Starting phenix.real_space_refine
on Fri Mar  6 18:24:33 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7a1d_11606/03_2026/7a1d_11606.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7a1d_11606/03_2026/7a1d_11606.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.19
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7a1d_11606/03_2026/7a1d_11606.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7a1d_11606/03_2026/7a1d_11606.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7a1d_11606/03_2026/7a1d_11606.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7a1d_11606/03_2026/7a1d_11606.cif"
  }
  resolution = 4.19
  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=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      76      5.16       5
     C   20744      2.51       5
     N    5888      2.21       5
     O    6324      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 128 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: 33032
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 8258
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1063, 8258
          Classifications: {'peptide': 1063}
          Link IDs: {'PTRANS': 42, 'TRANS': 1020}
          Chain breaks: 3
  Restraints were copied for chains:
    B, C, D
  Time building chain proxies: 9.44, per 1000 atoms: 0.29
  Number of scatterers: 33032
  At special positions: 0
  Unit cell: (233.2, 136.74, 126.14, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      76     16.00
     O    6324      8.00
     N    5888      7.00
     C   20744      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.68
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  8440 Ramachandran restraints generated.
    4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  7896

  Finding SS restraints...
    Secondary structure from input PDB file:
      172 helices and 16 sheets defined
      60.0% alpha, 6.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.04
  Creating SS restraints...
    Processing helix  chain 'A' and resid 500 through 509
    Processing helix  chain 'A' and resid 545 through 551
      removed outlier: 3.843A  pdb=" N   LEU A 549 " --> pdb=" O   LEU A 545 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 590 through 610
      removed outlier: 3.508A  pdb=" N   TRP A 609 " --> pdb=" O   VAL A 605 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 621 through 627
      removed outlier: 3.665A  pdb=" N   ALA A 625 " --> pdb=" O   LEU A 621 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 628 through 645
      removed outlier: 3.830A  pdb=" N   LEU A 635 " --> pdb=" O   GLN A 631 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 650 through 661
      removed outlier: 3.663A  pdb=" N   ILE A 654 " --> pdb=" O   SER A 650 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   ASN A 661 " --> pdb=" O   VAL A 657 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 661 through 673
      removed outlier: 3.593A  pdb=" N   THR A 665 " --> pdb=" O   ASN A 661 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 684 through 702
      removed outlier: 4.170A  pdb=" N   ASP A 700 " --> pdb=" O   ALA A 696 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 706 through 720
    Processing helix  chain 'A' and resid 791 through 806
      removed outlier: 3.706A  pdb=" N   LEU A 797 " --> pdb=" O   ARG A 793 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 830 through 856
      removed outlier: 3.617A  pdb=" N   VAL A 856 " --> pdb=" O   GLY A 852 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 894 through 906
    Processing helix  chain 'A' and resid 929 through 943
      removed outlier: 3.912A  pdb=" N   ALA A 933 " --> pdb=" O   THR A 929 " (cutoff:3.500A)
      removed outlier: 4.088A  pdb=" N   GLU A 943 " --> pdb=" O   ARG A 939 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 961 through 972
      removed outlier: 3.686A  pdb=" N   VAL A 965 " --> pdb=" O   MET A 961 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 995 through 1008
    Processing helix  chain 'A' and resid 1012 through 1023
      removed outlier: 3.843A  pdb=" N   TYR A1016 " --> pdb=" O   SER A1012 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   GLU A1023 " --> pdb=" O   SER A1019 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1038 through 1044
      removed outlier: 3.772A  pdb=" N   ARG A1042 " --> pdb=" O   SER A1038 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1055 through 1066
      removed outlier: 5.032A  pdb=" N   LYS A1061 " --> pdb=" O   PRO A1057 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1120 through 1128
    Processing helix  chain 'A' and resid 1137 through 1164
    Processing helix  chain 'A' and resid 1167 through 1178
      removed outlier: 3.975A  pdb=" N   ARG A1171 " --> pdb=" O   THR A1167 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   LEU A1176 " --> pdb=" O   THR A1172 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1182 through 1203
      removed outlier: 3.625A  pdb=" N   VAL A1186 " --> pdb=" O   VAL A1182 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   ASN A1203 " --> pdb=" O   THR A1199 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1208 through 1220
    Processing helix  chain 'A' and resid 1224 through 1229
    Processing helix  chain 'A' and resid 1236 through 1242
    Processing helix  chain 'A' and resid 1248 through 1268
      removed outlier: 3.963A  pdb=" N   LEU A1255 " --> pdb=" O   GLU A1251 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   LEU A1268 " --> pdb=" O   LYS A1264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1275 through 1282
      removed outlier: 3.696A  pdb=" N   ALA A1279 " --> pdb=" O   GLN A1275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1287 through 1299
      removed outlier: 3.528A  pdb=" N   ARG A1291 " --> pdb=" O   PRO A1287 " (cutoff:3.500A)
      removed outlier: 4.276A  pdb=" N   GLU A1293 " --> pdb=" O   ARG A1289 " (cutoff:3.500A)
      removed outlier: 7.229A  pdb=" N   GLY A1296 " --> pdb=" O   GLU A1292 " (cutoff:3.500A)
      removed outlier: 6.094A  pdb=" N   GLU A1297 " --> pdb=" O   GLU A1293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1303 through 1319
      removed outlier: 3.848A  pdb=" N   THR A1319 " --> pdb=" O   ASP A1315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1322 through 1330
      removed outlier: 4.254A  pdb=" N   TYR A1326 " --> pdb=" O   ILE A1322 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1335 through 1351
    Processing helix  chain 'A' and resid 1351 through 1361
    Processing helix  chain 'A' and resid 1368 through 1394
      removed outlier: 3.829A  pdb=" N   THR A1372 " --> pdb=" O   PRO A1368 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   ARG A1394 " --> pdb=" O   LEU A1390 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1399 through 1412
      removed outlier: 3.976A  pdb=" N   GLU A1403 " --> pdb=" O   ALA A1399 " (cutoff:3.500A)
      removed outlier: 5.322A  pdb=" N   LYS A1410 " --> pdb=" O   ARG A1406 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   ALA A1412 " --> pdb=" O   GLY A1408 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1415 through 1420
      removed outlier: 3.705A  pdb=" N   MET A1418 " --> pdb=" O   THR A1415 " (cutoff:3.500A)
      removed outlier: 3.975A  pdb=" N   GLU A1420 " --> pdb=" O   ARG A1417 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1423 through 1439
    Processing helix  chain 'A' and resid 1443 through 1470
      removed outlier: 3.923A  pdb=" N   ALA A1447 " --> pdb=" O   PRO A1443 " (cutoff:3.500A)
      removed outlier: 4.482A  pdb=" N   ALA A1451 " --> pdb=" O   ALA A1447 " (cutoff:3.500A)
      removed outlier: 5.071A  pdb=" N   SER A1458 " --> pdb=" O   LEU A1454 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   VAL A1469 " --> pdb=" O   ILE A1465 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1472 through 1488
      removed outlier: 3.563A  pdb=" N   VAL A1476 " --> pdb=" O   GLU A1472 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1489 through 1497
    Processing helix  chain 'A' and resid 1503 through 1532
      removed outlier: 3.948A  pdb=" N   GLY A1532 " --> pdb=" O   VAL A1528 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1537 through 1548
      removed outlier: 3.868A  pdb=" N   THR A1548 " --> pdb=" O   GLU A1544 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1549 through 1566
      removed outlier: 5.072A  pdb=" N   ARG A1555 " --> pdb=" O   SER A1551 " (cutoff:3.500A)
      removed outlier: 4.172A  pdb=" N   ASP A1566 " --> pdb=" O   GLU A1562 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1570 through 1587
      removed outlier: 3.569A  pdb=" N   LEU A1574 " --> pdb=" O   ASP A1570 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   THR A1587 " --> pdb=" O   SER A1583 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 501 through 509
    Processing helix  chain 'B' and resid 545 through 551
      removed outlier: 3.843A  pdb=" N   LEU B 549 " --> pdb=" O   LEU B 545 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 590 through 610
      removed outlier: 3.509A  pdb=" N   TRP B 609 " --> pdb=" O   VAL B 605 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 621 through 627
      removed outlier: 3.664A  pdb=" N   ALA B 625 " --> pdb=" O   LEU B 621 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 628 through 645
      removed outlier: 3.832A  pdb=" N   LEU B 635 " --> pdb=" O   GLN B 631 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 650 through 661
      removed outlier: 3.664A  pdb=" N   ILE B 654 " --> pdb=" O   SER B 650 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   ASN B 661 " --> pdb=" O   VAL B 657 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 661 through 673
      removed outlier: 3.593A  pdb=" N   THR B 665 " --> pdb=" O   ASN B 661 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 684 through 702
      removed outlier: 4.171A  pdb=" N   ASP B 700 " --> pdb=" O   ALA B 696 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 706 through 720
    Processing helix  chain 'B' and resid 791 through 806
      removed outlier: 3.706A  pdb=" N   LEU B 797 " --> pdb=" O   ARG B 793 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 830 through 856
      removed outlier: 3.616A  pdb=" N   VAL B 856 " --> pdb=" O   GLY B 852 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 894 through 906
    Processing helix  chain 'B' and resid 929 through 943
      removed outlier: 3.913A  pdb=" N   ALA B 933 " --> pdb=" O   THR B 929 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   GLU B 943 " --> pdb=" O   ARG B 939 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 961 through 972
      removed outlier: 3.686A  pdb=" N   VAL B 965 " --> pdb=" O   MET B 961 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 995 through 1008
    Processing helix  chain 'B' and resid 1012 through 1023
      removed outlier: 3.843A  pdb=" N   TYR B1016 " --> pdb=" O   SER B1012 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   GLU B1023 " --> pdb=" O   SER B1019 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1038 through 1044
      removed outlier: 3.772A  pdb=" N   ARG B1042 " --> pdb=" O   SER B1038 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1055 through 1066
      removed outlier: 5.032A  pdb=" N   LYS B1061 " --> pdb=" O   PRO B1057 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1120 through 1128
    Processing helix  chain 'B' and resid 1137 through 1164
    Processing helix  chain 'B' and resid 1167 through 1178
      removed outlier: 3.976A  pdb=" N   ARG B1171 " --> pdb=" O   THR B1167 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   LEU B1176 " --> pdb=" O   THR B1172 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1182 through 1203
      removed outlier: 3.624A  pdb=" N   VAL B1186 " --> pdb=" O   VAL B1182 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   ASN B1203 " --> pdb=" O   THR B1199 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1208 through 1220
    Processing helix  chain 'B' and resid 1224 through 1229
    Processing helix  chain 'B' and resid 1236 through 1242
    Processing helix  chain 'B' and resid 1248 through 1268
      removed outlier: 3.963A  pdb=" N   LEU B1255 " --> pdb=" O   GLU B1251 " (cutoff:3.500A)
      removed outlier: 4.260A  pdb=" N   LEU B1268 " --> pdb=" O   LYS B1264 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1275 through 1282
      removed outlier: 3.696A  pdb=" N   ALA B1279 " --> pdb=" O   GLN B1275 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1287 through 1299
      removed outlier: 3.529A  pdb=" N   ARG B1291 " --> pdb=" O   PRO B1287 " (cutoff:3.500A)
      removed outlier: 4.276A  pdb=" N   GLU B1293 " --> pdb=" O   ARG B1289 " (cutoff:3.500A)
      removed outlier: 7.229A  pdb=" N   GLY B1296 " --> pdb=" O   GLU B1292 " (cutoff:3.500A)
      removed outlier: 6.093A  pdb=" N   GLU B1297 " --> pdb=" O   GLU B1293 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1303 through 1319
      removed outlier: 3.848A  pdb=" N   THR B1319 " --> pdb=" O   ASP B1315 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1322 through 1330
      removed outlier: 4.253A  pdb=" N   TYR B1326 " --> pdb=" O   ILE B1322 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1335 through 1351
    Processing helix  chain 'B' and resid 1351 through 1361
    Processing helix  chain 'B' and resid 1368 through 1394
      removed outlier: 3.830A  pdb=" N   THR B1372 " --> pdb=" O   PRO B1368 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   ARG B1394 " --> pdb=" O   LEU B1390 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1399 through 1412
      removed outlier: 3.976A  pdb=" N   GLU B1403 " --> pdb=" O   ALA B1399 " (cutoff:3.500A)
      removed outlier: 5.321A  pdb=" N   LYS B1410 " --> pdb=" O   ARG B1406 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   ALA B1412 " --> pdb=" O   GLY B1408 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1415 through 1420
      removed outlier: 3.705A  pdb=" N   MET B1418 " --> pdb=" O   THR B1415 " (cutoff:3.500A)
      removed outlier: 3.975A  pdb=" N   GLU B1420 " --> pdb=" O   ARG B1417 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1423 through 1439
    Processing helix  chain 'B' and resid 1443 through 1470
      removed outlier: 3.923A  pdb=" N   ALA B1447 " --> pdb=" O   PRO B1443 " (cutoff:3.500A)
      removed outlier: 4.482A  pdb=" N   ALA B1451 " --> pdb=" O   ALA B1447 " (cutoff:3.500A)
      removed outlier: 5.071A  pdb=" N   SER B1458 " --> pdb=" O   LEU B1454 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   VAL B1469 " --> pdb=" O   ILE B1465 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1472 through 1488
      removed outlier: 3.563A  pdb=" N   VAL B1476 " --> pdb=" O   GLU B1472 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1489 through 1497
    Processing helix  chain 'B' and resid 1503 through 1532
      removed outlier: 3.949A  pdb=" N   GLY B1532 " --> pdb=" O   VAL B1528 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1537 through 1548
      removed outlier: 3.868A  pdb=" N   THR B1548 " --> pdb=" O   GLU B1544 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1549 through 1566
      removed outlier: 5.071A  pdb=" N   ARG B1555 " --> pdb=" O   SER B1551 " (cutoff:3.500A)
      removed outlier: 4.171A  pdb=" N   ASP B1566 " --> pdb=" O   GLU B1562 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1570 through 1587
      removed outlier: 3.569A  pdb=" N   LEU B1574 " --> pdb=" O   ASP B1570 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   THR B1587 " --> pdb=" O   SER B1583 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 501 through 509
    Processing helix  chain 'C' and resid 545 through 551
      removed outlier: 3.843A  pdb=" N   LEU C 549 " --> pdb=" O   LEU C 545 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 590 through 610
      removed outlier: 3.508A  pdb=" N   TRP C 609 " --> pdb=" O   VAL C 605 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 621 through 627
      removed outlier: 3.665A  pdb=" N   ALA C 625 " --> pdb=" O   LEU C 621 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 628 through 645
      removed outlier: 3.831A  pdb=" N   LEU C 635 " --> pdb=" O   GLN C 631 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 650 through 661
      removed outlier: 3.663A  pdb=" N   ILE C 654 " --> pdb=" O   SER C 650 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   ASN C 661 " --> pdb=" O   VAL C 657 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 661 through 673
      removed outlier: 3.593A  pdb=" N   THR C 665 " --> pdb=" O   ASN C 661 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 684 through 702
      removed outlier: 4.171A  pdb=" N   ASP C 700 " --> pdb=" O   ALA C 696 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 706 through 720
    Processing helix  chain 'C' and resid 791 through 806
      removed outlier: 3.706A  pdb=" N   LEU C 797 " --> pdb=" O   ARG C 793 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 830 through 856
      removed outlier: 3.617A  pdb=" N   VAL C 856 " --> pdb=" O   GLY C 852 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 894 through 906
    Processing helix  chain 'C' and resid 929 through 943
      removed outlier: 3.913A  pdb=" N   ALA C 933 " --> pdb=" O   THR C 929 " (cutoff:3.500A)
      removed outlier: 4.088A  pdb=" N   GLU C 943 " --> pdb=" O   ARG C 939 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 961 through 972
      removed outlier: 3.687A  pdb=" N   VAL C 965 " --> pdb=" O   MET C 961 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 995 through 1008
    Processing helix  chain 'C' and resid 1012 through 1023
      removed outlier: 3.843A  pdb=" N   TYR C1016 " --> pdb=" O   SER C1012 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   GLU C1023 " --> pdb=" O   SER C1019 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1038 through 1044
      removed outlier: 3.772A  pdb=" N   ARG C1042 " --> pdb=" O   SER C1038 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1055 through 1066
      removed outlier: 5.032A  pdb=" N   LYS C1061 " --> pdb=" O   PRO C1057 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1120 through 1128
    Processing helix  chain 'C' and resid 1137 through 1164
    Processing helix  chain 'C' and resid 1167 through 1178
      removed outlier: 3.975A  pdb=" N   ARG C1171 " --> pdb=" O   THR C1167 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   LEU C1176 " --> pdb=" O   THR C1172 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1182 through 1203
      removed outlier: 3.625A  pdb=" N   VAL C1186 " --> pdb=" O   VAL C1182 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   ASN C1203 " --> pdb=" O   THR C1199 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1208 through 1220
    Processing helix  chain 'C' and resid 1224 through 1229
    Processing helix  chain 'C' and resid 1236 through 1242
    Processing helix  chain 'C' and resid 1248 through 1268
      removed outlier: 3.963A  pdb=" N   LEU C1255 " --> pdb=" O   GLU C1251 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   LEU C1268 " --> pdb=" O   LYS C1264 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1275 through 1282
      removed outlier: 3.697A  pdb=" N   ALA C1279 " --> pdb=" O   GLN C1275 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1287 through 1299
      removed outlier: 3.528A  pdb=" N   ARG C1291 " --> pdb=" O   PRO C1287 " (cutoff:3.500A)
      removed outlier: 4.276A  pdb=" N   GLU C1293 " --> pdb=" O   ARG C1289 " (cutoff:3.500A)
      removed outlier: 7.229A  pdb=" N   GLY C1296 " --> pdb=" O   GLU C1292 " (cutoff:3.500A)
      removed outlier: 6.093A  pdb=" N   GLU C1297 " --> pdb=" O   GLU C1293 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1303 through 1319
      removed outlier: 3.848A  pdb=" N   THR C1319 " --> pdb=" O   ASP C1315 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1322 through 1330
      removed outlier: 4.254A  pdb=" N   TYR C1326 " --> pdb=" O   ILE C1322 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1335 through 1351
    Processing helix  chain 'C' and resid 1351 through 1361
    Processing helix  chain 'C' and resid 1368 through 1394
      removed outlier: 3.830A  pdb=" N   THR C1372 " --> pdb=" O   PRO C1368 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   ARG C1394 " --> pdb=" O   LEU C1390 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1399 through 1412
      removed outlier: 3.977A  pdb=" N   GLU C1403 " --> pdb=" O   ALA C1399 " (cutoff:3.500A)
      removed outlier: 5.322A  pdb=" N   LYS C1410 " --> pdb=" O   ARG C1406 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   ALA C1412 " --> pdb=" O   GLY C1408 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1415 through 1420
      removed outlier: 3.705A  pdb=" N   MET C1418 " --> pdb=" O   THR C1415 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   GLU C1420 " --> pdb=" O   ARG C1417 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1423 through 1439
    Processing helix  chain 'C' and resid 1443 through 1470
      removed outlier: 3.924A  pdb=" N   ALA C1447 " --> pdb=" O   PRO C1443 " (cutoff:3.500A)
      removed outlier: 4.482A  pdb=" N   ALA C1451 " --> pdb=" O   ALA C1447 " (cutoff:3.500A)
      removed outlier: 5.070A  pdb=" N   SER C1458 " --> pdb=" O   LEU C1454 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   VAL C1469 " --> pdb=" O   ILE C1465 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1472 through 1488
      removed outlier: 3.563A  pdb=" N   VAL C1476 " --> pdb=" O   GLU C1472 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1489 through 1497
    Processing helix  chain 'C' and resid 1503 through 1532
      removed outlier: 3.948A  pdb=" N   GLY C1532 " --> pdb=" O   VAL C1528 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1537 through 1548
      removed outlier: 3.868A  pdb=" N   THR C1548 " --> pdb=" O   GLU C1544 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1549 through 1566
      removed outlier: 5.072A  pdb=" N   ARG C1555 " --> pdb=" O   SER C1551 " (cutoff:3.500A)
      removed outlier: 4.172A  pdb=" N   ASP C1566 " --> pdb=" O   GLU C1562 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1570 through 1587
      removed outlier: 3.570A  pdb=" N   LEU C1574 " --> pdb=" O   ASP C1570 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   THR C1587 " --> pdb=" O   SER C1583 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 501 through 509
    Processing helix  chain 'D' and resid 545 through 551
      removed outlier: 3.843A  pdb=" N   LEU D 549 " --> pdb=" O   LEU D 545 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 590 through 610
      removed outlier: 3.508A  pdb=" N   TRP D 609 " --> pdb=" O   VAL D 605 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 621 through 627
      removed outlier: 3.665A  pdb=" N   ALA D 625 " --> pdb=" O   LEU D 621 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 628 through 645
      removed outlier: 3.831A  pdb=" N   LEU D 635 " --> pdb=" O   GLN D 631 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 650 through 661
      removed outlier: 3.663A  pdb=" N   ILE D 654 " --> pdb=" O   SER D 650 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   ASN D 661 " --> pdb=" O   VAL D 657 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 661 through 673
      removed outlier: 3.593A  pdb=" N   THR D 665 " --> pdb=" O   ASN D 661 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 684 through 702
      removed outlier: 4.171A  pdb=" N   ASP D 700 " --> pdb=" O   ALA D 696 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 706 through 720
    Processing helix  chain 'D' and resid 791 through 806
      removed outlier: 3.707A  pdb=" N   LEU D 797 " --> pdb=" O   ARG D 793 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 830 through 856
      removed outlier: 3.617A  pdb=" N   VAL D 856 " --> pdb=" O   GLY D 852 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 894 through 906
    Processing helix  chain 'D' and resid 929 through 943
      removed outlier: 3.913A  pdb=" N   ALA D 933 " --> pdb=" O   THR D 929 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   GLU D 943 " --> pdb=" O   ARG D 939 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 961 through 972
      removed outlier: 3.686A  pdb=" N   VAL D 965 " --> pdb=" O   MET D 961 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 995 through 1008
    Processing helix  chain 'D' and resid 1012 through 1023
      removed outlier: 3.843A  pdb=" N   TYR D1016 " --> pdb=" O   SER D1012 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   GLU D1023 " --> pdb=" O   SER D1019 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1038 through 1044
      removed outlier: 3.772A  pdb=" N   ARG D1042 " --> pdb=" O   SER D1038 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1055 through 1066
      removed outlier: 5.032A  pdb=" N   LYS D1061 " --> pdb=" O   PRO D1057 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1120 through 1128
    Processing helix  chain 'D' and resid 1137 through 1164
    Processing helix  chain 'D' and resid 1167 through 1178
      removed outlier: 3.976A  pdb=" N   ARG D1171 " --> pdb=" O   THR D1167 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   LEU D1176 " --> pdb=" O   THR D1172 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1182 through 1203
      removed outlier: 3.625A  pdb=" N   VAL D1186 " --> pdb=" O   VAL D1182 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   ASN D1203 " --> pdb=" O   THR D1199 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1208 through 1220
    Processing helix  chain 'D' and resid 1224 through 1229
    Processing helix  chain 'D' and resid 1236 through 1242
    Processing helix  chain 'D' and resid 1248 through 1268
      removed outlier: 3.964A  pdb=" N   LEU D1255 " --> pdb=" O   GLU D1251 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   LEU D1268 " --> pdb=" O   LYS D1264 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1275 through 1282
      removed outlier: 3.696A  pdb=" N   ALA D1279 " --> pdb=" O   GLN D1275 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1287 through 1299
      removed outlier: 3.528A  pdb=" N   ARG D1291 " --> pdb=" O   PRO D1287 " (cutoff:3.500A)
      removed outlier: 4.277A  pdb=" N   GLU D1293 " --> pdb=" O   ARG D1289 " (cutoff:3.500A)
      removed outlier: 7.230A  pdb=" N   GLY D1296 " --> pdb=" O   GLU D1292 " (cutoff:3.500A)
      removed outlier: 6.093A  pdb=" N   GLU D1297 " --> pdb=" O   GLU D1293 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1303 through 1319
      removed outlier: 3.849A  pdb=" N   THR D1319 " --> pdb=" O   ASP D1315 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1322 through 1330
      removed outlier: 4.254A  pdb=" N   TYR D1326 " --> pdb=" O   ILE D1322 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1335 through 1351
    Processing helix  chain 'D' and resid 1351 through 1361
    Processing helix  chain 'D' and resid 1368 through 1394
      removed outlier: 3.830A  pdb=" N   THR D1372 " --> pdb=" O   PRO D1368 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   ARG D1394 " --> pdb=" O   LEU D1390 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1399 through 1412
      removed outlier: 3.976A  pdb=" N   GLU D1403 " --> pdb=" O   ALA D1399 " (cutoff:3.500A)
      removed outlier: 5.321A  pdb=" N   LYS D1410 " --> pdb=" O   ARG D1406 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   ALA D1412 " --> pdb=" O   GLY D1408 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1415 through 1420
      removed outlier: 3.705A  pdb=" N   MET D1418 " --> pdb=" O   THR D1415 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   GLU D1420 " --> pdb=" O   ARG D1417 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1423 through 1439
    Processing helix  chain 'D' and resid 1443 through 1470
      removed outlier: 3.924A  pdb=" N   ALA D1447 " --> pdb=" O   PRO D1443 " (cutoff:3.500A)
      removed outlier: 4.482A  pdb=" N   ALA D1451 " --> pdb=" O   ALA D1447 " (cutoff:3.500A)
      removed outlier: 5.071A  pdb=" N   SER D1458 " --> pdb=" O   LEU D1454 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   VAL D1469 " --> pdb=" O   ILE D1465 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1472 through 1488
      removed outlier: 3.563A  pdb=" N   VAL D1476 " --> pdb=" O   GLU D1472 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1489 through 1497
    Processing helix  chain 'D' and resid 1503 through 1532
      removed outlier: 3.948A  pdb=" N   GLY D1532 " --> pdb=" O   VAL D1528 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1537 through 1548
      removed outlier: 3.868A  pdb=" N   THR D1548 " --> pdb=" O   GLU D1544 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1549 through 1566
      removed outlier: 5.072A  pdb=" N   ARG D1555 " --> pdb=" O   SER D1551 " (cutoff:3.500A)
      removed outlier: 4.172A  pdb=" N   ASP D1566 " --> pdb=" O   GLU D1562 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1570 through 1587
      removed outlier: 3.569A  pdb=" N   LEU D1574 " --> pdb=" O   ASP D1570 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   THR D1587 " --> pdb=" O   SER D1583 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 518 through 522
      removed outlier: 6.308A  pdb=" N   LEU A 570 " --> pdb=" O   ARG A 565 " (cutoff:3.500A)
      removed outlier: 4.783A  pdb=" N   ARG A 565 " --> pdb=" O   LEU A 570 " (cutoff:3.500A)
      removed outlier: 6.779A  pdb=" N   VAL A 572 " --> pdb=" O   THR A 563 " (cutoff:3.500A)
      removed outlier: 4.743A  pdb=" N   THR A 563 " --> pdb=" O   VAL A 572 " (cutoff:3.500A)
      removed outlier: 6.670A  pdb=" N   ILE A 574 " --> pdb=" O   PRO A 561 " (cutoff:3.500A)
      removed outlier: 6.731A  pdb=" N   GLN A 576 " --> pdb=" O   GLU A 559 " (cutoff:3.500A)
      removed outlier: 4.819A  pdb=" N   GLU A 559 " --> pdb=" O   GLN A 576 " (cutoff:3.500A)
      removed outlier: 7.095A  pdb=" N   LYS A 578 " --> pdb=" O   LEU A 557 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   LEU A 557 " --> pdb=" O   LYS A 578 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 721 through 727
      removed outlier: 4.172A  pdb=" N   ARG A 723 " --> pdb=" O   LYS A 743 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   LYS A 743 " --> pdb=" O   ARG A 723 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   ASN A 725 " --> pdb=" O   ALA A 741 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   ALA A 741 " --> pdb=" O   ASN A 725 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 780 through 783
      removed outlier: 3.913A  pdb=" N   LEU A 783 " --> pdb=" O   ALA A 886 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 988 through 989
      removed outlier: 3.595A  pdb=" N   PHE A 988 " --> pdb=" O   ALA A 981 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 518 through 522
      removed outlier: 6.308A  pdb=" N   LEU B 570 " --> pdb=" O   ARG B 565 " (cutoff:3.500A)
      removed outlier: 4.782A  pdb=" N   ARG B 565 " --> pdb=" O   LEU B 570 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   VAL B 572 " --> pdb=" O   THR B 563 " (cutoff:3.500A)
      removed outlier: 4.744A  pdb=" N   THR B 563 " --> pdb=" O   VAL B 572 " (cutoff:3.500A)
      removed outlier: 6.671A  pdb=" N   ILE B 574 " --> pdb=" O   PRO B 561 " (cutoff:3.500A)
      removed outlier: 6.730A  pdb=" N   GLN B 576 " --> pdb=" O   GLU B 559 " (cutoff:3.500A)
      removed outlier: 4.818A  pdb=" N   GLU B 559 " --> pdb=" O   GLN B 576 " (cutoff:3.500A)
      removed outlier: 7.095A  pdb=" N   LYS B 578 " --> pdb=" O   LEU B 557 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   LEU B 557 " --> pdb=" O   LYS B 578 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 721 through 727
      removed outlier: 4.173A  pdb=" N   ARG B 723 " --> pdb=" O   LYS B 743 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   LYS B 743 " --> pdb=" O   ARG B 723 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   ASN B 725 " --> pdb=" O   ALA B 741 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   ALA B 741 " --> pdb=" O   ASN B 725 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 780 through 783
      removed outlier: 3.914A  pdb=" N   LEU B 783 " --> pdb=" O   ALA B 886 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 988 through 989
      removed outlier: 3.595A  pdb=" N   PHE B 988 " --> pdb=" O   ALA B 981 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 518 through 522
      removed outlier: 6.308A  pdb=" N   LEU C 570 " --> pdb=" O   ARG C 565 " (cutoff:3.500A)
      removed outlier: 4.783A  pdb=" N   ARG C 565 " --> pdb=" O   LEU C 570 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   VAL C 572 " --> pdb=" O   THR C 563 " (cutoff:3.500A)
      removed outlier: 4.743A  pdb=" N   THR C 563 " --> pdb=" O   VAL C 572 " (cutoff:3.500A)
      removed outlier: 6.671A  pdb=" N   ILE C 574 " --> pdb=" O   PRO C 561 " (cutoff:3.500A)
      removed outlier: 6.731A  pdb=" N   GLN C 576 " --> pdb=" O   GLU C 559 " (cutoff:3.500A)
      removed outlier: 4.819A  pdb=" N   GLU C 559 " --> pdb=" O   GLN C 576 " (cutoff:3.500A)
      removed outlier: 7.095A  pdb=" N   LYS C 578 " --> pdb=" O   LEU C 557 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   LEU C 557 " --> pdb=" O   LYS C 578 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 721 through 727
      removed outlier: 4.174A  pdb=" N   ARG C 723 " --> pdb=" O   LYS C 743 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   LYS C 743 " --> pdb=" O   ARG C 723 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   ASN C 725 " --> pdb=" O   ALA C 741 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   ALA C 741 " --> pdb=" O   ASN C 725 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 780 through 783
      removed outlier: 3.913A  pdb=" N   LEU C 783 " --> pdb=" O   ALA C 886 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 988 through 989
      removed outlier: 3.594A  pdb=" N   PHE C 988 " --> pdb=" O   ALA C 981 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 518 through 522
      removed outlier: 6.308A  pdb=" N   LEU D 570 " --> pdb=" O   ARG D 565 " (cutoff:3.500A)
      removed outlier: 4.783A  pdb=" N   ARG D 565 " --> pdb=" O   LEU D 570 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   VAL D 572 " --> pdb=" O   THR D 563 " (cutoff:3.500A)
      removed outlier: 4.743A  pdb=" N   THR D 563 " --> pdb=" O   VAL D 572 " (cutoff:3.500A)
      removed outlier: 6.671A  pdb=" N   ILE D 574 " --> pdb=" O   PRO D 561 " (cutoff:3.500A)
      removed outlier: 6.730A  pdb=" N   GLN D 576 " --> pdb=" O   GLU D 559 " (cutoff:3.500A)
      removed outlier: 4.818A  pdb=" N   GLU D 559 " --> pdb=" O   GLN D 576 " (cutoff:3.500A)
      removed outlier: 7.095A  pdb=" N   LYS D 578 " --> pdb=" O   LEU D 557 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   LEU D 557 " --> pdb=" O   LYS D 578 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 721 through 727
      removed outlier: 4.173A  pdb=" N   ARG D 723 " --> pdb=" O   LYS D 743 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   LYS D 743 " --> pdb=" O   ARG D 723 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   ASN D 725 " --> pdb=" O   ALA D 741 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   ALA D 741 " --> pdb=" O   ASN D 725 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 780 through 783
      removed outlier: 3.914A  pdb=" N   LEU D 783 " --> pdb=" O   ALA D 886 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 988 through 989
      removed outlier: 3.595A  pdb=" N   PHE D 988 " --> pdb=" O   ALA D 981 " (cutoff:3.500A)

    1837 hydrogen bonds defined for protein.
    5439 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 6.47

  Time building geometry restraints manager: 3.55 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 10766
        1.34 -     1.46: 5085
        1.46 -     1.57: 17637
        1.57 -     1.69: 0
        1.69 -     1.81: 136
  Bond restraints: 33624
  Sorted by residual:
  bond pdb=" C   PRO A1056 "
       pdb=" N   PRO A1057 "
    ideal  model  delta    sigma   weight residual
    1.334  1.388 -0.054 2.34e-02 1.83e+03 5.31e+00
  bond pdb=" C   PRO B1056 "
       pdb=" N   PRO B1057 "
    ideal  model  delta    sigma   weight residual
    1.334  1.387 -0.053 2.34e-02 1.83e+03 5.22e+00
  bond pdb=" C   PRO D1056 "
       pdb=" N   PRO D1057 "
    ideal  model  delta    sigma   weight residual
    1.334  1.387 -0.053 2.34e-02 1.83e+03 5.17e+00
  bond pdb=" C   PRO C1056 "
       pdb=" N   PRO C1057 "
    ideal  model  delta    sigma   weight residual
    1.334  1.387 -0.053 2.34e-02 1.83e+03 5.15e+00
  bond pdb=" CB  TRP D 629 "
       pdb=" CG  TRP D 629 "
    ideal  model  delta    sigma   weight residual
    1.498  1.444  0.054 3.10e-02 1.04e+03 3.00e+00
  ... (remaining 33619 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.09: 43259
        2.09 -     4.17: 1985
        4.17 -     6.26: 309
        6.26 -     8.35: 75
        8.35 -    10.44: 28
  Bond angle restraints: 45656
  Sorted by residual:
  angle pdb=" C   PRO D 766 "
        pdb=" N   ARG D 767 "
        pdb=" CA  ARG D 767 "
      ideal   model   delta    sigma   weight residual
     126.45  133.80   -7.35 1.77e+00 3.19e-01 1.72e+01
  angle pdb=" C   PRO B 766 "
        pdb=" N   ARG B 767 "
        pdb=" CA  ARG B 767 "
      ideal   model   delta    sigma   weight residual
     126.45  133.79   -7.34 1.77e+00 3.19e-01 1.72e+01
  angle pdb=" C   PRO C 766 "
        pdb=" N   ARG C 767 "
        pdb=" CA  ARG C 767 "
      ideal   model   delta    sigma   weight residual
     126.45  133.75   -7.30 1.77e+00 3.19e-01 1.70e+01
  angle pdb=" C   PRO A 766 "
        pdb=" N   ARG A 767 "
        pdb=" CA  ARG A 767 "
      ideal   model   delta    sigma   weight residual
     126.45  133.75   -7.30 1.77e+00 3.19e-01 1.70e+01
  angle pdb=" N   GLY A 626 "
        pdb=" CA  GLY A 626 "
        pdb=" C   GLY A 626 "
      ideal   model   delta    sigma   weight residual
     113.18  122.46   -9.28 2.37e+00 1.78e-01 1.53e+01
  ... (remaining 45651 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.78: 19026
       15.78 -    31.56: 1002
       31.56 -    47.35: 212
       47.35 -    63.13: 16
       63.13 -    78.91: 16
  Dihedral angle restraints: 20272
    sinusoidal: 8040
      harmonic: 12232
  Sorted by residual:
  dihedral pdb=" CA  ASP B 952 "
           pdb=" C   ASP B 952 "
           pdb=" N   PHE B 953 "
           pdb=" CA  PHE B 953 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.13  -29.87     0      5.00e+00 4.00e-02 3.57e+01
  dihedral pdb=" CA  ASP C 952 "
           pdb=" C   ASP C 952 "
           pdb=" N   PHE C 953 "
           pdb=" CA  PHE C 953 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.17  -29.83     0      5.00e+00 4.00e-02 3.56e+01
  dihedral pdb=" CA  ASP A 952 "
           pdb=" C   ASP A 952 "
           pdb=" N   PHE A 953 "
           pdb=" CA  PHE A 953 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -150.21  -29.79     0      5.00e+00 4.00e-02 3.55e+01
  ... (remaining 20269 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.061: 3859
       0.061 -    0.121: 1081
       0.121 -    0.182: 236
       0.182 -    0.243: 22
       0.243 -    0.304: 18
  Chirality restraints: 5216
  Sorted by residual:
  chirality pdb=" CB  VAL A 703 "
            pdb=" CA  VAL A 703 "
            pdb=" CG1 VAL A 703 "
            pdb=" CG2 VAL A 703 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.33   -0.30 2.00e-01 2.50e+01 2.30e+00
  chirality pdb=" CB  VAL D 703 "
            pdb=" CA  VAL D 703 "
            pdb=" CG1 VAL D 703 "
            pdb=" CG2 VAL D 703 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.33   -0.30 2.00e-01 2.50e+01 2.29e+00
  chirality pdb=" CB  VAL C 703 "
            pdb=" CA  VAL C 703 "
            pdb=" CG1 VAL C 703 "
            pdb=" CG2 VAL C 703 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.33   -0.30 2.00e-01 2.50e+01 2.26e+00
  ... (remaining 5213 not shown)

  Planarity restraints: 5996
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A1305 "   -0.015 2.00e-02 2.50e+03   3.07e-02 9.45e+00
        pdb=" C   ARG A1305 "    0.053 2.00e-02 2.50e+03
        pdb=" O   ARG A1305 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   GLU A1306 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B1305 "    0.015 2.00e-02 2.50e+03   3.06e-02 9.38e+00
        pdb=" C   ARG B1305 "   -0.053 2.00e-02 2.50e+03
        pdb=" O   ARG B1305 "    0.020 2.00e-02 2.50e+03
        pdb=" N   GLU B1306 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG C1305 "   -0.015 2.00e-02 2.50e+03   3.04e-02 9.21e+00
        pdb=" C   ARG C1305 "    0.052 2.00e-02 2.50e+03
        pdb=" O   ARG C1305 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   GLU C1306 "   -0.018 2.00e-02 2.50e+03
  ... (remaining 5993 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 7233
        2.78 -     3.31: 32071
        3.31 -     3.84: 54040
        3.84 -     4.37: 60176
        4.37 -     4.90: 101228
  Nonbonded interactions: 254748
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP C 855 "
            pdb=" OH  TYR C 905 "
     model   vdw
     2.253 3.040
  nonbonded pdb=" OD1 ASP B 855 "
            pdb=" OH  TYR B 905 "
     model   vdw
     2.253 3.040
  nonbonded pdb=" OD1 ASP A 855 "
            pdb=" OH  TYR A 905 "
     model   vdw
     2.253 3.040
  nonbonded pdb=" OD1 ASP D 855 "
            pdb=" OH  TYR D 905 "
     model   vdw
     2.253 3.040
  nonbonded pdb=" O   PRO D 662 "
            pdb=" OG1 THR D 665 "
     model   vdw
     2.258 3.040
  ... (remaining 254743 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: 0.06
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.580
  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:          0.430
  Check model and map are aligned:         0.130
  Set scattering table:                    0.090
  Process input model:                     31.110
  Find NCS groups from input model:        0.360
  Set up NCS constraints:                  0.040
  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:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.050
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7420
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.082  33624  Z= 0.270
  Angle     :  1.037  10.435  45656  Z= 0.569
  Chirality :  0.060   0.304   5216
  Planarity :  0.008   0.067   5996
  Dihedral  : 10.620  78.910  12376
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.36 %
    Favored  : 91.64 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  :  3.11 %
    Favored  : 96.55 %
  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: -4.40 (0.10), residues: 4220
  helix: -2.58 (0.08), residues: 2420
  sheet: -1.77 (0.26), residues: 348
  loop : -3.55 (0.13), residues: 1452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.020   0.001   ARG D1582 
 TYR   0.024   0.003   TYR D1455 
 PHE   0.037   0.004   PHE D 714 
 TRP   0.018   0.003   TRP B 934 
 HIS   0.013   0.003   HIS A 940 

Details of bonding type rmsd
  covalent geometry    : bond        0.00587 (33624)
  covalent geometry    : angle       1.03706 (45656)
  hydrogen bonds       : bond        0.11693 ( 1837)
  hydrogen bonds       : angle       6.66105 ( 5439)

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

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

  8440 Ramachandran restraints generated.
    4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  8440 Ramachandran restraints generated.
    4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  887 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 875
  time to evaluate  : 1.356 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  500 ASP cc_start: 0.6238 (m-30) cc_final: 0.5994 (t0)
REVERT: A  531 LEU cc_start: 0.8830 (tt) cc_final: 0.8272 (tp)
REVERT: A  760 GLU cc_start: 0.8097 (tt0) cc_final: 0.7873 (tt0)
REVERT: A  796 ILE cc_start: 0.8717 (pt) cc_final: 0.8461 (mt)
REVERT: A  799 LEU cc_start: 0.8245 (mt) cc_final: 0.7983 (mt)
REVERT: A  883 LEU cc_start: 0.8930 (mp) cc_final: 0.8721 (tt)
REVERT: A 1017 ASP cc_start: 0.7537 (m-30) cc_final: 0.6805 (p0)
REVERT: A 1059 LEU cc_start: 0.7372 (tt) cc_final: 0.6594 (mt)
REVERT: A 1208 LEU cc_start: 0.7532 (mt) cc_final: 0.6561 (pp)
REVERT: A 1452 THR cc_start: 0.6288 (m) cc_final: 0.5489 (m)
REVERT: A 1459 LEU cc_start: 0.8959 (tp) cc_final: 0.8724 (mt)
REVERT: A 1511 LEU cc_start: 0.8667 (tt) cc_final: 0.8375 (mm)
REVERT: A 1513 ILE cc_start: 0.9108 (mt) cc_final: 0.8873 (tp)
REVERT: A 1537 ASN cc_start: 0.8065 (t0) cc_final: 0.7593 (p0)
REVERT: A 1565 LYS cc_start: 0.8303 (mmtt) cc_final: 0.7858 (tppt)
REVERT: B  519 VAL cc_start: 0.8215 (t) cc_final: 0.6677 (t)
REVERT: B  627 LEU cc_start: 0.9159 (mt) cc_final: 0.8702 (mp)
REVERT: B  718 ILE cc_start: 0.9416 (pt) cc_final: 0.9133 (pt)
REVERT: B 1017 ASP cc_start: 0.7757 (m-30) cc_final: 0.6888 (p0)
REVERT: B 1208 LEU cc_start: 0.7811 (mt) cc_final: 0.6859 (pp)
REVERT: B 1311 MET cc_start: 0.7832 (tpt) cc_final: 0.7494 (tpt)
REVERT: B 1452 THR cc_start: 0.6653 (m) cc_final: 0.5829 (m)
REVERT: B 1455 TYR cc_start: 0.8314 (m-10) cc_final: 0.8067 (m-80)
REVERT: B 1459 LEU cc_start: 0.8974 (tp) cc_final: 0.8674 (mt)
REVERT: B 1511 LEU cc_start: 0.8732 (tt) cc_final: 0.8510 (mm)
REVERT: B 1537 ASN cc_start: 0.7925 (t0) cc_final: 0.7462 (p0)
REVERT: B 1565 LYS cc_start: 0.8214 (mmtt) cc_final: 0.7767 (tppt)
REVERT: C  500 ASP cc_start: 0.6790 (m-30) cc_final: 0.6309 (t70)
REVERT: C  531 LEU cc_start: 0.8880 (tt) cc_final: 0.8515 (tt)
REVERT: C  577 PHE cc_start: 0.7245 (p90) cc_final: 0.6501 (p90)
REVERT: C  627 LEU cc_start: 0.9076 (mt) cc_final: 0.8804 (mt)
REVERT: C  718 ILE cc_start: 0.9570 (pt) cc_final: 0.9237 (pt)
REVERT: C 1017 ASP cc_start: 0.7842 (m-30) cc_final: 0.6930 (p0)
REVERT: C 1208 LEU cc_start: 0.7797 (mt) cc_final: 0.6823 (pp)
REVERT: C 1452 THR cc_start: 0.6467 (m) cc_final: 0.5575 (m)
REVERT: C 1459 LEU cc_start: 0.8938 (tp) cc_final: 0.8680 (mt)
REVERT: C 1464 ASP cc_start: 0.7407 (t70) cc_final: 0.7150 (t0)
REVERT: C 1511 LEU cc_start: 0.8779 (tt) cc_final: 0.8546 (mm)
REVERT: C 1537 ASN cc_start: 0.8211 (t0) cc_final: 0.7577 (p0)
REVERT: C 1565 LYS cc_start: 0.8354 (mmtt) cc_final: 0.7803 (tppt)
REVERT: D  883 LEU cc_start: 0.9007 (mp) cc_final: 0.8779 (tp)
REVERT: D  999 TRP cc_start: 0.7771 (t60) cc_final: 0.7557 (t60)
REVERT: D 1017 ASP cc_start: 0.7665 (m-30) cc_final: 0.7010 (p0)
REVERT: D 1059 LEU cc_start: 0.7321 (tt) cc_final: 0.6578 (mt)
REVERT: D 1187 LEU cc_start: 0.7245 (tt) cc_final: 0.6203 (tt)
REVERT: D 1208 LEU cc_start: 0.7667 (mt) cc_final: 0.6715 (pp)
REVERT: D 1452 THR cc_start: 0.6653 (m) cc_final: 0.5794 (m)
REVERT: D 1455 TYR cc_start: 0.8315 (m-10) cc_final: 0.8064 (m-80)
REVERT: D 1459 LEU cc_start: 0.8947 (tp) cc_final: 0.8664 (mt)
REVERT: D 1511 LEU cc_start: 0.8682 (tt) cc_final: 0.8390 (mm)
REVERT: D 1537 ASN cc_start: 0.7924 (t0) cc_final: 0.7451 (p0)
REVERT: D 1565 LYS cc_start: 0.8247 (mmtt) cc_final: 0.7809 (tppt)
  outliers start: 12
  outliers final: 8
  residues processed: 883
  average time/residue: 0.2422
  time to fit residues: 323.1167
Evaluate side-chains
  453 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 445
  time to evaluate  : 1.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 424
   random chunks:
   chunk 197 optimal weight:    6.9990
   chunk 388 optimal weight:    0.9980
   chunk 215 optimal weight:    7.9990
   chunk 20 optimal weight:    2.9990
   chunk 132 optimal weight:    1.9990
   chunk 261 optimal weight:    0.9990
   chunk 248 optimal weight:    1.9990
   chunk 207 optimal weight:    8.9990
   chunk 401 optimal weight:    0.5980
   chunk 155 optimal weight:    8.9990
   chunk 244 optimal weight:    0.8980
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
A 803 GLN
A1097 GLN
** A1104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1149 HIS
** A1190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1449 HIS
B1097 GLN
** B1104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1149 HIS
** B1190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 803 GLN
C1032 GLN
C1097 GLN
** C1104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C1149 HIS
** C1190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C1449 HIS
D 803 GLN
D1097 GLN
** D1104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D1149 HIS
** D1190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.092791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.077795 restraints weight = 146575.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.079401 restraints weight = 102247.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.080479 restraints weight = 78255.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.081308 restraints weight = 64533.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.081863 restraints weight = 55761.871|
|-----------------------------------------------------------------------------|
r_work (final): 0.3622
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7514
moved from start:          0.2689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  33624  Z= 0.160
  Angle     :  0.698   9.691  45656  Z= 0.369
  Chirality :  0.045   0.184   5216
  Planarity :  0.006   0.055   5996
  Dihedral  :  6.080  26.871   4688
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 12.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  2.73 %
    Favored  : 97.15 %
  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: -2.88 (0.11), residues: 4220
  helix: -1.07 (0.09), residues: 2416
  sheet: -1.30 (0.27), residues: 344
  loop : -3.41 (0.13), residues: 1460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D1191 
 TYR   0.024   0.002   TYR D 575 
 PHE   0.017   0.001   PHE B 894 
 TRP   0.026   0.002   TRP C1356 
 HIS   0.007   0.001   HIS A1149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 (33624)
  covalent geometry    : angle       0.69804 (45656)
  hydrogen bonds       : bond        0.04550 ( 1837)
  hydrogen bonds       : angle       5.17993 ( 5439)

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

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

  8440 Ramachandran restraints generated.
    4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  8440 Ramachandran restraints generated.
    4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  630 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 626
  time to evaluate  : 1.234 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  530 LYS cc_start: 0.8376 (tmtt) cc_final: 0.8050 (tptp)
REVERT: A  531 LEU cc_start: 0.8623 (tt) cc_final: 0.8336 (tt)
REVERT: A  577 PHE cc_start: 0.7847 (p90) cc_final: 0.6333 (p90)
REVERT: A  686 ARG cc_start: 0.7260 (mpp-170) cc_final: 0.6944 (ppt170)
REVERT: A  718 ILE cc_start: 0.9543 (pt) cc_final: 0.9267 (pt)
REVERT: A 1059 LEU cc_start: 0.7381 (tt) cc_final: 0.6550 (mt)
REVERT: A 1106 ARG cc_start: 0.7206 (ptt-90) cc_final: 0.6825 (ptm160)
REVERT: A 1208 LEU cc_start: 0.7647 (mt) cc_final: 0.6559 (pp)
REVERT: A 1226 ARG cc_start: 0.7031 (mmt180) cc_final: 0.5993 (mmp80)
REVERT: A 1452 THR cc_start: 0.6000 (m) cc_final: 0.4691 (m)
REVERT: A 1511 LEU cc_start: 0.8554 (tt) cc_final: 0.8273 (mm)
REVERT: A 1565 LYS cc_start: 0.8234 (mmtt) cc_final: 0.7779 (tppt)
REVERT: A 1584 MET cc_start: 0.8035 (mtp) cc_final: 0.7817 (mtt)
REVERT: B  519 VAL cc_start: 0.8121 (t) cc_final: 0.6665 (t)
REVERT: B  627 LEU cc_start: 0.9250 (mt) cc_final: 0.9018 (mt)
REVERT: B  641 TYR cc_start: 0.9178 (t80) cc_final: 0.8480 (t80)
REVERT: B  718 ILE cc_start: 0.9430 (pt) cc_final: 0.9117 (pt)
REVERT: B  749 ILE cc_start: 0.8295 (pt) cc_final: 0.7795 (pt)
REVERT: B 1017 ASP cc_start: 0.7749 (m-30) cc_final: 0.7053 (p0)
REVERT: B 1208 LEU cc_start: 0.7978 (mt) cc_final: 0.6830 (pp)
REVERT: B 1307 ILE cc_start: 0.8993 (tp) cc_final: 0.8646 (tp)
REVERT: B 1511 LEU cc_start: 0.8701 (tt) cc_final: 0.8401 (mm)
REVERT: B 1565 LYS cc_start: 0.8185 (mmtt) cc_final: 0.7693 (tppt)
REVERT: B 1579 ARG cc_start: 0.8086 (tpt90) cc_final: 0.7703 (tpt90)
REVERT: B 1584 MET cc_start: 0.8284 (mtp) cc_final: 0.8046 (mtt)
REVERT: C  500 ASP cc_start: 0.6514 (m-30) cc_final: 0.6259 (t70)
REVERT: C  623 MET cc_start: 0.9045 (ppp) cc_final: 0.8842 (ppp)
REVERT: C  627 LEU cc_start: 0.9169 (mt) cc_final: 0.8837 (mt)
REVERT: C  641 TYR cc_start: 0.9208 (t80) cc_final: 0.8306 (t80)
REVERT: C  718 ILE cc_start: 0.9573 (pt) cc_final: 0.9203 (pt)
REVERT: C  796 ILE cc_start: 0.8600 (pt) cc_final: 0.8330 (mt)
REVERT: C  998 SER cc_start: 0.6986 (t) cc_final: 0.6592 (p)
REVERT: C 1017 ASP cc_start: 0.7814 (m-30) cc_final: 0.6842 (p0)
REVERT: C 1208 LEU cc_start: 0.7792 (mt) cc_final: 0.6696 (pp)
REVERT: C 1307 ILE cc_start: 0.9012 (tp) cc_final: 0.8641 (tp)
REVERT: C 1511 LEU cc_start: 0.8726 (tt) cc_final: 0.8411 (mm)
REVERT: C 1565 LYS cc_start: 0.8185 (mmtt) cc_final: 0.7704 (tppt)
REVERT: C 1579 ARG cc_start: 0.7973 (tpt90) cc_final: 0.7705 (tpt90)
REVERT: D  627 LEU cc_start: 0.9286 (mt) cc_final: 0.9047 (mt)
REVERT: D  641 TYR cc_start: 0.9173 (t80) cc_final: 0.8331 (t80)
REVERT: D 1059 LEU cc_start: 0.7245 (tt) cc_final: 0.6426 (mt)
REVERT: D 1145 ASP cc_start: 0.8542 (t0) cc_final: 0.8079 (t70)
REVERT: D 1208 LEU cc_start: 0.7881 (mt) cc_final: 0.6763 (pp)
REVERT: D 1307 ILE cc_start: 0.9000 (tp) cc_final: 0.8659 (tp)
REVERT: D 1511 LEU cc_start: 0.8716 (tt) cc_final: 0.8309 (mm)
REVERT: D 1565 LYS cc_start: 0.8231 (mmtt) cc_final: 0.7793 (tppt)
  outliers start: 4
  outliers final: 0
  residues processed: 630
  average time/residue: 0.2239
  time to fit residues: 220.8416
Evaluate side-chains
  380 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 380
  time to evaluate  : 1.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 424
   random chunks:
   chunk 102 optimal weight:    8.9990
   chunk 345 optimal weight:    0.9990
   chunk 324 optimal weight:    8.9990
   chunk 351 optimal weight:    3.9990
   chunk 131 optimal weight:    0.9990
   chunk 276 optimal weight:    6.9990
   chunk 224 optimal weight:    5.9990
   chunk 85 optimal weight:    5.9990
   chunk 24 optimal weight:    1.9990
   chunk 235 optimal weight:    1.9990
   chunk 166 optimal weight:    2.9990
   overall best weight:    1.7990

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

Flipped N/Q/H residues before XYZ refinement:
B1449 HIS
C1032 GLN
C1221 ASN
D1221 ASN
D1449 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.089141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.073711 restraints weight = 151304.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.075234 restraints weight = 106143.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.076294 restraints weight = 82311.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.077032 restraints weight = 68518.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.077530 restraints weight = 60092.336|
|-----------------------------------------------------------------------------|
r_work (final): 0.3527
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7679
moved from start:          0.3820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  33624  Z= 0.201
  Angle     :  0.721   8.968  45656  Z= 0.380
  Chirality :  0.045   0.193   5216
  Planarity :  0.005   0.056   5996
  Dihedral  :  5.771  25.922   4688
  Min Nonbonded Distance : 2.317

Molprobity Statistics.
  All-atom Clashscore : 13.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.71 %
    Favored  : 93.29 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  :  4.89 %
    Favored  : 95.05 %
  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: -2.20 (0.12), residues: 4220
  helix: -0.39 (0.10), residues: 2424
  sheet: -1.41 (0.28), residues: 352
  loop : -3.32 (0.14), residues: 1444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.024   0.001   ARG B1171 
 TYR   0.027   0.002   TYR D1457 
 PHE   0.016   0.002   PHE D 941 
 TRP   0.022   0.002   TRP A 934 
 HIS   0.006   0.001   HIS A1301 

Details of bonding type rmsd
  covalent geometry    : bond        0.00426 (33624)
  covalent geometry    : angle       0.72091 (45656)
  hydrogen bonds       : bond        0.04525 ( 1837)
  hydrogen bonds       : angle       5.02105 ( 5439)

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

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

  8440 Ramachandran restraints generated.
    4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  8440 Ramachandran restraints generated.
    4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  524 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 522
  time to evaluate  : 1.381 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  531 LEU cc_start: 0.8291 (tt) cc_final: 0.7956 (mm)
REVERT: A  799 LEU cc_start: 0.8392 (mt) cc_final: 0.8114 (mt)
REVERT: A  883 LEU cc_start: 0.9076 (mp) cc_final: 0.8726 (tt)
REVERT: A 1059 LEU cc_start: 0.7421 (tt) cc_final: 0.6549 (mt)
REVERT: A 1208 LEU cc_start: 0.8259 (mt) cc_final: 0.7477 (mp)
REVERT: A 1226 ARG cc_start: 0.7411 (mmt180) cc_final: 0.6071 (mmp80)
REVERT: A 1452 THR cc_start: 0.5946 (m) cc_final: 0.5260 (m)
REVERT: A 1511 LEU cc_start: 0.8621 (tt) cc_final: 0.8238 (tp)
REVERT: A 1565 LYS cc_start: 0.8195 (mmtt) cc_final: 0.7646 (ttmm)
REVERT: A 1584 MET cc_start: 0.8261 (mtp) cc_final: 0.8040 (mtt)
REVERT: B  641 TYR cc_start: 0.8751 (t80) cc_final: 0.8422 (t80)
REVERT: B  771 VAL cc_start: 0.9514 (t) cc_final: 0.9236 (m)
REVERT: B 1017 ASP cc_start: 0.7806 (m-30) cc_final: 0.7125 (p0)
REVERT: B 1208 LEU cc_start: 0.8410 (mt) cc_final: 0.8126 (mp)
REVERT: B 1511 LEU cc_start: 0.8699 (tt) cc_final: 0.8359 (mm)
REVERT: B 1565 LYS cc_start: 0.8267 (mmtt) cc_final: 0.7788 (tppt)
REVERT: B 1579 ARG cc_start: 0.8207 (tpt90) cc_final: 0.7967 (tpt90)
REVERT: B 1584 MET cc_start: 0.8316 (mtp) cc_final: 0.8081 (mtt)
REVERT: C  500 ASP cc_start: 0.6782 (m-30) cc_final: 0.6488 (t70)
REVERT: C  627 LEU cc_start: 0.9187 (mt) cc_final: 0.8942 (mt)
REVERT: C  998 SER cc_start: 0.7119 (t) cc_final: 0.6788 (p)
REVERT: C 1145 ASP cc_start: 0.7940 (t0) cc_final: 0.7715 (t70)
REVERT: C 1208 LEU cc_start: 0.8277 (mt) cc_final: 0.7631 (mp)
REVERT: C 1226 ARG cc_start: 0.7475 (mmt180) cc_final: 0.6097 (mmp80)
REVERT: C 1511 LEU cc_start: 0.8650 (tt) cc_final: 0.8356 (mm)
REVERT: C 1565 LYS cc_start: 0.8330 (mmtt) cc_final: 0.7793 (tppt)
REVERT: C 1579 ARG cc_start: 0.8236 (tpt90) cc_final: 0.7969 (tpt90)
REVERT: D  799 LEU cc_start: 0.8457 (mt) cc_final: 0.8186 (mt)
REVERT: D 1190 ASN cc_start: 0.8262 (m-40) cc_final: 0.6556 (m-40)
REVERT: D 1208 LEU cc_start: 0.8340 (mt) cc_final: 0.7564 (mp)
REVERT: D 1226 ARG cc_start: 0.7535 (mmt180) cc_final: 0.6061 (mmp80)
REVERT: D 1508 LEU cc_start: 0.8997 (mp) cc_final: 0.8783 (mm)
REVERT: D 1511 LEU cc_start: 0.8609 (tt) cc_final: 0.8238 (mm)
REVERT: D 1565 LYS cc_start: 0.8294 (mmtt) cc_final: 0.7758 (ttmm)
REVERT: D 1579 ARG cc_start: 0.8293 (tpt90) cc_final: 0.8003 (tpt90)
  outliers start: 2
  outliers final: 0
  residues processed: 524
  average time/residue: 0.2174
  time to fit residues: 181.8669
Evaluate side-chains
  339 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 339
  time to evaluate  : 1.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 424
   random chunks:
   chunk 157 optimal weight:    0.2980
   chunk 405 optimal weight:    0.9990
   chunk 360 optimal weight:    3.9990
   chunk 332 optimal weight:    0.7980
   chunk 237 optimal weight:    2.9990
   chunk 252 optimal weight:    6.9990
   chunk 344 optimal weight:    1.9990
   chunk 118 optimal weight:    1.9990
   chunk 5 optimal weight:    4.9990
   chunk 215 optimal weight:    8.9990
   chunk 407 optimal weight:    0.7980
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
A 975 HIS
A1097 GLN
A1486 HIS
B 975 HIS
B1097 GLN
B1486 HIS
C 975 HIS
C1032 GLN
C1193 GLN
D 975 HIS
D1097 GLN
D1486 HIS

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.090198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.075012 restraints weight = 149512.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.076464 restraints weight = 106152.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.077534 restraints weight = 82887.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.078257 restraints weight = 69396.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.078691 restraints weight = 61013.732|
|-----------------------------------------------------------------------------|
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7645
moved from start:          0.4171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  33624  Z= 0.151
  Angle     :  0.675   8.949  45656  Z= 0.351
  Chirality :  0.045   0.219   5216
  Planarity :  0.005   0.067   5996
  Dihedral  :  5.485  24.750   4688
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 13.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.71 %
    Favored  : 94.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  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: -1.82 (0.12), residues: 4220
  helix: -0.03 (0.10), residues: 2408
  sheet: -1.13 (0.27), residues: 392
  loop : -3.31 (0.14), residues: 1420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG D 784 
 TYR   0.030   0.002   TYR D1457 
 PHE   0.014   0.002   PHE A 577 
 TRP   0.017   0.001   TRP A 934 
 HIS   0.004   0.001   HIS C1506 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 (33624)
  covalent geometry    : angle       0.67536 (45656)
  hydrogen bonds       : bond        0.04148 ( 1837)
  hydrogen bonds       : angle       4.87228 ( 5439)

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

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

  8440 Ramachandran restraints generated.
    4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  8440 Ramachandran restraints generated.
    4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  537 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 537
  time to evaluate  : 1.236 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  531 LEU cc_start: 0.8411 (tt) cc_final: 0.7916 (mm)
REVERT: A  883 LEU cc_start: 0.8946 (mp) cc_final: 0.8590 (tt)
REVERT: A 1059 LEU cc_start: 0.7358 (tt) cc_final: 0.6407 (mt)
REVERT: A 1208 LEU cc_start: 0.8317 (mt) cc_final: 0.8067 (mp)
REVERT: A 1226 ARG cc_start: 0.7372 (mmt180) cc_final: 0.6053 (mmp80)
REVERT: A 1511 LEU cc_start: 0.8643 (tt) cc_final: 0.8299 (mm)
REVERT: A 1584 MET cc_start: 0.8189 (mtp) cc_final: 0.7963 (mtt)
REVERT: B  548 MET cc_start: 0.8884 (mpp) cc_final: 0.8636 (mpp)
REVERT: B  550 GLN cc_start: 0.8385 (tp40) cc_final: 0.8170 (tp-100)
REVERT: B  718 ILE cc_start: 0.9570 (pt) cc_final: 0.9290 (pt)
REVERT: B  771 VAL cc_start: 0.9528 (t) cc_final: 0.9282 (m)
REVERT: B  998 SER cc_start: 0.6945 (t) cc_final: 0.6628 (p)
REVERT: B 1017 ASP cc_start: 0.7755 (m-30) cc_final: 0.7117 (p0)
REVERT: B 1145 ASP cc_start: 0.7866 (t70) cc_final: 0.7541 (t70)
REVERT: B 1208 LEU cc_start: 0.8504 (mt) cc_final: 0.8233 (mp)
REVERT: B 1324 TYR cc_start: 0.6756 (t80) cc_final: 0.5798 (t80)
REVERT: B 1511 LEU cc_start: 0.8633 (tt) cc_final: 0.8296 (mm)
REVERT: B 1565 LYS cc_start: 0.8129 (mmtt) cc_final: 0.7627 (tppt)
REVERT: B 1579 ARG cc_start: 0.8270 (tpt90) cc_final: 0.7915 (tpt90)
REVERT: B 1584 MET cc_start: 0.8242 (mtp) cc_final: 0.8038 (mtt)
REVERT: C  718 ILE cc_start: 0.9589 (pt) cc_final: 0.9343 (pt)
REVERT: C 1145 ASP cc_start: 0.8059 (t0) cc_final: 0.7726 (t70)
REVERT: C 1208 LEU cc_start: 0.8353 (mt) cc_final: 0.8076 (mp)
REVERT: C 1226 ARG cc_start: 0.7449 (mmt180) cc_final: 0.6070 (mmp80)
REVERT: C 1327 ARG cc_start: 0.7959 (mtm180) cc_final: 0.7605 (mpp80)
REVERT: C 1511 LEU cc_start: 0.8615 (tt) cc_final: 0.8298 (mm)
REVERT: C 1565 LYS cc_start: 0.8176 (mmtt) cc_final: 0.7659 (tppt)
REVERT: C 1579 ARG cc_start: 0.8314 (tpt90) cc_final: 0.7939 (tpt90)
REVERT: D  771 VAL cc_start: 0.9477 (t) cc_final: 0.9200 (m)
REVERT: D 1059 LEU cc_start: 0.7214 (tt) cc_final: 0.6271 (mt)
REVERT: D 1145 ASP cc_start: 0.7832 (t70) cc_final: 0.7493 (t70)
REVERT: D 1208 LEU cc_start: 0.8469 (mt) cc_final: 0.8167 (mp)
REVERT: D 1214 MET cc_start: 0.8315 (mmt) cc_final: 0.7958 (mmp)
REVERT: D 1226 ARG cc_start: 0.7396 (mmt180) cc_final: 0.5938 (mmp80)
REVERT: D 1330 GLU cc_start: 0.7890 (mp0) cc_final: 0.7571 (mp0)
REVERT: D 1508 LEU cc_start: 0.8996 (mp) cc_final: 0.8757 (mm)
REVERT: D 1511 LEU cc_start: 0.8634 (tt) cc_final: 0.8265 (mm)
REVERT: D 1579 ARG cc_start: 0.8393 (tpt90) cc_final: 0.7941 (tpt90)
  outliers start: 0
  outliers final: 0
  residues processed: 537
  average time/residue: 0.2139
  time to fit residues: 182.8287
Evaluate side-chains
  354 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 354
  time to evaluate  : 1.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 424
   random chunks:
   chunk 344 optimal weight:    1.9990
   chunk 373 optimal weight:    7.9990
   chunk 66 optimal weight:    4.9990
   chunk 128 optimal weight:    4.9990
   chunk 18 optimal weight:    1.9990
   chunk 62 optimal weight:    3.9990
   chunk 260 optimal weight:    8.9990
   chunk 321 optimal weight:   10.0000
   chunk 413 optimal weight:    3.9990
   chunk 283 optimal weight:    4.9990
   chunk 325 optimal weight:    0.9980
   overall best weight:    2.5988

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

Flipped N/Q/H residues before XYZ refinement:
A 653 HIS
A 940 HIS
** B 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 653 HIS
B 940 HIS
B 992 ASN
C 576 GLN
C 940 HIS
C1032 GLN
C1486 HIS
** D 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 940 HIS

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.085539 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.069824 restraints weight = 152810.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.071464 restraints weight = 102522.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.072586 restraints weight = 77579.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.073343 restraints weight = 63712.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.073865 restraints weight = 55565.567|
|-----------------------------------------------------------------------------|
r_work (final): 0.3439
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7784
moved from start:          0.5016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.066  33624  Z= 0.248
  Angle     :  0.778   8.632  45656  Z= 0.408
  Chirality :  0.048   0.272   5216
  Planarity :  0.006   0.100   5996
  Dihedral  :  5.766  25.378   4688
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 18.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.01 %
    Favored  : 91.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  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: -2.00 (0.12), residues: 4220
  helix: -0.20 (0.10), residues: 2404
  sheet: -1.17 (0.27), residues: 400
  loop : -3.34 (0.14), residues: 1416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG C 977 
 TYR   0.025   0.003   TYR A1455 
 PHE   0.023   0.003   PHE B 849 
 TRP   0.020   0.002   TRP B1013 
 HIS   0.007   0.002   HIS B1301 

Details of bonding type rmsd
  covalent geometry    : bond        0.00547 (33624)
  covalent geometry    : angle       0.77813 (45656)
  hydrogen bonds       : bond        0.04799 ( 1837)
  hydrogen bonds       : angle       5.10497 ( 5439)

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

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

  8440 Ramachandran restraints generated.
    4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  8440 Ramachandran restraints generated.
    4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  453 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 453
  time to evaluate  : 1.056 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1226 ARG cc_start: 0.7747 (mmt180) cc_final: 0.6497 (mmp80)
REVERT: A 1304 ARG cc_start: 0.7595 (mpt180) cc_final: 0.7349 (mmt180)
REVERT: A 1307 ILE cc_start: 0.9299 (tp) cc_final: 0.8974 (tp)
REVERT: A 1511 LEU cc_start: 0.8571 (tt) cc_final: 0.8265 (mm)
REVERT: B  550 GLN cc_start: 0.8444 (tp40) cc_final: 0.8208 (tp-100)
REVERT: B  769 GLU cc_start: 0.7941 (pm20) cc_final: 0.7697 (pm20)
REVERT: B  771 VAL cc_start: 0.9539 (t) cc_final: 0.9263 (m)
REVERT: B 1017 ASP cc_start: 0.7899 (m-30) cc_final: 0.7216 (p0)
REVERT: B 1226 ARG cc_start: 0.7605 (mmt180) cc_final: 0.6974 (mmm-85)
REVERT: B 1256 MET cc_start: 0.9403 (tmm) cc_final: 0.9186 (tmm)
REVERT: B 1324 TYR cc_start: 0.6751 (t80) cc_final: 0.5763 (t80)
REVERT: B 1508 LEU cc_start: 0.8965 (mp) cc_final: 0.8531 (tp)
REVERT: B 1511 LEU cc_start: 0.8695 (tt) cc_final: 0.8396 (mm)
REVERT: B 1579 ARG cc_start: 0.8462 (tpt90) cc_final: 0.8089 (tpt90)
REVERT: C 1145 ASP cc_start: 0.7925 (t0) cc_final: 0.7718 (t70)
REVERT: C 1226 ARG cc_start: 0.7738 (mmt180) cc_final: 0.7180 (mmm-85)
REVERT: C 1256 MET cc_start: 0.9421 (tmm) cc_final: 0.9197 (tmm)
REVERT: C 1327 ARG cc_start: 0.8237 (mtm180) cc_final: 0.7832 (mpp80)
REVERT: C 1508 LEU cc_start: 0.8963 (mp) cc_final: 0.8528 (tp)
REVERT: C 1511 LEU cc_start: 0.8648 (tt) cc_final: 0.8432 (mm)
REVERT: C 1579 ARG cc_start: 0.8516 (tpt90) cc_final: 0.8092 (tpt90)
REVERT: D  771 VAL cc_start: 0.9531 (t) cc_final: 0.9232 (m)
REVERT: D 1226 ARG cc_start: 0.7674 (mmt180) cc_final: 0.7048 (mmm-85)
REVERT: D 1256 MET cc_start: 0.9388 (tmm) cc_final: 0.9177 (tmm)
REVERT: D 1508 LEU cc_start: 0.8991 (mp) cc_final: 0.8577 (tp)
REVERT: D 1511 LEU cc_start: 0.8650 (tt) cc_final: 0.8322 (mm)
REVERT: D 1579 ARG cc_start: 0.8492 (tpt90) cc_final: 0.7989 (tpt90)
  outliers start: 0
  outliers final: 0
  residues processed: 453
  average time/residue: 0.2128
  time to fit residues: 153.5982
Evaluate side-chains
  309 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 309
  time to evaluate  : 1.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 424
   random chunks:
   chunk 359 optimal weight:    5.9990
   chunk 333 optimal weight:    3.9990
   chunk 255 optimal weight:    7.9990
   chunk 163 optimal weight:    8.9990
   chunk 352 optimal weight:    2.9990
   chunk 13 optimal weight:    0.6980
   chunk 393 optimal weight:    0.3980
   chunk 139 optimal weight:    0.8980
   chunk 353 optimal weight:    6.9990
   chunk 313 optimal weight:    5.9990
   chunk 231 optimal weight:    5.9990
   overall best weight:    1.7984

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

Flipped N/Q/H residues before XYZ refinement:
A 738 ASN
A1193 GLN
** B 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 738 ASN
B1032 GLN
B1193 GLN
C1032 GLN
D 550 GLN
** D 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 738 ASN
D1193 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.086480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.070774 restraints weight = 148005.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.072425 restraints weight = 99152.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.073561 restraints weight = 74646.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.074344 restraints weight = 60883.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.074886 restraints weight = 52659.324|
|-----------------------------------------------------------------------------|
r_work (final): 0.3469
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7745
moved from start:          0.5336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  33624  Z= 0.183
  Angle     :  0.710   9.319  45656  Z= 0.370
  Chirality :  0.046   0.245   5216
  Planarity :  0.005   0.041   5996
  Dihedral  :  5.586  24.641   4688
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 16.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.35 %
    Favored  : 93.65 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  2.30 %
    Favored  : 97.58 %
  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: -1.82 (0.12), residues: 4220
  helix: -0.01 (0.10), residues: 2400
  sheet: -0.91 (0.27), residues: 396
  loop : -3.41 (0.14), residues: 1424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D 784 
 TYR   0.030   0.002   TYR A 638 
 PHE   0.016   0.002   PHE C 577 
 TRP   0.025   0.001   TRP A 533 
 HIS   0.005   0.001   HIS A1301 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 (33624)
  covalent geometry    : angle       0.71046 (45656)
  hydrogen bonds       : bond        0.04435 ( 1837)
  hydrogen bonds       : angle       4.99515 ( 5439)

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

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

  8440 Ramachandran restraints generated.
    4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  8440 Ramachandran restraints generated.
    4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  456 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 452
  time to evaluate  : 1.157 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  531 LEU cc_start: 0.8580 (tt) cc_final: 0.8110 (mm)
REVERT: A  738 ASN cc_start: 0.5896 (OUTLIER) cc_final: 0.5592 (p0)
REVERT: A  944 MET cc_start: 0.6416 (mpp) cc_final: 0.6210 (mpp)
REVERT: A 1226 ARG cc_start: 0.7774 (mmt180) cc_final: 0.6558 (mmp80)
REVERT: A 1511 LEU cc_start: 0.8627 (tt) cc_final: 0.8298 (mm)
REVERT: B  550 GLN cc_start: 0.8304 (tp40) cc_final: 0.8091 (tp-100)
REVERT: B  576 GLN cc_start: 0.7695 (tm-30) cc_final: 0.7355 (tm-30)
REVERT: B  738 ASN cc_start: 0.5838 (OUTLIER) cc_final: 0.5442 (p0)
REVERT: B  769 GLU cc_start: 0.8111 (pm20) cc_final: 0.7884 (pm20)
REVERT: B  771 VAL cc_start: 0.9534 (t) cc_final: 0.9312 (m)
REVERT: B  941 PHE cc_start: 0.8141 (t80) cc_final: 0.7886 (t80)
REVERT: B 1017 ASP cc_start: 0.7839 (m-30) cc_final: 0.7235 (p0)
REVERT: B 1226 ARG cc_start: 0.7575 (mmt180) cc_final: 0.7318 (mmt90)
REVERT: B 1508 LEU cc_start: 0.8972 (mp) cc_final: 0.8515 (tp)
REVERT: B 1579 ARG cc_start: 0.8447 (tpt90) cc_final: 0.7974 (tpt90)
REVERT: C  941 PHE cc_start: 0.8094 (t80) cc_final: 0.7864 (t80)
REVERT: C 1145 ASP cc_start: 0.8038 (t0) cc_final: 0.7829 (t70)
REVERT: C 1226 ARG cc_start: 0.7712 (mmt180) cc_final: 0.7249 (mmm-85)
REVERT: C 1256 MET cc_start: 0.9404 (tmm) cc_final: 0.9165 (tmm)
REVERT: C 1311 MET cc_start: 0.7896 (tpt) cc_final: 0.6878 (tpp)
REVERT: C 1508 LEU cc_start: 0.8964 (mp) cc_final: 0.8519 (tp)
REVERT: C 1511 LEU cc_start: 0.8649 (tt) cc_final: 0.8339 (mm)
REVERT: C 1579 ARG cc_start: 0.8552 (tpt90) cc_final: 0.8023 (tpt90)
REVERT: C 1584 MET cc_start: 0.8320 (mtp) cc_final: 0.7957 (mtt)
REVERT: D  517 LYS cc_start: 0.8906 (tptp) cc_final: 0.8678 (tppt)
REVERT: D  738 ASN cc_start: 0.5871 (OUTLIER) cc_final: 0.5504 (p0)
REVERT: D  771 VAL cc_start: 0.9535 (t) cc_final: 0.9253 (m)
REVERT: D  788 ARG cc_start: 0.7422 (mtm-85) cc_final: 0.7041 (mtm-85)
REVERT: D 1145 ASP cc_start: 0.8487 (t0) cc_final: 0.8163 (t0)
REVERT: D 1214 MET cc_start: 0.8496 (mmt) cc_final: 0.8067 (mmp)
REVERT: D 1256 MET cc_start: 0.9390 (tmm) cc_final: 0.8934 (tmm)
REVERT: D 1311 MET cc_start: 0.7841 (tpt) cc_final: 0.6883 (tpp)
REVERT: D 1508 LEU cc_start: 0.8992 (mp) cc_final: 0.8782 (mm)
REVERT: D 1511 LEU cc_start: 0.8627 (tt) cc_final: 0.8243 (mm)
REVERT: D 1579 ARG cc_start: 0.8321 (tpt90) cc_final: 0.7899 (tpt90)
  outliers start: 4
  outliers final: 1
  residues processed: 453
  average time/residue: 0.2145
  time to fit residues: 154.6322
Evaluate side-chains
  306 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 302
  time to evaluate  : 0.984 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 424
   random chunks:
   chunk 249 optimal weight:    4.9990
   chunk 368 optimal weight:   20.0000
   chunk 158 optimal weight:    0.2980
   chunk 213 optimal weight:    0.4980
   chunk 107 optimal weight:    1.9990
   chunk 211 optimal weight:    0.9990
   chunk 102 optimal weight:    7.9990
   chunk 251 optimal weight:    0.7980
   chunk 284 optimal weight:    6.9990
   chunk 215 optimal weight:    7.9990
   chunk 254 optimal weight:    5.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
B 576 GLN
B1032 GLN
C 738 ASN
C1032 GLN
C1140 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.087782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.072325 restraints weight = 148960.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.074432 restraints weight = 106614.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.075485 restraints weight = 74167.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.075816 restraints weight = 62625.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.076065 restraints weight = 55953.961|
|-----------------------------------------------------------------------------|
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7720
moved from start:          0.5505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  33624  Z= 0.142
  Angle     :  0.681   7.709  45656  Z= 0.351
  Chirality :  0.045   0.243   5216
  Planarity :  0.005   0.053   5996
  Dihedral  :  5.309  23.109   4688
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 14.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.11 %
    Favored  : 93.89 %
  Rotamer:
    Outliers :  0.03 %
    Allowed  :  1.75 %
    Favored  : 98.22 %
  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: -1.64 (0.12), residues: 4220
  helix:  0.14 (0.10), residues: 2440
  sheet: -0.98 (0.26), residues: 396
  loop : -3.38 (0.14), residues: 1384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D 784 
 TYR   0.033   0.002   TYR B1457 
 PHE   0.020   0.002   PHE B 982 
 TRP   0.028   0.001   TRP D 533 
 HIS   0.003   0.001   HIS B 984 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 (33624)
  covalent geometry    : angle       0.68054 (45656)
  hydrogen bonds       : bond        0.04094 ( 1837)
  hydrogen bonds       : angle       4.86735 ( 5439)

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

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

  8440 Ramachandran restraints generated.
    4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  8440 Ramachandran restraints generated.
    4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  483 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 482
  time to evaluate  : 1.316 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  531 LEU cc_start: 0.8570 (tt) cc_final: 0.8186 (mm)
REVERT: A 1017 ASP cc_start: 0.7921 (m-30) cc_final: 0.7292 (p0)
REVERT: A 1226 ARG cc_start: 0.7647 (mmt180) cc_final: 0.7341 (mmm-85)
REVERT: A 1511 LEU cc_start: 0.8566 (tt) cc_final: 0.8225 (mm)
REVERT: B  576 GLN cc_start: 0.7547 (tm130) cc_final: 0.6646 (tm130)
REVERT: B  641 TYR cc_start: 0.8751 (t80) cc_final: 0.8454 (t80)
REVERT: B  771 VAL cc_start: 0.9543 (t) cc_final: 0.9325 (m)
REVERT: B  998 SER cc_start: 0.7042 (t) cc_final: 0.6729 (p)
REVERT: B 1017 ASP cc_start: 0.7800 (m-30) cc_final: 0.7213 (p0)
REVERT: B 1145 ASP cc_start: 0.8434 (t0) cc_final: 0.7992 (t0)
REVERT: B 1227 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7950 (tp30)
REVERT: B 1508 LEU cc_start: 0.8873 (mp) cc_final: 0.8439 (tp)
REVERT: B 1579 ARG cc_start: 0.8457 (tpt90) cc_final: 0.7945 (tpt90)
REVERT: C  649 TYR cc_start: 0.5341 (m-80) cc_final: 0.5140 (m-10)
REVERT: C  738 ASN cc_start: 0.5789 (OUTLIER) cc_final: 0.5336 (p0)
REVERT: C  771 VAL cc_start: 0.9543 (t) cc_final: 0.9277 (m)
REVERT: C 1145 ASP cc_start: 0.7987 (t0) cc_final: 0.7699 (t70)
REVERT: C 1226 ARG cc_start: 0.7684 (mmt180) cc_final: 0.7200 (mmm-85)
REVERT: C 1508 LEU cc_start: 0.8947 (mp) cc_final: 0.8487 (tp)
REVERT: C 1511 LEU cc_start: 0.8575 (tt) cc_final: 0.8323 (mm)
REVERT: C 1579 ARG cc_start: 0.8477 (tpt90) cc_final: 0.7918 (tpt90)
REVERT: D  517 LYS cc_start: 0.8925 (tptp) cc_final: 0.8645 (tppt)
REVERT: D  531 LEU cc_start: 0.9076 (tt) cc_final: 0.8537 (mm)
REVERT: D  771 VAL cc_start: 0.9530 (t) cc_final: 0.9274 (m)
REVERT: D  788 ARG cc_start: 0.7513 (mtm-85) cc_final: 0.7104 (mtm-85)
REVERT: D  941 PHE cc_start: 0.8015 (t80) cc_final: 0.7804 (t80)
REVERT: D  998 SER cc_start: 0.7145 (t) cc_final: 0.6791 (p)
REVERT: D 1145 ASP cc_start: 0.8376 (t0) cc_final: 0.8033 (t0)
REVERT: D 1226 ARG cc_start: 0.7600 (mmt180) cc_final: 0.7112 (mmm-85)
REVERT: D 1330 GLU cc_start: 0.7992 (mp0) cc_final: 0.7685 (mp0)
REVERT: D 1511 LEU cc_start: 0.8511 (tt) cc_final: 0.8276 (mm)
REVERT: D 1579 ARG cc_start: 0.8324 (tpt90) cc_final: 0.7819 (tpt90)
  outliers start: 1
  outliers final: 0
  residues processed: 482
  average time/residue: 0.2078
  time to fit residues: 160.3881
Evaluate side-chains
  325 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 324
  time to evaluate  : 1.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 424
   random chunks:
   chunk 341 optimal weight:    2.9990
   chunk 414 optimal weight:    3.9990
   chunk 253 optimal weight:    0.7980
   chunk 305 optimal weight:    6.9990
   chunk 221 optimal weight:    2.9990
   chunk 233 optimal weight:    1.9990
   chunk 109 optimal weight:    8.9990
   chunk 101 optimal weight:    9.9990
   chunk 73 optimal weight:    0.9990
   chunk 213 optimal weight:    1.9990
   chunk 220 optimal weight:    0.8980
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
B 550 GLN
B1032 GLN
C1032 GLN
C1190 ASN
** D 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.087167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.072107 restraints weight = 147458.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.073562 restraints weight = 102882.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.074588 restraints weight = 79615.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.075309 restraints weight = 66090.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.075773 restraints weight = 57848.042|
|-----------------------------------------------------------------------------|
r_work (final): 0.3495
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7714
moved from start:          0.5749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  33624  Z= 0.160
  Angle     :  0.692   9.466  45656  Z= 0.358
  Chirality :  0.046   0.262   5216
  Planarity :  0.004   0.041   5996
  Dihedral  :  5.269  23.273   4688
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 15.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.40 %
    Favored  : 93.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  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: -1.58 (0.12), residues: 4220
  helix:  0.23 (0.10), residues: 2412
  sheet: -1.05 (0.26), residues: 396
  loop : -3.36 (0.14), residues: 1412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.001   ARG B 977 
 TYR   0.030   0.002   TYR C 641 
 PHE   0.020   0.002   PHE C 577 
 TRP   0.017   0.001   TRP D 533 
 HIS   0.004   0.001   HIS A1506 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 (33624)
  covalent geometry    : angle       0.69152 (45656)
  hydrogen bonds       : bond        0.04128 ( 1837)
  hydrogen bonds       : angle       4.89672 ( 5439)

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

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

  8440 Ramachandran restraints generated.
    4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  8440 Ramachandran restraints generated.
    4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  440 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 440
  time to evaluate  : 1.134 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  749 ILE cc_start: 0.8141 (pt) cc_final: 0.7599 (pt)
REVERT: A  872 GLU cc_start: 0.3589 (mm-30) cc_final: 0.3266 (mm-30)
REVERT: A 1017 ASP cc_start: 0.7747 (m-30) cc_final: 0.7246 (p0)
REVERT: A 1226 ARG cc_start: 0.7736 (mmt180) cc_final: 0.6512 (mmp80)
REVERT: A 1330 GLU cc_start: 0.8063 (mp0) cc_final: 0.7712 (mp0)
REVERT: B  641 TYR cc_start: 0.8722 (t80) cc_final: 0.8375 (t80)
REVERT: B  771 VAL cc_start: 0.9563 (t) cc_final: 0.9322 (m)
REVERT: B  998 SER cc_start: 0.6886 (t) cc_final: 0.6642 (p)
REVERT: B 1017 ASP cc_start: 0.7748 (m-30) cc_final: 0.7188 (p0)
REVERT: B 1226 ARG cc_start: 0.7676 (mmt180) cc_final: 0.7470 (mmt90)
REVERT: B 1508 LEU cc_start: 0.8894 (mp) cc_final: 0.8440 (tp)
REVERT: B 1579 ARG cc_start: 0.8440 (tpt90) cc_final: 0.7886 (tpt90)
REVERT: C 1145 ASP cc_start: 0.7898 (t0) cc_final: 0.7635 (t70)
REVERT: C 1226 ARG cc_start: 0.7658 (mmt180) cc_final: 0.7271 (mmm-85)
REVERT: C 1508 LEU cc_start: 0.8935 (mp) cc_final: 0.8486 (tp)
REVERT: C 1511 LEU cc_start: 0.8607 (tt) cc_final: 0.8336 (mm)
REVERT: C 1579 ARG cc_start: 0.8473 (tpt90) cc_final: 0.7868 (tpt90)
REVERT: C 1584 MET cc_start: 0.8234 (mtp) cc_final: 0.7889 (mtt)
REVERT: D  531 LEU cc_start: 0.8903 (tt) cc_final: 0.8448 (mm)
REVERT: D  771 VAL cc_start: 0.9540 (t) cc_final: 0.9268 (m)
REVERT: D  941 PHE cc_start: 0.8058 (t80) cc_final: 0.7825 (t80)
REVERT: D  977 ARG cc_start: 0.8073 (mmt180) cc_final: 0.7405 (tpp80)
REVERT: D  998 SER cc_start: 0.6990 (t) cc_final: 0.6617 (p)
REVERT: D 1214 MET cc_start: 0.8429 (mmt) cc_final: 0.7998 (mmp)
REVERT: D 1511 LEU cc_start: 0.8537 (tt) cc_final: 0.8313 (mm)
REVERT: D 1579 ARG cc_start: 0.8303 (tpt90) cc_final: 0.7821 (tpt90)
  outliers start: 0
  outliers final: 0
  residues processed: 440
  average time/residue: 0.2063
  time to fit residues: 147.3219
Evaluate side-chains
  304 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 304
  time to evaluate  : 1.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 424
   random chunks:
   chunk 294 optimal weight:    2.9990
   chunk 377 optimal weight:    0.9990
   chunk 217 optimal weight:    5.9990
   chunk 60 optimal weight:    4.9990
   chunk 381 optimal weight:    0.8980
   chunk 29 optimal weight:    0.8980
   chunk 290 optimal weight:    0.6980
   chunk 250 optimal weight:    6.9990
   chunk 91 optimal weight:    3.9990
   chunk 109 optimal weight:    8.9990
   chunk 282 optimal weight:    1.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
B1032 GLN
C1032 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.087943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.072949 restraints weight = 147707.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.074377 restraints weight = 103235.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.075376 restraints weight = 80203.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.076091 restraints weight = 66982.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.076573 restraints weight = 58761.895|
|-----------------------------------------------------------------------------|
r_work (final): 0.3508
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7721
moved from start:          0.5903

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  33624  Z= 0.147
  Angle     :  0.688   9.345  45656  Z= 0.354
  Chirality :  0.046   0.268   5216
  Planarity :  0.005   0.075   5996
  Dihedral  :  5.181  24.066   4688
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 15.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.16 %
    Favored  : 93.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.63 %
    Favored  : 99.37 %
  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: -1.48 (0.12), residues: 4220
  helix:  0.28 (0.10), residues: 2448
  sheet: -1.03 (0.25), residues: 416
  loop : -3.35 (0.14), residues: 1356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG C1171 
 TYR   0.034   0.002   TYR B1457 
 PHE   0.028   0.002   PHE C 577 
 TRP   0.015   0.001   TRP B 629 
 HIS   0.004   0.001   HIS A1506 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 (33624)
  covalent geometry    : angle       0.68794 (45656)
  hydrogen bonds       : bond        0.04065 ( 1837)
  hydrogen bonds       : angle       4.83409 ( 5439)

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

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

  8440 Ramachandran restraints generated.
    4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  8440 Ramachandran restraints generated.
    4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  443 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 443
  time to evaluate  : 1.315 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  531 LEU cc_start: 0.8561 (tt) cc_final: 0.8237 (mm)
REVERT: A  749 ILE cc_start: 0.8057 (pt) cc_final: 0.7619 (pt)
REVERT: A  872 GLU cc_start: 0.3546 (mm-30) cc_final: 0.3250 (mm-30)
REVERT: A 1017 ASP cc_start: 0.7682 (m-30) cc_final: 0.7305 (p0)
REVERT: A 1226 ARG cc_start: 0.7728 (mmt180) cc_final: 0.6470 (mmp80)
REVERT: A 1330 GLU cc_start: 0.8118 (mp0) cc_final: 0.7771 (mp0)
REVERT: B  530 LYS cc_start: 0.7897 (tptm) cc_final: 0.7560 (tptp)
REVERT: B  771 VAL cc_start: 0.9549 (t) cc_final: 0.9318 (m)
REVERT: B  977 ARG cc_start: 0.8254 (mmt180) cc_final: 0.7305 (tpp80)
REVERT: B  998 SER cc_start: 0.7063 (t) cc_final: 0.6809 (p)
REVERT: B 1017 ASP cc_start: 0.7759 (m-30) cc_final: 0.7209 (p0)
REVERT: B 1226 ARG cc_start: 0.7695 (mmt180) cc_final: 0.7480 (mmt90)
REVERT: B 1508 LEU cc_start: 0.8930 (mp) cc_final: 0.8479 (tp)
REVERT: B 1579 ARG cc_start: 0.8510 (tpt90) cc_final: 0.7867 (tpt90)
REVERT: C 1145 ASP cc_start: 0.8046 (t0) cc_final: 0.7800 (t70)
REVERT: C 1171 ARG cc_start: 0.6874 (mpp-170) cc_final: 0.6249 (mpp-170)
REVERT: C 1226 ARG cc_start: 0.7740 (mmt180) cc_final: 0.7346 (mmm-85)
REVERT: C 1508 LEU cc_start: 0.8967 (mp) cc_final: 0.8576 (tp)
REVERT: C 1511 LEU cc_start: 0.8551 (tt) cc_final: 0.8315 (mm)
REVERT: C 1579 ARG cc_start: 0.8574 (tpt90) cc_final: 0.7942 (tpt90)
REVERT: D  531 LEU cc_start: 0.8997 (tt) cc_final: 0.8560 (mm)
REVERT: D  771 VAL cc_start: 0.9548 (t) cc_final: 0.9270 (m)
REVERT: D  941 PHE cc_start: 0.8124 (t80) cc_final: 0.7825 (t80)
REVERT: D  977 ARG cc_start: 0.8061 (mmt180) cc_final: 0.7181 (tpp80)
REVERT: D  998 SER cc_start: 0.6961 (t) cc_final: 0.6676 (p)
REVERT: D 1214 MET cc_start: 0.8445 (mmt) cc_final: 0.8115 (mmp)
REVERT: D 1511 LEU cc_start: 0.8534 (tt) cc_final: 0.8224 (mm)
REVERT: D 1579 ARG cc_start: 0.8499 (tpt90) cc_final: 0.7996 (tpt90)
  outliers start: 0
  outliers final: 0
  residues processed: 443
  average time/residue: 0.2005
  time to fit residues: 144.4349
Evaluate side-chains
  310 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 310
  time to evaluate  : 1.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 424
   random chunks:
   chunk 211 optimal weight:    6.9990
   chunk 337 optimal weight:    8.9990
   chunk 36 optimal weight:    0.9980
   chunk 58 optimal weight:    7.9990
   chunk 388 optimal weight:    4.9990
   chunk 351 optimal weight:    4.9990
   chunk 66 optimal weight:    0.8980
   chunk 114 optimal weight:    0.6980
   chunk 268 optimal weight:    9.9990
   chunk 151 optimal weight:    7.9990
   chunk 359 optimal weight:    0.6980
   overall best weight:    1.6582

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

Flipped N/Q/H residues before XYZ refinement:
B1032 GLN
** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C1032 GLN
C1190 ASN
D1190 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.086477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.070677 restraints weight = 150970.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.072161 restraints weight = 104959.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.073198 restraints weight = 81270.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.073834 restraints weight = 67710.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.074407 restraints weight = 59898.057|
|-----------------------------------------------------------------------------|
r_work (final): 0.3459
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7765
moved from start:          0.6146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  33624  Z= 0.176
  Angle     :  0.716   9.307  45656  Z= 0.371
  Chirality :  0.046   0.273   5216
  Planarity :  0.005   0.069   5996
  Dihedral  :  5.262  23.802   4688
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 15.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.04 %
    Favored  : 92.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.63 %
    Favored  : 99.37 %
  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: -1.47 (0.12), residues: 4220
  helix:  0.29 (0.10), residues: 2396
  sheet: -0.80 (0.26), residues: 368
  loop : -3.24 (0.14), residues: 1456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG C 784 
 TYR   0.020   0.002   TYR D1343 
 PHE   0.033   0.002   PHE C 982 
 TRP   0.013   0.001   TRP B 629 
 HIS   0.005   0.001   HIS D1301 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 (33624)
  covalent geometry    : angle       0.71551 (45656)
  hydrogen bonds       : bond        0.04192 ( 1837)
  hydrogen bonds       : angle       4.89656 ( 5439)

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

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

  8440 Ramachandran restraints generated.
    4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  8440 Ramachandran restraints generated.
    4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  411 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 411
  time to evaluate  : 1.146 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  749 ILE cc_start: 0.8206 (pt) cc_final: 0.7721 (pt)
REVERT: A 1017 ASP cc_start: 0.7729 (m-30) cc_final: 0.7486 (p0)
REVERT: A 1330 GLU cc_start: 0.8031 (mp0) cc_final: 0.7719 (mp0)
REVERT: B  576 GLN cc_start: 0.7176 (pp30) cc_final: 0.6909 (pp30)
REVERT: B  718 ILE cc_start: 0.9454 (pt) cc_final: 0.9146 (tt)
REVERT: B  771 VAL cc_start: 0.9580 (t) cc_final: 0.9338 (m)
REVERT: B  977 ARG cc_start: 0.8189 (mmt180) cc_final: 0.7273 (tpp80)
REVERT: B  998 SER cc_start: 0.7077 (t) cc_final: 0.6830 (p)
REVERT: B 1017 ASP cc_start: 0.7777 (m-30) cc_final: 0.7219 (p0)
REVERT: B 1226 ARG cc_start: 0.7744 (mmt180) cc_final: 0.7430 (mmt90)
REVERT: B 1508 LEU cc_start: 0.8931 (mp) cc_final: 0.8494 (tp)
REVERT: B 1579 ARG cc_start: 0.8466 (tpt90) cc_final: 0.7864 (tpt90)
REVERT: C 1226 ARG cc_start: 0.7763 (mmt180) cc_final: 0.7514 (mmt90)
REVERT: C 1508 LEU cc_start: 0.8957 (mp) cc_final: 0.8498 (tp)
REVERT: C 1511 LEU cc_start: 0.8583 (tt) cc_final: 0.8314 (mm)
REVERT: C 1579 ARG cc_start: 0.8526 (tpt90) cc_final: 0.7881 (tpt90)
REVERT: D  531 LEU cc_start: 0.9008 (tt) cc_final: 0.8456 (mm)
REVERT: D  576 GLN cc_start: 0.7415 (tm-30) cc_final: 0.7129 (tm-30)
REVERT: D  941 PHE cc_start: 0.8112 (t80) cc_final: 0.7829 (t80)
REVERT: D  998 SER cc_start: 0.6864 (t) cc_final: 0.6597 (p)
REVERT: D 1004 ARG cc_start: 0.8957 (tpt-90) cc_final: 0.8432 (tpp-160)
REVERT: D 1214 MET cc_start: 0.8477 (mmt) cc_final: 0.8135 (mmp)
REVERT: D 1252 LEU cc_start: 0.9506 (mt) cc_final: 0.9293 (mt)
REVERT: D 1579 ARG cc_start: 0.8438 (tpt90) cc_final: 0.7962 (tpt90)
  outliers start: 0
  outliers final: 0
  residues processed: 411
  average time/residue: 0.2015
  time to fit residues: 135.5161
Evaluate side-chains
  283 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 283
  time to evaluate  : 1.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 424
   random chunks:
   chunk 254 optimal weight:    2.9990
   chunk 292 optimal weight:    0.9980
   chunk 154 optimal weight:    0.0770
   chunk 139 optimal weight:    0.9990
   chunk 74 optimal weight:    3.9990
   chunk 257 optimal weight:    1.9990
   chunk 201 optimal weight:    0.7980
   chunk 302 optimal weight:   10.0000
   chunk 357 optimal weight:    6.9990
   chunk 204 optimal weight:    4.9990
   chunk 350 optimal weight:    0.0050
   overall best weight:    0.5754

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

Flipped N/Q/H residues before XYZ refinement:
B 968 ASN
B1032 GLN
** B1314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C1032 GLN
D 968 ASN
** D1190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.088536 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.073544 restraints weight = 147911.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.075002 restraints weight = 103266.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.076048 restraints weight = 79797.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.076766 restraints weight = 66192.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.077284 restraints weight = 57936.517|
|-----------------------------------------------------------------------------|
r_work (final): 0.3523
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7699
moved from start:          0.6218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  33624  Z= 0.135
  Angle     :  0.692   9.184  45656  Z= 0.352
  Chirality :  0.046   0.268   5216
  Planarity :  0.005   0.054   5996
  Dihedral  :  5.087  24.654   4688
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 14.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  0.03 %
    Allowed  :  0.40 %
    Favored  : 99.57 %
  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: -1.28 (0.12), residues: 4220
  helix:  0.43 (0.10), residues: 2432
  sheet: -0.95 (0.26), residues: 380
  loop : -3.14 (0.14), residues: 1408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG C 784 
 TYR   0.036   0.002   TYR B1457 
 PHE   0.032   0.002   PHE C 577 
 TRP   0.022   0.001   TRP B 533 
 HIS   0.003   0.001   HIS A 975 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 (33624)
  covalent geometry    : angle       0.69162 (45656)
  hydrogen bonds       : bond        0.03947 ( 1837)
  hydrogen bonds       : angle       4.80403 ( 5439)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5398.08 seconds
wall clock time: 94 minutes 7.47 seconds (5647.47 seconds total)