
B1366 HIS
B1729 ASN
B1730 ASN
B1796 GLN
** B1933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.122333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 90)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.086715 restraints weight = 45401.721|
|-----------------------------------------------------------------------------|
r_work (start): 0.3010 rms_B_bonded: 1.80
r_work: 0.2904 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.2788 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.2788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8499
moved from start:          0.2045

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  28200  Z= 0.106
  Angle     :  0.533   9.325  38199  Z= 0.280
  Chirality :  0.043   0.206   4266
  Planarity :  0.004   0.050   4927
  Dihedral  :  5.254  58.906   3794
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 11.90 %
    Favored  : 85.88 %
  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: -2.17 (0.13), residues: 3506
  helix: -1.11 (0.13), residues: 1472
  sheet: -1.44 (0.22), residues: 488
  loop : -1.65 (0.15), residues: 1546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B1133 
 TYR   0.017   0.001   TYR A 347 
 PHE   0.021   0.001   PHE B1935 
 TRP   0.013   0.001   TRP A1017 
 HIS   0.014   0.001   HIS A1135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 (28199)
  covalent geometry    : angle       0.53293 (38199)
  hydrogen bonds       : bond        0.03766 ( 1055)
  hydrogen bonds       : angle       4.79331 ( 3081)
  Misc. bond           : bond        0.00023 (    1)

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

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

  7012 Ramachandran restraints generated.
    3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7012 Ramachandran restraints generated.
    3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  331 residues out of total 3017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 264
  time to evaluate  : 0.972 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  375 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8331 (tt0)
REVERT: A  524 MET cc_start: 0.8936 (mmp) cc_final: 0.8728 (mmp)
REVERT: A  746 ASP cc_start: 0.8514 (m-30) cc_final: 0.8154 (m-30)
REVERT: A  866 MET cc_start: 0.4277 (mmt) cc_final: 0.3363 (mmt)
REVERT: A  951 ILE cc_start: 0.9004 (mm) cc_final: 0.8771 (mt)
REVERT: A  954 ARG cc_start: 0.8210 (mtm-85) cc_final: 0.7933 (mtm-85)
REVERT: B   14 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7724 (pp)
REVERT: B  208 ARG cc_start: 0.7187 (tmm160) cc_final: 0.6897 (tmm-80)
REVERT: B  235 ASP cc_start: 0.7892 (p0) cc_final: 0.7688 (p0)
REVERT: B  674 MET cc_start: 0.8877 (ttp) cc_final: 0.8646 (ttp)
REVERT: B  704 ILE cc_start: 0.9332 (OUTLIER) cc_final: 0.9038 (mp)
REVERT: B 1638 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8569 (pp)
  outliers start: 67
  outliers final: 38
  residues processed: 319
  average time/residue: 0.1840
  time to fit residues: 92.0157
Evaluate side-chains
  264 residues out of total 3017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 223
  time to evaluate  : 1.008 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 VAL
Chi-restraints excluded: chain A residue   73 SER
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  398 ASP
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue 1115 GLU
Chi-restraints excluded: chain A residue 1162 VAL
Chi-restraints excluded: chain A residue 1254 ASP
Chi-restraints excluded: chain A residue 1400 LYS
Chi-restraints excluded: chain A residue 1420 HIS
Chi-restraints excluded: chain A residue 1478 SER
Chi-restraints excluded: chain A residue 1584 LEU
Chi-restraints excluded: chain A residue 1713 VAL
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   22 THR
Chi-restraints excluded: chain B residue  105 SER
Chi-restraints excluded: chain B residue  314 ILE
Chi-restraints excluded: chain B residue  386 VAL
Chi-restraints excluded: chain B residue  397 LEU
Chi-restraints excluded: chain B residue  419 GLU
Chi-restraints excluded: chain B residue  522 VAL
Chi-restraints excluded: chain B residue  601 LEU
Chi-restraints excluded: chain B residue  677 GLU
Chi-restraints excluded: chain B residue  704 ILE
Chi-restraints excluded: chain B residue  732 HIS
Chi-restraints excluded: chain B residue  756 HIS
Chi-restraints excluded: chain B residue 1095 LEU
Chi-restraints excluded: chain B residue 1127 VAL
Chi-restraints excluded: chain B residue 1140 VAL
Chi-restraints excluded: chain B residue 1193 VAL
Chi-restraints excluded: chain B residue 1194 VAL
Chi-restraints excluded: chain B residue 1287 VAL
Chi-restraints excluded: chain B residue 1357 VAL
Chi-restraints excluded: chain B residue 1400 THR
Chi-restraints excluded: chain B residue 1420 VAL
Chi-restraints excluded: chain B residue 1617 VAL
Chi-restraints excluded: chain B residue 1638 LEU
Chi-restraints excluded: chain B residue 1707 VAL
Chi-restraints excluded: chain B residue 1833 LEU
Chi-restraints excluded: chain B residue 1883 THR
Chi-restraints excluded: chain B residue 1999 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 351
   random chunks:
   chunk 266 optimal weight:    6.9990
   chunk 6 optimal weight:    6.9990
   chunk 152 optimal weight:    7.9990
   chunk 128 optimal weight:    0.8980
   chunk 64 optimal weight:    6.9990
   chunk 118 optimal weight:    0.2980
   chunk 71 optimal weight:    6.9990
   chunk 338 optimal weight:   10.0000
   chunk 269 optimal weight:    8.9990
   chunk 111 optimal weight:    0.6980
   chunk 158 optimal weight:    3.9990
   overall best weight:    2.5784

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

Flipped N/Q/H residues before XYZ refinement:
A 383 GLN
** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1050 HIS
** A1367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1501 ASN
B 104 HIS
** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 373 HIS
B 525 HIS
B 669 GLN
B 732 HIS
** B1018 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1059 GLN
B1088 HIS
B1366 HIS
B1616 ASN
B1729 ASN
B1730 ASN
B1796 GLN
** B1933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.119407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.081806 restraints weight = 45087.715|
|-----------------------------------------------------------------------------|
r_work (start): 0.2943 rms_B_bonded: 1.80
r_work: 0.2814 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.2695 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.2695
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8581
moved from start:          0.2213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060  28200  Z= 0.201
  Angle     :  0.592   8.968  38199  Z= 0.308
  Chirality :  0.047   0.188   4266
  Planarity :  0.005   0.051   4927
  Dihedral  :  5.289  58.830   3791
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.99 %
    Favored  : 94.01 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 12.63 %
    Favored  : 84.69 %
  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: -1.73 (0.14), residues: 3506
  helix: -0.66 (0.13), residues: 1463
  sheet: -1.24 (0.23), residues: 463
  loop : -1.48 (0.15), residues: 1580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B1133 
 TYR   0.017   0.002   TYR B 132 
 PHE   0.023   0.002   PHE B1935 
 TRP   0.019   0.001   TRP A1017 
 HIS   0.016   0.001   HIS A1135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00485 (28199)
  covalent geometry    : angle       0.59222 (38199)
  hydrogen bonds       : bond        0.04106 ( 1055)
  hydrogen bonds       : angle       4.68248 ( 3081)
  Misc. bond           : bond        0.00006 (    1)

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

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

  7012 Ramachandran restraints generated.
    3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7012 Ramachandran restraints generated.
    3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  318 residues out of total 3017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 81
    poor density    : 237
  time to evaluate  : 0.997 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  375 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8269 (tt0)
REVERT: A  732 ASP cc_start: 0.8684 (OUTLIER) cc_final: 0.8329 (t0)
REVERT: A  866 MET cc_start: 0.4465 (mmt) cc_final: 0.3414 (mmt)
REVERT: A  951 ILE cc_start: 0.8997 (mm) cc_final: 0.8777 (mt)
REVERT: A  954 ARG cc_start: 0.8185 (mtm-85) cc_final: 0.7886 (mtm-85)
REVERT: A 1135 HIS cc_start: 0.7860 (OUTLIER) cc_final: 0.6806 (p-80)
REVERT: A 1140 ASP cc_start: 0.8406 (p0) cc_final: 0.8113 (p0)
REVERT: A 1319 TYR cc_start: 0.8314 (OUTLIER) cc_final: 0.6845 (p90)
REVERT: B   14 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7839 (pp)
REVERT: B  704 ILE cc_start: 0.9339 (OUTLIER) cc_final: 0.9044 (mp)
REVERT: B 1268 GLU cc_start: 0.8473 (pp20) cc_final: 0.8156 (pp20)
REVERT: B 1638 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8602 (pp)
  outliers start: 81
  outliers final: 59
  residues processed: 307
  average time/residue: 0.1861
  time to fit residues: 89.1383
Evaluate side-chains
  287 residues out of total 3017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 222
  time to evaluate  : 0.881 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 VAL
Chi-restraints excluded: chain A residue   73 SER
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  681 LEU
Chi-restraints excluded: chain A residue  732 ASP
Chi-restraints excluded: chain A residue  772 LEU
Chi-restraints excluded: chain A residue 1014 VAL
Chi-restraints excluded: chain A residue 1071 VAL
Chi-restraints excluded: chain A residue 1110 GLN
Chi-restraints excluded: chain A residue 1135 HIS
Chi-restraints excluded: chain A residue 1162 VAL
Chi-restraints excluded: chain A residue 1254 ASP
Chi-restraints excluded: chain A residue 1319 TYR
Chi-restraints excluded: chain A residue 1320 ASP
Chi-restraints excluded: chain A residue 1341 ASP
Chi-restraints excluded: chain A residue 1357 THR
Chi-restraints excluded: chain A residue 1394 THR
Chi-restraints excluded: chain A residue 1398 THR
Chi-restraints excluded: chain A residue 1400 LYS
Chi-restraints excluded: chain A residue 1420 HIS
Chi-restraints excluded: chain A residue 1478 SER
Chi-restraints excluded: chain A residue 1501 ASN
Chi-restraints excluded: chain A residue 1519 THR
Chi-restraints excluded: chain A residue 1584 LEU
Chi-restraints excluded: chain A residue 1713 VAL
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   22 THR
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue  207 ILE
Chi-restraints excluded: chain B residue  386 VAL
Chi-restraints excluded: chain B residue  397 LEU
Chi-restraints excluded: chain B residue  419 GLU
Chi-restraints excluded: chain B residue  446 LYS
Chi-restraints excluded: chain B residue  522 VAL
Chi-restraints excluded: chain B residue  557 PHE
Chi-restraints excluded: chain B residue  677 GLU
Chi-restraints excluded: chain B residue  704 ILE
Chi-restraints excluded: chain B residue  756 HIS
Chi-restraints excluded: chain B residue  859 MET
Chi-restraints excluded: chain B residue  863 ILE
Chi-restraints excluded: chain B residue  973 THR
Chi-restraints excluded: chain B residue 1095 LEU
Chi-restraints excluded: chain B residue 1127 VAL
Chi-restraints excluded: chain B residue 1140 VAL
Chi-restraints excluded: chain B residue 1193 VAL
Chi-restraints excluded: chain B residue 1194 VAL
Chi-restraints excluded: chain B residue 1357 VAL
Chi-restraints excluded: chain B residue 1400 THR
Chi-restraints excluded: chain B residue 1420 VAL
Chi-restraints excluded: chain B residue 1421 ASN
Chi-restraints excluded: chain B residue 1511 ILE
Chi-restraints excluded: chain B residue 1616 ASN
Chi-restraints excluded: chain B residue 1617 VAL
Chi-restraints excluded: chain B residue 1638 LEU
Chi-restraints excluded: chain B residue 1656 VAL
Chi-restraints excluded: chain B residue 1663 THR
Chi-restraints excluded: chain B residue 1707 VAL
Chi-restraints excluded: chain B residue 1729 ASN
Chi-restraints excluded: chain B residue 1833 LEU
Chi-restraints excluded: chain B residue 1883 THR
Chi-restraints excluded: chain B residue 1884 PHE
Chi-restraints excluded: chain B residue 1940 ILE
Chi-restraints excluded: chain B residue 1999 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 351
   random chunks:
   chunk 13 optimal weight:    5.9990
   chunk 171 optimal weight:    0.8980
   chunk 288 optimal weight:   10.0000
   chunk 23 optimal weight:    0.9980
   chunk 81 optimal weight:    0.8980
   chunk 20 optimal weight:    2.9990
   chunk 161 optimal weight:    5.9990
   chunk 314 optimal weight:    2.9990
   chunk 283 optimal weight:    8.9990
   chunk 239 optimal weight:    3.9990
   chunk 90 optimal weight:    5.9990
   overall best weight:    1.7584

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

Flipped N/Q/H residues before XYZ refinement:
A 383 GLN
** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1501 ASN
B 104 HIS
** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 373 HIS
B 525 HIS
B 669 GLN
** B1018 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1616 ASN
B1729 ASN
B1730 ASN
B1796 GLN
** B1933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.119870 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.083472 restraints weight = 45006.249|
|-----------------------------------------------------------------------------|
r_work (start): 0.2968 rms_B_bonded: 1.76
r_work: 0.2827 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.2707 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.2707
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8567
moved from start:          0.2342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  28200  Z= 0.151
  Angle     :  0.552   8.589  38199  Z= 0.288
  Chirality :  0.045   0.175   4266
  Planarity :  0.004   0.046   4927
  Dihedral  :  5.155  59.807   3790
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.16 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 13.92 %
    Favored  : 83.92 %
  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: -1.44 (0.14), residues: 3506
  helix: -0.39 (0.13), residues: 1479
  sheet: -1.11 (0.24), residues: 453
  loop : -1.36 (0.16), residues: 1574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B1133 
 TYR   0.017   0.001   TYR B 132 
 PHE   0.022   0.001   PHE B1935 
 TRP   0.019   0.001   TRP A1017 
 HIS   0.015   0.001   HIS A1135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 (28199)
  covalent geometry    : angle       0.55201 (38199)
  hydrogen bonds       : bond        0.03767 ( 1055)
  hydrogen bonds       : angle       4.55448 ( 3081)
  Misc. bond           : bond        0.00008 (    1)

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

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

  7012 Ramachandran restraints generated.
    3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7012 Ramachandran restraints generated.
    3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  300 residues out of total 3017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 235
  time to evaluate  : 0.861 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  375 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8271 (tt0)
REVERT: A  732 ASP cc_start: 0.8754 (OUTLIER) cc_final: 0.8397 (t0)
REVERT: A  866 MET cc_start: 0.4503 (mmt) cc_final: 0.3436 (mmt)
REVERT: A  954 ARG cc_start: 0.8209 (mtm-85) cc_final: 0.7902 (mtm-85)
REVERT: A 1054 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8023 (pt)
REVERT: A 1135 HIS cc_start: 0.7831 (OUTLIER) cc_final: 0.6653 (p-80)
REVERT: A 1140 ASP cc_start: 0.8327 (p0) cc_final: 0.8019 (p0)
REVERT: A 1319 TYR cc_start: 0.8298 (OUTLIER) cc_final: 0.6865 (p90)
REVERT: A 1458 ARG cc_start: 0.8203 (mtm110) cc_final: 0.7996 (mtm-85)
REVERT: A 1460 GLU cc_start: 0.8081 (tt0) cc_final: 0.7780 (tt0)
REVERT: B   14 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7816 (pp)
REVERT: B  704 ILE cc_start: 0.9324 (OUTLIER) cc_final: 0.9065 (mp)
REVERT: B 1268 GLU cc_start: 0.8516 (pp20) cc_final: 0.8165 (pp20)
REVERT: B 1638 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8609 (pp)
  outliers start: 65
  outliers final: 46
  residues processed: 290
  average time/residue: 0.1819
  time to fit residues: 82.8079
Evaluate side-chains
  273 residues out of total 3017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 220
  time to evaluate  : 0.949 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 VAL
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  681 LEU
Chi-restraints excluded: chain A residue  732 ASP
Chi-restraints excluded: chain A residue 1054 LEU
Chi-restraints excluded: chain A residue 1071 VAL
Chi-restraints excluded: chain A residue 1122 VAL
Chi-restraints excluded: chain A residue 1135 HIS
Chi-restraints excluded: chain A residue 1162 VAL
Chi-restraints excluded: chain A residue 1254 ASP
Chi-restraints excluded: chain A residue 1319 TYR
Chi-restraints excluded: chain A residue 1394 THR
Chi-restraints excluded: chain A residue 1400 LYS
Chi-restraints excluded: chain A residue 1420 HIS
Chi-restraints excluded: chain A residue 1478 SER
Chi-restraints excluded: chain A residue 1501 ASN
Chi-restraints excluded: chain A residue 1584 LEU
Chi-restraints excluded: chain A residue 1611 ASP
Chi-restraints excluded: chain A residue 1713 VAL
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue  207 ILE
Chi-restraints excluded: chain B residue  386 VAL
Chi-restraints excluded: chain B residue  397 LEU
Chi-restraints excluded: chain B residue  419 GLU
Chi-restraints excluded: chain B residue  446 LYS
Chi-restraints excluded: chain B residue  522 VAL
Chi-restraints excluded: chain B residue  535 VAL
Chi-restraints excluded: chain B residue  677 GLU
Chi-restraints excluded: chain B residue  704 ILE
Chi-restraints excluded: chain B residue  756 HIS
Chi-restraints excluded: chain B residue  859 MET
Chi-restraints excluded: chain B residue  863 ILE
Chi-restraints excluded: chain B residue  973 THR
Chi-restraints excluded: chain B residue 1095 LEU
Chi-restraints excluded: chain B residue 1127 VAL
Chi-restraints excluded: chain B residue 1140 VAL
Chi-restraints excluded: chain B residue 1193 VAL
Chi-restraints excluded: chain B residue 1194 VAL
Chi-restraints excluded: chain B residue 1357 VAL
Chi-restraints excluded: chain B residue 1400 THR
Chi-restraints excluded: chain B residue 1420 VAL
Chi-restraints excluded: chain B residue 1421 ASN
Chi-restraints excluded: chain B residue 1616 ASN
Chi-restraints excluded: chain B residue 1617 VAL
Chi-restraints excluded: chain B residue 1638 LEU
Chi-restraints excluded: chain B residue 1686 GLN
Chi-restraints excluded: chain B residue 1707 VAL
Chi-restraints excluded: chain B residue 1833 LEU
Chi-restraints excluded: chain B residue 1883 THR
Chi-restraints excluded: chain B residue 1884 PHE
Chi-restraints excluded: chain B residue 1999 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 351
   random chunks:
   chunk 68 optimal weight:    0.8980
   chunk 273 optimal weight:    1.9990
   chunk 46 optimal weight:    5.9990
   chunk 258 optimal weight:    0.1980
   chunk 339 optimal weight:   20.0000
   chunk 200 optimal weight:    3.9990
   chunk 146 optimal weight:    8.9990
   chunk 18 optimal weight:    1.9990
   chunk 184 optimal weight:    3.9990
   chunk 304 optimal weight:   10.0000
   chunk 154 optimal weight:    3.9990
   overall best weight:    1.8186

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

Flipped N/Q/H residues before XYZ refinement:
A 383 GLN
** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1501 ASN
A1742 ASN
B 104 HIS
** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 373 HIS
B 525 HIS
B 669 GLN
B1616 ASN
B1729 ASN
B1730 ASN
** B1933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.120115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.2966 r_free = 0.2966 target = 0.082336 restraints weight = 45170.397|
|-----------------------------------------------------------------------------|
r_work (start): 0.2954 rms_B_bonded: 1.78
r_work: 0.2850 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.2733 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.2733
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8552
moved from start:          0.2453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  28200  Z= 0.154
  Angle     :  0.554  10.590  38199  Z= 0.288
  Chirality :  0.045   0.171   4266
  Planarity :  0.004   0.046   4927
  Dihedral  :  5.092  59.901   3790
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.65 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 13.62 %
    Favored  : 83.56 %
  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: -1.27 (0.14), residues: 3506
  helix: -0.23 (0.14), residues: 1475
  sheet: -1.04 (0.24), residues: 453
  loop : -1.27 (0.16), residues: 1578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1458 
 TYR   0.016   0.001   TYR A 827 
 PHE   0.021   0.001   PHE B1935 
 TRP   0.017   0.001   TRP A1017 
 HIS   0.015   0.001   HIS A1135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 (28199)
  covalent geometry    : angle       0.55393 (38199)
  hydrogen bonds       : bond        0.03692 ( 1055)
  hydrogen bonds       : angle       4.48897 ( 3081)
  Misc. bond           : bond        0.00007 (    1)

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

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

  7012 Ramachandran restraints generated.
    3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7012 Ramachandran restraints generated.
    3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  310 residues out of total 3017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 85
    poor density    : 225
  time to evaluate  : 1.094 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  375 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8259 (tt0)
REVERT: A  732 ASP cc_start: 0.8733 (OUTLIER) cc_final: 0.8351 (t0)
REVERT: A  866 MET cc_start: 0.4421 (mmt) cc_final: 0.3334 (mmt)
REVERT: A  933 ASN cc_start: 0.8244 (m-40) cc_final: 0.7772 (t0)
REVERT: A  954 ARG cc_start: 0.8253 (mtm-85) cc_final: 0.7922 (mtm-85)
REVERT: A 1054 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8066 (pt)
REVERT: A 1135 HIS cc_start: 0.7873 (OUTLIER) cc_final: 0.6713 (p-80)
REVERT: A 1140 ASP cc_start: 0.8277 (p0) cc_final: 0.7962 (p0)
REVERT: A 1319 TYR cc_start: 0.8276 (OUTLIER) cc_final: 0.6850 (p90)
REVERT: A 1460 GLU cc_start: 0.8020 (tt0) cc_final: 0.7722 (tt0)
REVERT: B   14 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7907 (pp)
REVERT: B  667 MET cc_start: 0.7550 (ttt) cc_final: 0.7318 (ttt)
REVERT: B  704 ILE cc_start: 0.9311 (OUTLIER) cc_final: 0.9055 (mp)
REVERT: B 1638 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8589 (pp)
  outliers start: 85
  outliers final: 61
  residues processed: 300
  average time/residue: 0.1883
  time to fit residues: 89.2819
Evaluate side-chains
  283 residues out of total 3017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 215
  time to evaluate  : 0.970 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 VAL
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  681 LEU
Chi-restraints excluded: chain A residue  732 ASP
Chi-restraints excluded: chain A residue 1020 THR
Chi-restraints excluded: chain A residue 1054 LEU
Chi-restraints excluded: chain A residue 1071 VAL
Chi-restraints excluded: chain A residue 1122 VAL
Chi-restraints excluded: chain A residue 1135 HIS
Chi-restraints excluded: chain A residue 1162 VAL
Chi-restraints excluded: chain A residue 1254 ASP
Chi-restraints excluded: chain A residue 1319 TYR
Chi-restraints excluded: chain A residue 1341 ASP
Chi-restraints excluded: chain A residue 1357 THR
Chi-restraints excluded: chain A residue 1358 THR
Chi-restraints excluded: chain A residue 1394 THR
Chi-restraints excluded: chain A residue 1400 LYS
Chi-restraints excluded: chain A residue 1420 HIS
Chi-restraints excluded: chain A residue 1478 SER
Chi-restraints excluded: chain A residue 1501 ASN
Chi-restraints excluded: chain A residue 1519 THR
Chi-restraints excluded: chain A residue 1584 LEU
Chi-restraints excluded: chain A residue 1611 ASP
Chi-restraints excluded: chain A residue 1713 VAL
Chi-restraints excluded: chain A residue 1747 VAL
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue  207 ILE
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  386 VAL
Chi-restraints excluded: chain B residue  397 LEU
Chi-restraints excluded: chain B residue  419 GLU
Chi-restraints excluded: chain B residue  446 LYS
Chi-restraints excluded: chain B residue  522 VAL
Chi-restraints excluded: chain B residue  557 PHE
Chi-restraints excluded: chain B residue  601 LEU
Chi-restraints excluded: chain B residue  677 GLU
Chi-restraints excluded: chain B residue  704 ILE
Chi-restraints excluded: chain B residue  732 HIS
Chi-restraints excluded: chain B residue  756 HIS
Chi-restraints excluded: chain B residue  859 MET
Chi-restraints excluded: chain B residue  863 ILE
Chi-restraints excluded: chain B residue  973 THR
Chi-restraints excluded: chain B residue 1095 LEU
Chi-restraints excluded: chain B residue 1127 VAL
Chi-restraints excluded: chain B residue 1140 VAL
Chi-restraints excluded: chain B residue 1193 VAL
Chi-restraints excluded: chain B residue 1194 VAL
Chi-restraints excluded: chain B residue 1357 VAL
Chi-restraints excluded: chain B residue 1385 VAL
Chi-restraints excluded: chain B residue 1400 THR
Chi-restraints excluded: chain B residue 1420 VAL
Chi-restraints excluded: chain B residue 1421 ASN
Chi-restraints excluded: chain B residue 1511 ILE
Chi-restraints excluded: chain B residue 1616 ASN
Chi-restraints excluded: chain B residue 1617 VAL
Chi-restraints excluded: chain B residue 1631 MET
Chi-restraints excluded: chain B residue 1638 LEU
Chi-restraints excluded: chain B residue 1656 VAL
Chi-restraints excluded: chain B residue 1686 GLN
Chi-restraints excluded: chain B residue 1707 VAL
Chi-restraints excluded: chain B residue 1729 ASN
Chi-restraints excluded: chain B residue 1833 LEU
Chi-restraints excluded: chain B residue 1883 THR
Chi-restraints excluded: chain B residue 1940 ILE
Chi-restraints excluded: chain B residue 1999 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 351
   random chunks:
   chunk 306 optimal weight:    0.5980
   chunk 250 optimal weight:    0.0870
   chunk 115 optimal weight:    0.9980
   chunk 285 optimal weight:    8.9990
   chunk 67 optimal weight:    0.2980
   chunk 83 optimal weight:    5.9990
   chunk 91 optimal weight:    0.9990
   chunk 167 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 72 optimal weight:    0.8980
   chunk 256 optimal weight:    6.9990
   overall best weight:    0.5758

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

Flipped N/Q/H residues before XYZ refinement:
A 383 GLN
** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1501 ASN
B 104 HIS
B 338 ASN
B 373 HIS
B 525 HIS
** B 750 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1616 ASN
B1729 ASN
B1730 ASN
B1933 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.121920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.085083 restraints weight = 44659.736|
|-----------------------------------------------------------------------------|
r_work (start): 0.2994 rms_B_bonded: 1.86
r_work: 0.2869 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.2748 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.2748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8530
moved from start:          0.2586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  28200  Z= 0.098
  Angle     :  0.524  11.989  38199  Z= 0.272
  Chirality :  0.043   0.157   4266
  Planarity :  0.004   0.087   4927
  Dihedral  :  4.901  59.890   3790
  Min Nonbonded Distance : 2.287

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 14.39 %
    Favored  : 83.16 %
  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: -1.03 (0.14), residues: 3506
  helix:  0.03 (0.14), residues: 1473
  sheet: -0.89 (0.24), residues: 450
  loop : -1.22 (0.16), residues: 1583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.022   0.000   ARG B1133 
 TYR   0.015   0.001   TYR B 132 
 PHE   0.020   0.001   PHE B1935 
 TRP   0.016   0.001   TRP A1017 
 HIS   0.013   0.001   HIS A1135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 (28199)
  covalent geometry    : angle       0.52390 (38199)
  hydrogen bonds       : bond        0.03310 ( 1055)
  hydrogen bonds       : angle       4.35689 ( 3081)
  Misc. bond           : bond        0.00026 (    1)

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

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

  7012 Ramachandran restraints generated.
    3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7012 Ramachandran restraints generated.
    3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  309 residues out of total 3017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 74
    poor density    : 235
  time to evaluate  : 1.017 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  375 GLU cc_start: 0.8697 (mm-30) cc_final: 0.8311 (tt0)
REVERT: A  682 GLN cc_start: 0.8707 (OUTLIER) cc_final: 0.8438 (pt0)
REVERT: A  732 ASP cc_start: 0.8596 (OUTLIER) cc_final: 0.8247 (t0)
REVERT: A  866 MET cc_start: 0.4395 (mmt) cc_final: 0.3316 (mmt)
REVERT: A  933 ASN cc_start: 0.8247 (m-40) cc_final: 0.7758 (t0)
REVERT: A  954 ARG cc_start: 0.8171 (mtm-85) cc_final: 0.7866 (mtm-85)
REVERT: A 1135 HIS cc_start: 0.7806 (OUTLIER) cc_final: 0.6242 (p-80)
REVERT: A 1319 TYR cc_start: 0.8221 (OUTLIER) cc_final: 0.6818 (p90)
REVERT: A 1458 ARG cc_start: 0.8234 (mtm110) cc_final: 0.7897 (mtm-85)
REVERT: A 1460 GLU cc_start: 0.8031 (tt0) cc_final: 0.7739 (tt0)
REVERT: B   14 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7926 (pp)
REVERT: B  704 ILE cc_start: 0.9298 (OUTLIER) cc_final: 0.9067 (mp)
REVERT: B 1095 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8683 (mt)
REVERT: B 1599 MET cc_start: 0.8141 (mmm) cc_final: 0.7693 (mtp)
REVERT: B 1638 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8591 (pp)
REVERT: B 1833 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8515 (mp)
  outliers start: 74
  outliers final: 45
  residues processed: 297
  average time/residue: 0.1812
  time to fit residues: 84.1082
Evaluate side-chains
  270 residues out of total 3017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 216
  time to evaluate  : 0.932 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 VAL
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  681 LEU
Chi-restraints excluded: chain A residue  682 GLN
Chi-restraints excluded: chain A residue  732 ASP
Chi-restraints excluded: chain A residue 1071 VAL
Chi-restraints excluded: chain A residue 1135 HIS
Chi-restraints excluded: chain A residue 1162 VAL
Chi-restraints excluded: chain A residue 1254 ASP
Chi-restraints excluded: chain A residue 1319 TYR
Chi-restraints excluded: chain A residue 1394 THR
Chi-restraints excluded: chain A residue 1400 LYS
Chi-restraints excluded: chain A residue 1420 HIS
Chi-restraints excluded: chain A residue 1478 SER
Chi-restraints excluded: chain A residue 1501 ASN
Chi-restraints excluded: chain A residue 1519 THR
Chi-restraints excluded: chain A residue 1584 LEU
Chi-restraints excluded: chain A residue 1611 ASP
Chi-restraints excluded: chain A residue 1713 VAL
Chi-restraints excluded: chain A residue 1747 VAL
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue  207 ILE
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  386 VAL
Chi-restraints excluded: chain B residue  419 GLU
Chi-restraints excluded: chain B residue  522 VAL
Chi-restraints excluded: chain B residue  601 LEU
Chi-restraints excluded: chain B residue  677 GLU
Chi-restraints excluded: chain B residue  704 ILE
Chi-restraints excluded: chain B residue  732 HIS
Chi-restraints excluded: chain B residue  756 HIS
Chi-restraints excluded: chain B residue  863 ILE
Chi-restraints excluded: chain B residue  973 THR
Chi-restraints excluded: chain B residue 1095 LEU
Chi-restraints excluded: chain B residue 1127 VAL
Chi-restraints excluded: chain B residue 1140 VAL
Chi-restraints excluded: chain B residue 1193 VAL
Chi-restraints excluded: chain B residue 1357 VAL
Chi-restraints excluded: chain B residue 1385 VAL
Chi-restraints excluded: chain B residue 1400 THR
Chi-restraints excluded: chain B residue 1420 VAL
Chi-restraints excluded: chain B residue 1616 ASN
Chi-restraints excluded: chain B residue 1617 VAL
Chi-restraints excluded: chain B residue 1638 LEU
Chi-restraints excluded: chain B residue 1686 GLN
Chi-restraints excluded: chain B residue 1707 VAL
Chi-restraints excluded: chain B residue 1833 LEU
Chi-restraints excluded: chain B residue 1883 THR
Chi-restraints excluded: chain B residue 1884 PHE
Chi-restraints excluded: chain B residue 1940 ILE
Chi-restraints excluded: chain B residue 1999 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 351
   random chunks:
   chunk 193 optimal weight:    0.8980
   chunk 143 optimal weight:    2.9990
   chunk 328 optimal weight:    1.9990
   chunk 29 optimal weight:    3.9990
   chunk 144 optimal weight:    9.9990
   chunk 273 optimal weight:    0.9980
   chunk 34 optimal weight:    1.9990
   chunk 43 optimal weight:    0.7980
   chunk 152 optimal weight:    0.0570
   chunk 19 optimal weight:    5.9990
   chunk 167 optimal weight:    0.0370
   overall best weight:    0.5576

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

Flipped N/Q/H residues before XYZ refinement:
A  40 ASN
A 383 GLN
** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1501 ASN
B 104 HIS
** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 373 HIS
B 669 GLN
** B 750 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1616 ASN
B1729 ASN
B1730 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.122648 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.087202 restraints weight = 45073.847|
|-----------------------------------------------------------------------------|
r_work (start): 0.3022 rms_B_bonded: 1.79
r_work: 0.2868 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2748 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.2748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8524
moved from start:          0.2692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  28200  Z= 0.097
  Angle     :  0.521  12.243  38199  Z= 0.269
  Chirality :  0.043   0.153   4266
  Planarity :  0.004   0.062   4927
  Dihedral  :  4.772  59.900   3790
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 15.01 %
    Favored  : 82.63 %
  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 (0.14), residues: 3506
  helix:  0.21 (0.14), residues: 1468
  sheet: -0.85 (0.24), residues: 458
  loop : -1.16 (0.16), residues: 1580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.000   ARG B1133 
 TYR   0.013   0.001   TYR B 132 
 PHE   0.018   0.001   PHE B1891 
 TRP   0.012   0.001   TRP A1017 
 HIS   0.012   0.001   HIS A1135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 (28199)
  covalent geometry    : angle       0.52109 (38199)
  hydrogen bonds       : bond        0.03186 ( 1055)
  hydrogen bonds       : angle       4.27620 ( 3081)
  Misc. bond           : bond        0.00031 (    1)

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

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

  7012 Ramachandran restraints generated.
    3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7012 Ramachandran restraints generated.
    3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  294 residues out of total 3017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 223
  time to evaluate  : 0.928 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  375 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8280 (tt0)
REVERT: A  477 GLN cc_start: 0.8369 (mt0) cc_final: 0.8086 (pt0)
REVERT: A  488 ILE cc_start: 0.8769 (tp) cc_final: 0.8564 (mm)
REVERT: A  732 ASP cc_start: 0.8593 (OUTLIER) cc_final: 0.8270 (t0)
REVERT: A  866 MET cc_start: 0.4386 (mmt) cc_final: 0.3300 (mmt)
REVERT: A  933 ASN cc_start: 0.8249 (m-40) cc_final: 0.7764 (t0)
REVERT: A  954 ARG cc_start: 0.8195 (mtm-85) cc_final: 0.7898 (mtm-85)
REVERT: A 1054 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8040 (pt)
REVERT: A 1135 HIS cc_start: 0.7776 (OUTLIER) cc_final: 0.5925 (p-80)
REVERT: A 1319 TYR cc_start: 0.8181 (OUTLIER) cc_final: 0.6787 (p90)
REVERT: A 1458 ARG cc_start: 0.8238 (mtm110) cc_final: 0.7844 (mtm-85)
REVERT: A 1460 GLU cc_start: 0.8061 (tt0) cc_final: 0.7757 (tt0)
REVERT: B   14 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.7945 (pp)
REVERT: B  704 ILE cc_start: 0.9297 (OUTLIER) cc_final: 0.9071 (mp)
REVERT: B 1095 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8682 (mt)
REVERT: B 1638 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8592 (pp)
REVERT: B 1833 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8506 (mp)
  outliers start: 71
  outliers final: 53
  residues processed: 283
  average time/residue: 0.1852
  time to fit residues: 82.7220
Evaluate side-chains
  282 residues out of total 3017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 220
  time to evaluate  : 0.775 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 VAL
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  681 LEU
Chi-restraints excluded: chain A residue  682 GLN
Chi-restraints excluded: chain A residue  732 ASP
Chi-restraints excluded: chain A residue 1054 LEU
Chi-restraints excluded: chain A residue 1071 VAL
Chi-restraints excluded: chain A residue 1115 GLU
Chi-restraints excluded: chain A residue 1135 HIS
Chi-restraints excluded: chain A residue 1162 VAL
Chi-restraints excluded: chain A residue 1254 ASP
Chi-restraints excluded: chain A residue 1319 TYR
Chi-restraints excluded: chain A residue 1341 ASP
Chi-restraints excluded: chain A residue 1394 THR
Chi-restraints excluded: chain A residue 1400 LYS
Chi-restraints excluded: chain A residue 1420 HIS
Chi-restraints excluded: chain A residue 1478 SER
Chi-restraints excluded: chain A residue 1501 ASN
Chi-restraints excluded: chain A residue 1519 THR
Chi-restraints excluded: chain A residue 1584 LEU
Chi-restraints excluded: chain A residue 1611 ASP
Chi-restraints excluded: chain A residue 1713 VAL
Chi-restraints excluded: chain A residue 1747 VAL
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue  207 ILE
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  386 VAL
Chi-restraints excluded: chain B residue  419 GLU
Chi-restraints excluded: chain B residue  522 VAL
Chi-restraints excluded: chain B residue  557 PHE
Chi-restraints excluded: chain B residue  601 LEU
Chi-restraints excluded: chain B residue  677 GLU
Chi-restraints excluded: chain B residue  704 ILE
Chi-restraints excluded: chain B residue  732 HIS
Chi-restraints excluded: chain B residue  750 HIS
Chi-restraints excluded: chain B residue  756 HIS
Chi-restraints excluded: chain B residue  859 MET
Chi-restraints excluded: chain B residue  863 ILE
Chi-restraints excluded: chain B residue  973 THR
Chi-restraints excluded: chain B residue 1095 LEU
Chi-restraints excluded: chain B residue 1127 VAL
Chi-restraints excluded: chain B residue 1140 VAL
Chi-restraints excluded: chain B residue 1193 VAL
Chi-restraints excluded: chain B residue 1194 VAL
Chi-restraints excluded: chain B residue 1234 GLU
Chi-restraints excluded: chain B residue 1357 VAL
Chi-restraints excluded: chain B residue 1385 VAL
Chi-restraints excluded: chain B residue 1400 THR
Chi-restraints excluded: chain B residue 1420 VAL
Chi-restraints excluded: chain B residue 1492 VAL
Chi-restraints excluded: chain B residue 1631 MET
Chi-restraints excluded: chain B residue 1638 LEU
Chi-restraints excluded: chain B residue 1686 GLN
Chi-restraints excluded: chain B residue 1707 VAL
Chi-restraints excluded: chain B residue 1729 ASN
Chi-restraints excluded: chain B residue 1833 LEU
Chi-restraints excluded: chain B residue 1883 THR
Chi-restraints excluded: chain B residue 1884 PHE
Chi-restraints excluded: chain B residue 1940 ILE
Chi-restraints excluded: chain B residue 1999 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 351
   random chunks:
   chunk 114 optimal weight:    2.9990
   chunk 7 optimal weight:    9.9990
   chunk 64 optimal weight:    2.9990
   chunk 128 optimal weight:    0.7980
   chunk 341 optimal weight:   10.0000
   chunk 309 optimal weight:    0.9980
   chunk 249 optimal weight:    7.9990
   chunk 111 optimal weight:    0.0770
   chunk 169 optimal weight:    0.6980
   chunk 109 optimal weight:    3.9990
   chunk 278 optimal weight:    4.9990
   overall best weight:    1.1140

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

Flipped N/Q/H residues before XYZ refinement:
A 383 GLN
** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1501 ASN
B 104 HIS
** B 750 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1729 ASN
B1730 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.122079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.086424 restraints weight = 44942.709|
|-----------------------------------------------------------------------------|
r_work (start): 0.3009 rms_B_bonded: 1.75
r_work: 0.2877 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.2760 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.2760
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8528
moved from start:          0.2715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  28200  Z= 0.116
  Angle     :  0.533  13.213  38199  Z= 0.275
  Chirality :  0.044   0.292   4266
  Planarity :  0.004   0.056   4927
  Dihedral  :  4.732  59.913   3789
  Min Nonbonded Distance : 2.317

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 15.21 %
    Favored  : 82.40 %
  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: -0.80 (0.14), residues: 3506
  helix:  0.26 (0.14), residues: 1474
  sheet: -0.81 (0.24), residues: 458
  loop : -1.13 (0.16), residues: 1574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.000   ARG B1133 
 TYR   0.017   0.001   TYR A 827 
 PHE   0.016   0.001   PHE A1363 
 TRP   0.012   0.001   TRP A1017 
 HIS   0.013   0.001   HIS A1135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 (28199)
  covalent geometry    : angle       0.53300 (38199)
  hydrogen bonds       : bond        0.03275 ( 1055)
  hydrogen bonds       : angle       4.26567 ( 3081)
  Misc. bond           : bond        0.00024 (    1)

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

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

  7012 Ramachandran restraints generated.
    3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7012 Ramachandran restraints generated.
    3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  296 residues out of total 3017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 224
  time to evaluate  : 0.706 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  375 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8290 (tt0)
REVERT: A  732 ASP cc_start: 0.8598 (OUTLIER) cc_final: 0.8233 (t0)
REVERT: A  866 MET cc_start: 0.4461 (mmt) cc_final: 0.3362 (mmt)
REVERT: A  933 ASN cc_start: 0.8218 (m-40) cc_final: 0.7741 (t0)
REVERT: A  954 ARG cc_start: 0.8213 (mtm-85) cc_final: 0.7923 (mtm-85)
REVERT: A 1054 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8059 (pt)
REVERT: A 1135 HIS cc_start: 0.7748 (OUTLIER) cc_final: 0.6132 (p-80)
REVERT: A 1319 TYR cc_start: 0.8201 (OUTLIER) cc_final: 0.6804 (p90)
REVERT: A 1458 ARG cc_start: 0.8206 (mtm110) cc_final: 0.7827 (mtm-85)
REVERT: A 1460 GLU cc_start: 0.8014 (tt0) cc_final: 0.7726 (tt0)
REVERT: A 1688 MET cc_start: 0.8925 (ttm) cc_final: 0.8708 (ttm)
REVERT: B   14 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.7934 (pp)
REVERT: B   98 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8512 (pp)
REVERT: B  667 MET cc_start: 0.8513 (tpp) cc_final: 0.8206 (ttt)
REVERT: B  704 ILE cc_start: 0.9304 (OUTLIER) cc_final: 0.9074 (mp)
REVERT: B 1095 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8710 (mt)
REVERT: B 1599 MET cc_start: 0.8001 (mmm) cc_final: 0.7596 (mtp)
REVERT: B 1638 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8574 (pp)
REVERT: B 1833 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8469 (mp)
  outliers start: 72
  outliers final: 56
  residues processed: 284
  average time/residue: 0.1855
  time to fit residues: 82.5579
Evaluate side-chains
  284 residues out of total 3017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 218
  time to evaluate  : 1.061 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 VAL
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  681 LEU
Chi-restraints excluded: chain A residue  682 GLN
Chi-restraints excluded: chain A residue  732 ASP
Chi-restraints excluded: chain A residue 1054 LEU
Chi-restraints excluded: chain A residue 1071 VAL
Chi-restraints excluded: chain A residue 1122 VAL
Chi-restraints excluded: chain A residue 1135 HIS
Chi-restraints excluded: chain A residue 1162 VAL
Chi-restraints excluded: chain A residue 1254 ASP
Chi-restraints excluded: chain A residue 1319 TYR
Chi-restraints excluded: chain A residue 1320 ASP
Chi-restraints excluded: chain A residue 1341 ASP
Chi-restraints excluded: chain A residue 1358 THR
Chi-restraints excluded: chain A residue 1394 THR
Chi-restraints excluded: chain A residue 1400 LYS
Chi-restraints excluded: chain A residue 1420 HIS
Chi-restraints excluded: chain A residue 1478 SER
Chi-restraints excluded: chain A residue 1501 ASN
Chi-restraints excluded: chain A residue 1519 THR
Chi-restraints excluded: chain A residue 1584 LEU
Chi-restraints excluded: chain A residue 1611 ASP
Chi-restraints excluded: chain A residue 1713 VAL
Chi-restraints excluded: chain A residue 1747 VAL
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue   98 LEU
Chi-restraints excluded: chain B residue  207 ILE
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  386 VAL
Chi-restraints excluded: chain B residue  419 GLU
Chi-restraints excluded: chain B residue  522 VAL
Chi-restraints excluded: chain B residue  557 PHE
Chi-restraints excluded: chain B residue  677 GLU
Chi-restraints excluded: chain B residue  704 ILE
Chi-restraints excluded: chain B residue  732 HIS
Chi-restraints excluded: chain B residue  750 HIS
Chi-restraints excluded: chain B residue  756 HIS
Chi-restraints excluded: chain B residue  859 MET
Chi-restraints excluded: chain B residue  863 ILE
Chi-restraints excluded: chain B residue  973 THR
Chi-restraints excluded: chain B residue 1095 LEU
Chi-restraints excluded: chain B residue 1127 VAL
Chi-restraints excluded: chain B residue 1140 VAL
Chi-restraints excluded: chain B residue 1193 VAL
Chi-restraints excluded: chain B residue 1194 VAL
Chi-restraints excluded: chain B residue 1234 GLU
Chi-restraints excluded: chain B residue 1357 VAL
Chi-restraints excluded: chain B residue 1385 VAL
Chi-restraints excluded: chain B residue 1400 THR
Chi-restraints excluded: chain B residue 1420 VAL
Chi-restraints excluded: chain B residue 1492 VAL
Chi-restraints excluded: chain B residue 1631 MET
Chi-restraints excluded: chain B residue 1638 LEU
Chi-restraints excluded: chain B residue 1656 VAL
Chi-restraints excluded: chain B residue 1686 GLN
Chi-restraints excluded: chain B residue 1707 VAL
Chi-restraints excluded: chain B residue 1730 ASN
Chi-restraints excluded: chain B residue 1833 LEU
Chi-restraints excluded: chain B residue 1883 THR
Chi-restraints excluded: chain B residue 1884 PHE
Chi-restraints excluded: chain B residue 1940 ILE
Chi-restraints excluded: chain B residue 1999 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 351
   random chunks:
   chunk 71 optimal weight:    5.9990
   chunk 312 optimal weight:    6.9990
   chunk 307 optimal weight:    1.9990
   chunk 105 optimal weight:    3.9990
   chunk 219 optimal weight:    7.9990
   chunk 223 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9990
   chunk 271 optimal weight:    2.9990
   chunk 266 optimal weight:    7.9990
   chunk 333 optimal weight:    7.9990
   chunk 185 optimal weight:    3.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
A 383 GLN
** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 104 HIS
B 373 HIS
B 669 GLN
B 724 GLN
** B 750 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1729 ASN
B1730 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.120611 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.083616 restraints weight = 45044.590|
|-----------------------------------------------------------------------------|
r_work (start): 0.2963 rms_B_bonded: 1.89
r_work: 0.2827 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.2706 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.2706
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8567
moved from start:          0.2693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  28200  Z= 0.174
  Angle     :  0.568  13.686  38199  Z= 0.294
  Chirality :  0.046   0.289   4266
  Planarity :  0.004   0.070   4927
  Dihedral  :  4.835  59.038   3789
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 15.55 %
    Favored  : 82.20 %
  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: -0.85 (0.14), residues: 3506
  helix:  0.20 (0.14), residues: 1474
  sheet: -0.84 (0.24), residues: 462
  loop : -1.13 (0.16), residues: 1570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.020   0.000   ARG B1133 
 TYR   0.017   0.001   TYR A 347 
 PHE   0.023   0.002   PHE A1363 
 TRP   0.014   0.001   TRP B 670 
 HIS   0.014   0.001   HIS A1135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00421 (28199)
  covalent geometry    : angle       0.56806 (38199)
  hydrogen bonds       : bond        0.03594 ( 1055)
  hydrogen bonds       : angle       4.33713 ( 3081)
  Misc. bond           : bond        0.00006 (    1)

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

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

  7012 Ramachandran restraints generated.
    3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7012 Ramachandran restraints generated.
    3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  289 residues out of total 3017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 221
  time to evaluate  : 0.806 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  375 GLU cc_start: 0.8713 (mm-30) cc_final: 0.8253 (tt0)
REVERT: A  379 GLU cc_start: 0.7938 (tp30) cc_final: 0.7735 (tp30)
REVERT: A  732 ASP cc_start: 0.8771 (OUTLIER) cc_final: 0.8396 (t0)
REVERT: A  866 MET cc_start: 0.4411 (mmt) cc_final: 0.3293 (mmt)
REVERT: A  933 ASN cc_start: 0.8241 (m-40) cc_final: 0.7751 (t0)
REVERT: A  954 ARG cc_start: 0.8224 (mtm-85) cc_final: 0.7927 (mtm-85)
REVERT: A 1054 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8030 (pt)
REVERT: A 1135 HIS cc_start: 0.7948 (OUTLIER) cc_final: 0.6799 (p-80)
REVERT: A 1319 TYR cc_start: 0.8273 (OUTLIER) cc_final: 0.6851 (p90)
REVERT: A 1458 ARG cc_start: 0.8266 (mtm110) cc_final: 0.7841 (mtm-85)
REVERT: A 1460 GLU cc_start: 0.8025 (tt0) cc_final: 0.7805 (tt0)
REVERT: A 1688 MET cc_start: 0.8995 (ttm) cc_final: 0.8787 (ttm)
REVERT: B   14 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8001 (pp)
REVERT: B   98 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8557 (pp)
REVERT: B  704 ILE cc_start: 0.9323 (OUTLIER) cc_final: 0.9071 (mp)
REVERT: B 1599 MET cc_start: 0.8151 (mmm) cc_final: 0.7761 (mtp)
REVERT: B 1638 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8592 (pp)
REVERT: B 1833 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8451 (mp)
  outliers start: 68
  outliers final: 53
  residues processed: 279
  average time/residue: 0.1871
  time to fit residues: 81.1699
Evaluate side-chains
  279 residues out of total 3017 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 217
  time to evaluate  : 0.976 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 VAL
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  681 LEU
Chi-restraints excluded: chain A residue  732 ASP
Chi-restraints excluded: chain A residue  869 ASN
Chi-restraints excluded: chain A residue 1054 LEU
Chi-restraints excluded: chain A residue 1071 VAL
Chi-restraints excluded: chain A residue 1122 VAL
Chi-restraints excluded: chain A residue 1135 HIS
Chi-restraints excluded: chain A residue 1162 VAL
Chi-restraints excluded: chain A residue 1254 ASP
Chi-restraints excluded: chain A residue 1319 TYR
Chi-restraints excluded: chain A residue 1341 ASP
Chi-restraints excluded: chain A residue 1358 THR
Chi-restraints excluded: chain A residue 1394 THR
Chi-restraints excluded: chain A residue 1400 LYS
Chi-restraints excluded: chain A residue 1420 HIS
Chi-restraints excluded: chain A residue 1478 SER
Chi-restraints excluded: chain A residue 1519 THR
Chi-restraints excluded: chain A residue 1584 LEU
Chi-restraints excluded: chain A residue 1611 ASP
Chi-restraints excluded: chain A residue 1713 VAL
Chi-restraints excluded: chain A residue 1747 VAL
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue   98 LEU
Chi-restraints excluded: chain B residue  207 ILE
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  386 VAL
Chi-restraints excluded: chain B residue  419 GLU
Chi-restraints excluded: chain B residue  522 VAL
Chi-restraints excluded: chain B residue  677 GLU
Chi-restraints excluded: chain B residue  704 ILE
Chi-restraints excluded: chain B residue  732 HIS
Chi-restraints excluded: chain B residue  750 HIS
Chi-restraints excluded: chain B residue  756 HIS
Chi-restraints excluded: chain B residue  859 MET
Chi-restraints excluded: chain B residue  863 ILE
Chi-restraints excluded: chain B residue  973 THR
Chi-restraints excluded: chain B residue 1095 LEU
Chi-restraints excluded: chain B residue 1127 VAL
Chi-restraints excluded: chain B residue 1140 VAL
Chi-restraints excluded: chain B residue 1193 VAL
Chi-restraints excluded: chain B residue 1194 VAL
Chi-restraints excluded: chain B residue 1234 GLU
Chi-restraints excluded: chain B residue 1357 VAL
Chi-restraints excluded: chain B residue 1385 VAL
Chi-restraints excluded: chain B residue 1400 THR
Chi-restraints excluded: chain B residue 1420 VAL
Chi-restraints excluded: chain B residue 1492 VAL
Chi-restraints excluded: chain B residue 1638 LEU
Chi-restraints excluded: chain B residue 1656 VAL
Chi-restraints excluded: chain B residue 1686 GLN
Chi-restraints excluded: chain B residue 1707 VAL
Chi-restraints excluded: chain B residue 1729 ASN
Chi-restraints excluded: chain B residue 1833 LEU
Chi-restraints excluded: chain B residue 1883 THR
Chi-restraints excluded: chain B residue 1884 PHE
Chi-restraints excluded: chain B residue 1940 ILE
Chi-restraints excluded: chain B residue 1999 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 351
   random chunks:
   chunk 246 optimal weight:    0.9980
   chunk 238 optimal weight:    2.9990
   chunk 144 optimal weight:    9.9990
   chunk 159 optimal weight:    0.8980
   chunk 172 optimal weight:    5.9990
   chunk 311 optimal weight:   10.0000
   chunk 216 optimal weight:    6.9990
   chunk 127 optimal weight:    0.9990
   chunk 268 optimal weight:    5.9990
   chunk 221 optimal weight:    2.9990
   chunk 141 optimal weight:    0.0980
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
A 383 GLN
** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 104 HIS
B 373 HIS
** B 750 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1729 ASN
B1730 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.120724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.085045 restraints weight = 44885.331|
|-----------------------------------------------------------------------------|
r_work (start): 0.2992 rms_B_bonded: 1.72
r_work: 0.2858 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.2745 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.2745
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8543
moved from start:          0.2696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.162  28200  Z= 0.188
  Angle     :  0.696  59.180  38199  Z= 0.392
  Chirality :  0.046   0.533   4266
  Planarity :  0.004   0.063   4927
  Dihedral  :  4.844  59.031   3789
  Min Nonbonded Distance : 2.162

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.42 %
    Favored  : 94.58 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 15.71 %
    Favored  : 82.00 %
  Cbeta Deviations :  0.03 %
  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: -0.84 (0.14), residues: 3506
  helix:  0.21 (0.14), residues: 1474
  sheet: -0.84 (0.24), residues: 462
  loop : -1.14 (0.16), residues: 1570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG B1133 
 TYR   0.017   0.001   TYR A 347 
 PHE   0.022   0.001   PHE A1363 
 TRP   0.013   0.001   TRP B 670 
 HIS   0.014   0.001   HIS A1135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00423 (28199)
  covalent geometry    : angle       0.69591 (38199)
  hydrogen bonds       : bond        0.03627 ( 1055)
  hydrogen bonds       : angle       4.34944 ( 3081)
  Misc. bond           : bond        0.00005 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8633.57 seconds
wall clock time: 147 minutes 53.63 seconds (8873.63 seconds total)