Starting phenix.real_space_refine
on Sun Aug 24 21:23:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8p52_17440/08_2025/8p52_17440.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8p52_17440/08_2025/8p52_17440.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8p52_17440/08_2025/8p52_17440.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8p52_17440/08_2025/8p52_17440.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8p52_17440/08_2025/8p52_17440.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8p52_17440/08_2025/8p52_17440.cif"
  }
  resolution = 3.6
  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
-------------------------------------------------------------------------------
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      54      5.16       5
     C   14343      2.51       5
     N    4022      2.21       5
     O    4364      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 182 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 22783
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 22783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2914, 22783
          Classifications: {'peptide': 2914}
          Link IDs: {'PTRANS': 97, 'TRANS': 2816}
          Chain breaks: 1
  Residues with excluded nonbonded symmetry interactions: 19
    residue:
      pdb=" N   ALA A 993 " occ=0.00
      ... (3 atoms not shown)
      pdb=" CB  ALA A 993 " occ=0.00
    residue:
      pdb=" N   ASP A1113 " occ=0.00
      ... (6 atoms not shown)
      pdb=" OD2 ASP A1113 " occ=0.00
    residue:
      pdb=" N   GLN A1120 " occ=0.40
      ... (7 atoms not shown)
      pdb=" NE2 GLN A1120 " occ=0.00
    residue:
      pdb=" N   ALA A1262 " occ=0.00
      ... (3 atoms not shown)
      pdb=" CB  ALA A1262 " occ=0.00
    residue:
      pdb=" N   ASP A2674 " occ=0.00
      ... (6 atoms not shown)
      pdb=" OD2 ASP A2674 " occ=0.00
    residue:
      pdb=" N   GLY A2675 " occ=0.00
      ... (2 atoms not shown)
      pdb=" O   GLY A2675 " occ=0.00
    residue:
      pdb=" N   LYS A2676 " occ=0.00
      ... (7 atoms not shown)
      pdb=" NZ  LYS A2676 " occ=0.00
    residue:
      pdb=" N   THR A2831 " occ=0.00
      ... (5 atoms not shown)
      pdb=" CG2 THR A2831 " occ=0.00
    residue:
      pdb=" N   VAL A2833 " occ=0.56
      ... (5 atoms not shown)
      pdb=" CG2 VAL A2833 " occ=0.38
    residue:
      pdb=" N   ASP A2835 " occ=0.00
      ... (6 atoms not shown)
      pdb=" OD2 ASP A2835 " occ=0.33
    residue:
      pdb=" N   VAL A2858 " occ=0.89
      ... (5 atoms not shown)
      pdb=" CG2 VAL A2858 " occ=0.78
    residue:
      pdb=" N   SER A2859 " occ=0.00
      ... (4 atoms not shown)
      pdb=" OG  SER A2859 " occ=0.00
    ... (remaining 7 not shown)
  Time building chain proxies: 4.38, per 1000 atoms: 0.19
  Number of scatterers: 22783
  At special positions: 0
  Unit cell: (180, 184.5, 162.9, 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      54     16.00
     O    4364      8.00
     N    4022      7.00
     C   14343      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.70
  Conformation dependent library (CDL) restraints added in 978.1 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  5820 Ramachandran restraints generated.
    2910 Oldfield, 0 Emsley, 2910 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  5372

  Finding SS restraints...
    Secondary structure from input PDB file:
      98 helices and 29 sheets defined
      42.1% alpha, 20.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.64
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 22
    Processing helix  chain 'A' and resid 35 through 55
      removed outlier: 3.518A  pdb=" N   ASP A  39 " --> pdb=" O   ASP A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 64
      removed outlier: 3.559A  pdb=" N   GLN A  62 " --> pdb=" O   VAL A  58 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 75 through 86
    Processing helix  chain 'A' and resid 93 through 132
    Processing helix  chain 'A' and resid 140 through 147
    Processing helix  chain 'A' and resid 147 through 170
      removed outlier: 4.442A  pdb=" N   ALA A 153 " --> pdb=" O   VAL A 149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 176 through 202
    Processing helix  chain 'A' and resid 206 through 216
    Processing helix  chain 'A' and resid 225 through 233
    Processing helix  chain 'A' and resid 283 through 290
    Processing helix  chain 'A' and resid 296 through 301
      removed outlier: 4.196A  pdb=" N   ARG A 300 " --> pdb=" O   PRO A 296 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 314 through 321
      removed outlier: 3.529A  pdb=" N   TYR A 320 " --> pdb=" O   PHE A 316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 322 through 324
      No H-bonds generated for 'chain 'A' and resid 322 through 324'
    Processing helix  chain 'A' and resid 378 through 390
    Processing helix  chain 'A' and resid 399 through 405
    Processing helix  chain 'A' and resid 418 through 425
    Processing helix  chain 'A' and resid 465 through 489
      removed outlier: 3.688A  pdb=" N   SER A 488 " --> pdb=" O   GLU A 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 489 through 495
    Processing helix  chain 'A' and resid 500 through 517
      removed outlier: 3.832A  pdb=" N   ARG A 512 " --> pdb=" O   GLN A 508 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 520 through 525
    Processing helix  chain 'A' and resid 541 through 558
    Processing helix  chain 'A' and resid 561 through 573
      removed outlier: 3.518A  pdb=" N   ARG A 567 " --> pdb=" O   PRO A 563 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 574 through 584
      removed outlier: 6.192A  pdb=" N   ALA A 577 " --> pdb=" O   LYS A 574 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 586 through 598
      removed outlier: 4.074A  pdb=" N   ASP A 590 " --> pdb=" O   TYR A 586 " (cutoff:3.500A)
      removed outlier: 4.260A  pdb=" N   ALA A 592 " --> pdb=" O   GLN A 588 " (cutoff:3.500A)
      removed outlier: 4.436A  pdb=" N   GLN A 593 " --> pdb=" O   SER A 589 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 598 through 610
    Processing helix  chain 'A' and resid 611 through 623
      removed outlier: 3.648A  pdb=" N   GLN A 615 " --> pdb=" O   GLU A 611 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 635 through 653
    Processing helix  chain 'A' and resid 654 through 658
    Processing helix  chain 'A' and resid 659 through 664
    Processing helix  chain 'A' and resid 665 through 674
    Processing helix  chain 'A' and resid 675 through 698
      removed outlier: 3.872A  pdb=" N   ARG A 691 " --> pdb=" O   PHE A 687 " (cutoff:3.500A)
      Proline residue:  A 692  - end of helix
      removed outlier: 3.542A  pdb=" N   PHE A 697 " --> pdb=" O   VAL A 693 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   SER A 698 " --> pdb=" O   ALA A 694 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 725 through 731
    Processing helix  chain 'A' and resid 735 through 740
      removed outlier: 3.559A  pdb=" N   ARG A 740 " --> pdb=" O   GLN A 737 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 749 through 756
      removed outlier: 4.110A  pdb=" N   SER A 753 " --> pdb=" O   ASP A 749 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   TYR A 754 " --> pdb=" O   LYS A 750 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 763 through 773
    Processing helix  chain 'A' and resid 781 through 789
    Processing helix  chain 'A' and resid 790 through 795
    Processing helix  chain 'A' and resid 800 through 818
    Processing helix  chain 'A' and resid 823 through 834
      removed outlier: 4.921A  pdb=" N   VAL A 829 " --> pdb=" O   GLU A 825 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 841 through 857
      removed outlier: 3.602A  pdb=" N   GLU A 855 " --> pdb=" O   LYS A 851 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 863 through 878
      removed outlier: 3.892A  pdb=" N   ARG A 872 " --> pdb=" O   GLY A 868 " (cutoff:3.500A)
      Proline residue:  A 875  - end of helix
    Processing helix  chain 'A' and resid 879 through 881
      No H-bonds generated for 'chain 'A' and resid 879 through 881'
    Processing helix  chain 'A' and resid 902 through 906
    Processing helix  chain 'A' and resid 930 through 937
    Processing helix  chain 'A' and resid 937 through 945
    Processing helix  chain 'A' and resid 949 through 953
    Processing helix  chain 'A' and resid 985 through 988
    Processing helix  chain 'A' and resid 1052 through 1056
    Processing helix  chain 'A' and resid 1065 through 1069
    Processing helix  chain 'A' and resid 1125 through 1152
      removed outlier: 3.863A  pdb=" N   GLN A1133 " --> pdb=" O   ARG A1129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1173 through 1209
      removed outlier: 4.624A  pdb=" N   ALA A1178 " --> pdb=" O   PRO A1174 " (cutoff:3.500A)
      removed outlier: 6.023A  pdb=" N   TRP A1179 " --> pdb=" O   ALA A1175 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ILE A1190 " --> pdb=" O   VAL A1186 " (cutoff:3.500A)
      removed outlier: 4.411A  pdb=" N   ASP A1193 " --> pdb=" O   ARG A1189 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   GLN A1196 " --> pdb=" O   ALA A1192 " (cutoff:3.500A)
      removed outlier: 4.254A  pdb=" N   LEU A1197 " --> pdb=" O   ASP A1193 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   LYS A1200 " --> pdb=" O   GLN A1196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1213 through 1259
      removed outlier: 4.110A  pdb=" N   ILE A1217 " --> pdb=" O   ARG A1213 " (cutoff:3.500A)
      removed outlier: 4.410A  pdb=" N   GLN A1219 " --> pdb=" O   ASP A1215 " (cutoff:3.500A)
      removed outlier: 4.831A  pdb=" N   GLN A1220 " --> pdb=" O   LEU A1216 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   TYR A1231 " --> pdb=" O   THR A1227 " (cutoff:3.500A)
      removed outlier: 4.647A  pdb=" N   THR A1237 " --> pdb=" O   ALA A1233 " (cutoff:3.500A)
      removed outlier: 5.072A  pdb=" N   VAL A1238 " --> pdb=" O   GLN A1234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1260 through 1263
    Processing helix  chain 'A' and resid 1281 through 1289
    Processing helix  chain 'A' and resid 1298 through 1307
      removed outlier: 3.788A  pdb=" N   SER A1302 " --> pdb=" O   GLY A1298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1321 through 1331
    Processing helix  chain 'A' and resid 1335 through 1358
    Processing helix  chain 'A' and resid 1361 through 1372
      removed outlier: 3.861A  pdb=" N   PHE A1365 " --> pdb=" O   GLN A1361 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   SER A1366 " --> pdb=" O   THR A1362 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   GLU A1367 " --> pdb=" O   ALA A1363 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1391 through 1396
      removed outlier: 3.916A  pdb=" N   GLY A1395 " --> pdb=" O   ASP A1391 " (cutoff:3.500A)
      removed outlier: 4.574A  pdb=" N   ARG A1396 " --> pdb=" O   ARG A1392 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1391 through 1396'
    Processing helix  chain 'A' and resid 1396 through 1429
      removed outlier: 3.588A  pdb=" N   ARG A1402 " --> pdb=" O   TYR A1398 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   VAL A1406 " --> pdb=" O   ARG A1402 " (cutoff:3.500A)
      removed outlier: 8.662A  pdb=" N   GLU A1413 " --> pdb=" O   ALA A1409 " (cutoff:3.500A)
      removed outlier: 8.313A  pdb=" N   ALA A1414 " --> pdb=" O   SER A1410 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1432 through 1443
    Processing helix  chain 'A' and resid 1448 through 1454
      removed outlier: 3.550A  pdb=" N   VAL A1452 " --> pdb=" O   ASN A1448 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1463 through 1473
    Processing helix  chain 'A' and resid 1515 through 1528
      removed outlier: 3.506A  pdb=" N   GLN A1525 " --> pdb=" O   ARG A1521 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1531 through 1536
    Processing helix  chain 'A' and resid 1553 through 1558
      removed outlier: 3.708A  pdb=" N   ALA A1558 " --> pdb=" O   THR A1554 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1576 through 1599
      removed outlier: 3.645A  pdb=" N   GLU A1588 " --> pdb=" O   ARG A1584 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   GLU A1599 " --> pdb=" O   GLU A1595 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1600 through 1630
      removed outlier: 3.702A  pdb=" N   GLN A1608 " --> pdb=" O   SER A1604 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1640 through 1643
    Processing helix  chain 'A' and resid 1672 through 1691
      removed outlier: 4.473A  pdb=" N   ARG A1678 " --> pdb=" O   PHE A1674 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   HIS A1684 " --> pdb=" O   PHE A1680 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1709 through 1735
      removed outlier: 4.485A  pdb=" N   ASN A1715 " --> pdb=" O   VAL A1711 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   ALA A1719 " --> pdb=" O   ASN A1715 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1743 through 1757
      removed outlier: 4.266A  pdb=" N   ALA A1747 " --> pdb=" O   ASP A1743 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1766 through 1779
    Processing helix  chain 'A' and resid 1788 through 1809
      removed outlier: 3.737A  pdb=" N   GLY A1797 " --> pdb=" O   ALA A1793 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   VAL A1800 " --> pdb=" O   LEU A1796 " (cutoff:3.500A)
      removed outlier: 4.629A  pdb=" N   GLY A1805 " --> pdb=" O   ASN A1801 " (cutoff:3.500A)
      removed outlier: 4.342A  pdb=" N   VAL A1806 " --> pdb=" O   GLU A1802 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1837 through 1848
    Processing helix  chain 'A' and resid 1873 through 1907
      removed outlier: 3.712A  pdb=" N   GLY A1877 " --> pdb=" O   GLY A1873 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   PHE A1878 " --> pdb=" O   LEU A1874 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ALA A1884 " --> pdb=" O   ALA A1880 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   ASP A1891 " --> pdb=" O   ALA A1887 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1981 through 1985
    Processing helix  chain 'A' and resid 2028 through 2036
      removed outlier: 3.546A  pdb=" N   ILE A2032 " --> pdb=" O   GLY A2028 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2083 through 2087
      removed outlier: 3.917A  pdb=" N   HIS A2087 " --> pdb=" O   LYS A2084 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2194 through 2211
      removed outlier: 3.505A  pdb=" N   LYS A2206 " --> pdb=" O   SER A2202 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   ALA A2207 " --> pdb=" O   ASP A2203 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   HIS A2208 " --> pdb=" O   LEU A2204 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   GLN A2209 " --> pdb=" O   ALA A2205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2248 through 2252
    Processing helix  chain 'A' and resid 2339 through 2347
      removed outlier: 3.795A  pdb=" N   LEU A2345 " --> pdb=" O   ALA A2341 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2358 through 2364
    Processing helix  chain 'A' and resid 2365 through 2367
      No H-bonds generated for 'chain 'A' and resid 2365 through 2367'
    Processing helix  chain 'A' and resid 2369 through 2374
    Processing helix  chain 'A' and resid 2529 through 2534
    Processing helix  chain 'A' and resid 2538 through 2543
      removed outlier: 3.638A  pdb=" N   ASP A2542 " --> pdb=" O   HIS A2538 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2544 through 2546
      No H-bonds generated for 'chain 'A' and resid 2544 through 2546'
    Processing helix  chain 'A' and resid 2583 through 2587
      removed outlier: 3.688A  pdb=" N   HIS A2587 " --> pdb=" O   GLN A2584 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2617 through 2625
    Processing helix  chain 'A' and resid 2683 through 2691
    Processing helix  chain 'A' and resid 2693 through 2705
    Processing helix  chain 'A' and resid 2822 through 2829
    Processing helix  chain 'A' and resid 2883 through 2889
      removed outlier: 3.960A  pdb=" N   VAL A2887 " --> pdb=" O   SER A2884 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2905 through 2915
      removed outlier: 4.053A  pdb=" N   LEU A2915 " --> pdb=" O   GLY A2911 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2916 through 2919
    Processing helix  chain 'A' and resid 2925 through 2931
      removed outlier: 3.585A  pdb=" N   GLU A2930 " --> pdb=" O   PRO A2926 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 234 through 236
      removed outlier: 7.568A  pdb=" N   GLU A 234 " --> pdb=" O   ARG A 241 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   ARG A 241 " --> pdb=" O   GLU A 234 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   ARG A 236 " --> pdb=" O   TYR A 239 " (cutoff:3.500A)
      removed outlier: 5.305A  pdb=" N   ASN A 274 " --> pdb=" O   ALA A 245 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   ASN A 274 " --> pdb=" O   ILE A 359 " (cutoff:3.500A)
      removed outlier: 5.877A  pdb=" N   ILE A 359 " --> pdb=" O   ASN A 274 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 335 through 339
      removed outlier: 5.877A  pdb=" N   ILE A 359 " --> pdb=" O   ASN A 274 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   ASN A 274 " --> pdb=" O   ILE A 359 " (cutoff:3.500A)
      removed outlier: 5.305A  pdb=" N   ASN A 274 " --> pdb=" O   ALA A 245 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   ILE A 307 " --> pdb=" O   ILE A 398 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 258 through 261
    Processing sheet with id=AA4, first strand: chain 'A' and resid 435 through 436
    Processing sheet with id=AA5, first strand: chain 'A' and resid 450 through 454
    Processing sheet with id=AA6, first strand: chain 'A' and resid 720 through 722
    Processing sheet with id=AA7, first strand: chain 'A' and resid 946 through 948
      removed outlier: 6.787A  pdb=" N   LEU A 973 " --> pdb=" O   VAL A 969 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   SER A 963 " --> pdb=" O   THR A 979 " (cutoff:3.500A)
      removed outlier: 4.687A  pdb=" N   PHE A1022 " --> pdb=" O   PRO A 992 " (cutoff:3.500A)
      removed outlier: 4.124A  pdb=" N   THR A1025 " --> pdb=" O   ALA A1081 " (cutoff:3.500A)
      removed outlier: 5.588A  pdb=" N   ALA A1081 " --> pdb=" O   THR A1025 " (cutoff:3.500A)
      removed outlier: 4.193A  pdb=" N   LEU A1078 " --> pdb=" O   GLN A1097 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 946 through 948
      removed outlier: 6.787A  pdb=" N   LEU A 973 " --> pdb=" O   VAL A 969 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   SER A 963 " --> pdb=" O   THR A 979 " (cutoff:3.500A)
      removed outlier: 4.687A  pdb=" N   PHE A1022 " --> pdb=" O   PRO A 992 " (cutoff:3.500A)
      removed outlier: 4.124A  pdb=" N   THR A1025 " --> pdb=" O   ALA A1081 " (cutoff:3.500A)
      removed outlier: 5.588A  pdb=" N   ALA A1081 " --> pdb=" O   THR A1025 " (cutoff:3.500A)
      removed outlier: 4.193A  pdb=" N   LEU A1078 " --> pdb=" O   GLN A1097 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 1009 through 1014
      removed outlier: 6.822A  pdb=" N   SER A1037 " --> pdb=" O   VAL A1060 " (cutoff:3.500A)
      removed outlier: 7.082A  pdb=" N   VAL A1060 " --> pdb=" O   SER A1037 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 1376 through 1379
      removed outlier: 4.287A  pdb=" N   PHE A1376 " --> pdb=" O   ALA A1512 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 1457 through 1462
      removed outlier: 5.016A  pdb=" N   GLY A1459 " --> pdb=" O   LEU A1549 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   LEU A1549 " --> pdb=" O   GLY A1459 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 1636 through 1638
    Processing sheet with id=AB4, first strand: chain 'A' and resid 1636 through 1638
    Processing sheet with id=AB5, first strand: chain 'A' and resid 1692 through 1695
    Processing sheet with id=AB6, first strand: chain 'A' and resid 1911 through 1913
      removed outlier: 6.678A  pdb=" N   LEU A1920 " --> pdb=" O   ILE A2002 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   TRP A2121 " --> pdb=" O   LEU A2162 " (cutoff:3.500A)
      removed outlier: 7.920A  pdb=" N   VAL A2164 " --> pdb=" O   TRP A2121 " (cutoff:3.500A)
      removed outlier: 6.645A  pdb=" N   ILE A2123 " --> pdb=" O   VAL A2164 " (cutoff:3.500A)
      removed outlier: 5.765A  pdb=" N   VAL A2161 " --> pdb=" O   VAL A2173 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   VAL A2173 " --> pdb=" O   VAL A2161 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 1990 through 1992
      removed outlier: 6.459A  pdb=" N   GLN A1937 " --> pdb=" O   LEU A1931 " (cutoff:3.500A)
      removed outlier: 4.857A  pdb=" N   LEU A1931 " --> pdb=" O   GLN A1937 " (cutoff:3.500A)
      removed outlier: 6.952A  pdb=" N   ASP A1939 " --> pdb=" O   LYS A1929 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   LYS A1929 " --> pdb=" O   GLU A2067 " (cutoff:3.500A)
      removed outlier: 8.218A  pdb=" N   VAL A2069 " --> pdb=" O   LYS A1929 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   LEU A1931 " --> pdb=" O   VAL A2069 " (cutoff:3.500A)
      removed outlier: 4.158A  pdb=" N   GLU A2144 " --> pdb=" O   LYS A2147 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   SER A2132 " --> pdb=" O   GLY A2143 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'A' and resid 1977 through 1978
      removed outlier: 6.970A  pdb=" N   TYR A1944 " --> pdb=" O   ILE A2011 " (cutoff:3.500A)
      removed outlier: 8.535A  pdb=" N   TYR A2013 " --> pdb=" O   TYR A1944 " (cutoff:3.500A)
      removed outlier: 8.479A  pdb=" N   TYR A1946 " --> pdb=" O   TYR A2013 " (cutoff:3.500A)
      removed outlier: 11.677A  pdb=" N   TYR A2015 " --> pdb=" O   TYR A1946 " (cutoff:3.500A)
      removed outlier: 4.099A  pdb=" N   LYS A2008 " --> pdb=" O   VAL A2062 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   ARG A2056 " --> pdb=" O   GLU A2014 " (cutoff:3.500A)
      removed outlier: 5.804A  pdb=" N   MET A2016 " --> pdb=" O   ILE A2054 " (cutoff:3.500A)
      removed outlier: 5.030A  pdb=" N   ILE A2054 " --> pdb=" O   MET A2016 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   GLU A2052 " --> pdb=" O   PHE A2045 " (cutoff:3.500A)
      removed outlier: 4.567A  pdb=" N   PHE A2045 " --> pdb=" O   GLU A2052 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'A' and resid 1977 through 1978
      removed outlier: 6.970A  pdb=" N   TYR A1944 " --> pdb=" O   ILE A2011 " (cutoff:3.500A)
      removed outlier: 8.535A  pdb=" N   TYR A2013 " --> pdb=" O   TYR A1944 " (cutoff:3.500A)
      removed outlier: 8.479A  pdb=" N   TYR A1946 " --> pdb=" O   TYR A2013 " (cutoff:3.500A)
      removed outlier: 11.677A  pdb=" N   TYR A2015 " --> pdb=" O   TYR A1946 " (cutoff:3.500A)
      removed outlier: 4.099A  pdb=" N   LYS A2008 " --> pdb=" O   VAL A2062 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   ARG A2056 " --> pdb=" O   GLU A2014 " (cutoff:3.500A)
      removed outlier: 5.804A  pdb=" N   MET A2016 " --> pdb=" O   ILE A2054 " (cutoff:3.500A)
      removed outlier: 5.030A  pdb=" N   ILE A2054 " --> pdb=" O   MET A2016 " (cutoff:3.500A)
      removed outlier: 9.335A  pdb=" N   TYR A2214 " --> pdb=" O   ARG A2055 " (cutoff:3.500A)
      removed outlier: 6.712A  pdb=" N   ILE A2057 " --> pdb=" O   TYR A2214 " (cutoff:3.500A)
      removed outlier: 7.816A  pdb=" N   VAL A2216 " --> pdb=" O   ILE A2057 " (cutoff:3.500A)
      removed outlier: 7.027A  pdb=" N   HIS A2059 " --> pdb=" O   VAL A2216 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   LEU A2240 " --> pdb=" O   PHE A2231 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'A' and resid 1948 through 1949
    Processing sheet with id=AC2, first strand: chain 'A' and resid 2253 through 2258
      removed outlier: 4.891A  pdb=" N   LEU A2254 " --> pdb=" O   TYR A2265 " (cutoff:3.500A)
      removed outlier: 5.996A  pdb=" N   TYR A2265 " --> pdb=" O   LEU A2254 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   TYR A2261 " --> pdb=" O   MET A2258 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'A' and resid 2285 through 2286
      removed outlier: 6.941A  pdb=" N   GLN A2285 " --> pdb=" O   ILE A2382 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC3
    Processing sheet with id=AC4, first strand: chain 'A' and resid 2295 through 2303
      removed outlier: 5.628A  pdb=" N   GLY A2295 " --> pdb=" O   ARG A2314 " (cutoff:3.500A)
      removed outlier: 6.028A  pdb=" N   ARG A2314 " --> pdb=" O   GLY A2295 " (cutoff:3.500A)
      removed outlier: 4.977A  pdb=" N   ILE A2297 " --> pdb=" O   ARG A2312 " (cutoff:3.500A)
      removed outlier: 6.086A  pdb=" N   ARG A2312 " --> pdb=" O   ILE A2297 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   VAL A2307 " --> pdb=" O   ILE A2326 " (cutoff:3.500A)
      removed outlier: 7.446A  pdb=" N   GLU A2321 " --> pdb=" O   ALA A2336 " (cutoff:3.500A)
      removed outlier: 5.129A  pdb=" N   ALA A2336 " --> pdb=" O   GLU A2321 " (cutoff:3.500A)
      removed outlier: 6.728A  pdb=" N   GLY A2323 " --> pdb=" O   VAL A2334 " (cutoff:3.500A)
      removed outlier: 6.296A  pdb=" N   MET A2331 " --> pdb=" O   THR A2385 " (cutoff:3.500A)
      removed outlier: 7.087A  pdb=" N   ALA A2387 " --> pdb=" O   MET A2331 " (cutoff:3.500A)
      removed outlier: 6.783A  pdb=" N   LEU A2333 " --> pdb=" O   ALA A2387 " (cutoff:3.500A)
      removed outlier: 6.976A  pdb=" N   LEU A2389 " --> pdb=" O   LEU A2333 " (cutoff:3.500A)
      removed outlier: 5.890A  pdb=" N   SER A2335 " --> pdb=" O   LEU A2389 " (cutoff:3.500A)
      removed outlier: 6.460A  pdb=" N   THR A2391 " --> pdb=" O   SER A2335 " (cutoff:3.500A)
      removed outlier: 7.154A  pdb=" N   VAL A2400 " --> pdb=" O   ASP A2396 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'A' and resid 2445 through 2451
      removed outlier: 5.762A  pdb=" N   LEU A2446 " --> pdb=" O   TYR A2462 " (cutoff:3.500A)
      removed outlier: 6.685A  pdb=" N   TYR A2462 " --> pdb=" O   LEU A2446 " (cutoff:3.500A)
      removed outlier: 5.137A  pdb=" N   GLY A2448 " --> pdb=" O   PHE A2460 " (cutoff:3.500A)
      removed outlier: 4.641A  pdb=" N   PHE A2460 " --> pdb=" O   GLY A2448 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   THR A2468 " --> pdb=" O   SER A2463 " (cutoff:3.500A)
      removed outlier: 4.725A  pdb=" N   LEU A2469 " --> pdb=" O   VAL A2490 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'A' and resid 2495 through 2501
      removed outlier: 4.790A  pdb=" N   LEU A2505 " --> pdb=" O   LEU A2517 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   LEU A2517 " --> pdb=" O   LEU A2505 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ALA A2515 " --> pdb=" O   VAL A2507 " (cutoff:3.500A)
      removed outlier: 4.335A  pdb=" N   ARG A2513 " --> pdb=" O   THR A2509 " (cutoff:3.500A)
      removed outlier: 6.540A  pdb=" N   VAL A2514 " --> pdb=" O   ALA A2526 " (cutoff:3.500A)
      removed outlier: 9.800A  pdb=" N   SER A2524 " --> pdb=" O   THR A2552 " (cutoff:3.500A)
      removed outlier: 9.888A  pdb=" N   ALA A2554 " --> pdb=" O   SER A2524 " (cutoff:3.500A)
      removed outlier: 7.249A  pdb=" N   ALA A2526 " --> pdb=" O   ALA A2554 " (cutoff:3.500A)
      removed outlier: 4.535A  pdb=" N   VAL A2569 " --> pdb=" O   VAL A2555 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'A' and resid 2589 through 2590
      removed outlier: 3.723A  pdb=" N   LYS A2609 " --> pdb=" O   GLU A2604 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'A' and resid 2649 through 2655
      removed outlier: 6.718A  pdb=" N   THR A2662 " --> pdb=" O   LYS A2650 " (cutoff:3.500A)
      removed outlier: 4.504A  pdb=" N   ALA A2652 " --> pdb=" O   ARG A2660 " (cutoff:3.500A)
      removed outlier: 6.902A  pdb=" N   ARG A2660 " --> pdb=" O   ALA A2652 " (cutoff:3.500A)
      removed outlier: 4.971A  pdb=" N   GLN A2654 " --> pdb=" O   GLY A2658 " (cutoff:3.500A)
      removed outlier: 6.930A  pdb=" N   GLY A2658 " --> pdb=" O   GLN A2654 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   GLU A2667 " --> pdb=" O   THR A2663 " (cutoff:3.500A)
      removed outlier: 5.796A  pdb=" N   LEU A2670 " --> pdb=" O   LEU A2679 " (cutoff:3.500A)
      removed outlier: 5.320A  pdb=" N   LEU A2679 " --> pdb=" O   LEU A2670 " (cutoff:3.500A)
      removed outlier: 7.175A  pdb=" N   THR A2672 " --> pdb=" O   LEU A2677 " (cutoff:3.500A)
      removed outlier: 6.305A  pdb=" N   LEU A2677 " --> pdb=" O   THR A2672 " (cutoff:3.500A)
      removed outlier: 11.881A  pdb=" N   VAL A2710 " --> pdb=" O   GLN A2678 " (cutoff:3.500A)
      removed outlier: 7.080A  pdb=" N   VAL A2680 " --> pdb=" O   VAL A2710 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   THR A2712 " --> pdb=" O   VAL A2680 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   VAL A2682 " --> pdb=" O   THR A2712 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   GLN A2719 " --> pdb=" O   ILE A2732 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'A' and resid 2742 through 2746
      removed outlier: 3.551A  pdb=" N   ILE A2744 " --> pdb=" O   TYR A2754 " (cutoff:3.500A)
      removed outlier: 7.149A  pdb=" N   TYR A2754 " --> pdb=" O   ILE A2744 " (cutoff:3.500A)
      removed outlier: 5.877A  pdb=" N   GLN A2765 " --> pdb=" O   LYS A2773 " (cutoff:3.500A)
      removed outlier: 5.341A  pdb=" N   LYS A2773 " --> pdb=" O   GLN A2765 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'A' and resid 2779 through 2783
      removed outlier: 4.184A  pdb=" N   ASP A2779 " --> pdb=" O   GLN A2790 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'A' and resid 2819 through 2821
      removed outlier: 6.813A  pdb=" N   TYR A2819 " --> pdb=" O   ILE A2848 " (cutoff:3.500A)
      removed outlier: 8.025A  pdb=" N   ALA A2850 " --> pdb=" O   TYR A2819 " (cutoff:3.500A)
      removed outlier: 8.877A  pdb=" N   LEU A2821 " --> pdb=" O   ALA A2850 " (cutoff:3.500A)
      removed outlier: 8.971A  pdb=" N   ASP A2852 " --> pdb=" O   LEU A2821 " (cutoff:3.500A)
      removed outlier: 5.919A  pdb=" N   ILE A2847 " --> pdb=" O   ASP A2895 " (cutoff:3.500A)
      removed outlier: 7.630A  pdb=" N   GLU A2897 " --> pdb=" O   ILE A2847 " (cutoff:3.500A)
      removed outlier: 8.140A  pdb=" N   LEU A2849 " --> pdb=" O   GLU A2897 " (cutoff:3.500A)

    1119 hydrogen bonds defined for protein.
    3135 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 7.80

  Time building geometry restraints manager: 2.28 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: 7643
        1.34 -     1.46: 2962
        1.46 -     1.57: 12515
        1.57 -     1.69: 0
        1.69 -     1.81: 105
  Bond restraints: 23225
  Sorted by residual:
  bond pdb=" CZ  ARG A1573 "
       pdb=" NH2 ARG A1573 "
    ideal  model  delta    sigma   weight residual
    1.330  1.291  0.039 1.30e-02 5.92e+03 8.89e+00
  bond pdb=" N   ARG A1573 "
       pdb=" CA  ARG A1573 "
    ideal  model  delta    sigma   weight residual
    1.456  1.492 -0.037 1.44e-02 4.82e+03 6.49e+00
  bond pdb=" CA  GLU A1575 "
       pdb=" C   GLU A1575 "
    ideal  model  delta    sigma   weight residual
    1.526  1.552 -0.027 1.36e-02 5.41e+03 3.92e+00
  bond pdb=" CD  ARG A1530 "
       pdb=" NE  ARG A1530 "
    ideal  model  delta    sigma   weight residual
    1.458  1.480 -0.022 1.40e-02 5.10e+03 2.58e+00
  bond pdb=" CZ  ARG A1573 "
       pdb=" NH1 ARG A1573 "
    ideal  model  delta    sigma   weight residual
    1.323  1.301  0.022 1.40e-02 5.10e+03 2.46e+00
  ... (remaining 23220 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.41: 30115
        1.41 -     2.82: 1152
        2.82 -     4.23: 161
        4.23 -     5.64: 43
        5.64 -     7.04: 7
  Bond angle restraints: 31478
  Sorted by residual:
  angle pdb=" CA  ARG A1573 "
        pdb=" C   ARG A1573 "
        pdb=" N   PHE A1574 "
      ideal   model   delta    sigma   weight residual
     115.71  121.07   -5.36 1.60e+00 3.91e-01 1.12e+01
  angle pdb=" N   LYS A2880 "
        pdb=" CA  LYS A2880 "
        pdb=" C   LYS A2880 "
      ideal   model   delta    sigma   weight residual
     110.41  114.30   -3.89 1.18e+00 7.18e-01 1.09e+01
  angle pdb=" CA  GLU A1575 "
        pdb=" C   GLU A1575 "
        pdb=" N   GLU A1576 "
      ideal   model   delta    sigma   weight residual
     115.21  119.38   -4.17 1.33e+00 5.65e-01 9.83e+00
  angle pdb=" N   GLN A1660 "
        pdb=" CA  GLN A1660 "
        pdb=" C   GLN A1660 "
      ideal   model   delta    sigma   weight residual
     109.81  116.42   -6.61 2.21e+00 2.05e-01 8.94e+00
  angle pdb=" CA  GLN A2484 "
        pdb=" CB  GLN A2484 "
        pdb=" CG  GLN A2484 "
      ideal   model   delta    sigma   weight residual
     114.10  120.01   -5.91 2.00e+00 2.50e-01 8.73e+00
  ... (remaining 31473 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.94: 12813
       17.94 -    35.88: 860
       35.88 -    53.83: 130
       53.83 -    71.77: 57
       71.77 -    89.71: 30
  Dihedral angle restraints: 13890
    sinusoidal: 5504
      harmonic: 8386
  Sorted by residual:
  dihedral pdb=" CA  ARG A2238 "
           pdb=" C   ARG A2238 "
           pdb=" N   MET A2239 "
           pdb=" CA  MET A2239 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.67  -29.33     0      5.00e+00 4.00e-02 3.44e+01
  dihedral pdb=" CA  GLY A2592 "
           pdb=" C   GLY A2592 "
           pdb=" N   PHE A2593 "
           pdb=" CA  PHE A2593 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -150.70  -29.30     0      5.00e+00 4.00e-02 3.43e+01
  dihedral pdb=" CA  MET A2239 "
           pdb=" C   MET A2239 "
           pdb=" N   LEU A2240 "
           pdb=" CA  LEU A2240 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -150.92  -29.08     0      5.00e+00 4.00e-02 3.38e+01
  ... (remaining 13887 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 2523
       0.040 -    0.080: 708
       0.080 -    0.120: 218
       0.120 -    0.160: 37
       0.160 -    0.201: 7
  Chirality restraints: 3493
  Sorted by residual:
  chirality pdb=" CA  ILE A2920 "
            pdb=" N   ILE A2920 "
            pdb=" C   ILE A2920 "
            pdb=" CB  ILE A2920 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.20 2.00e-01 2.50e+01 1.01e+00
  chirality pdb=" CA  GLN A2213 "
            pdb=" N   GLN A2213 "
            pdb=" C   GLN A2213 "
            pdb=" CB  GLN A2213 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.74e-01
  chirality pdb=" CB  ILE A2297 "
            pdb=" CA  ILE A2297 "
            pdb=" CG1 ILE A2297 "
            pdb=" CG2 ILE A2297 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.18 2.00e-01 2.50e+01 8.56e-01
  ... (remaining 3490 not shown)

  Planarity restraints: 4152
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A1572 "    0.019 2.00e-02 2.50e+03   3.58e-02 1.28e+01
        pdb=" C   THR A1572 "   -0.062 2.00e-02 2.50e+03
        pdb=" O   THR A1572 "    0.023 2.00e-02 2.50e+03
        pdb=" N   ARG A1573 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A1722 "    0.016 2.00e-02 2.50e+03   3.25e-02 1.05e+01
        pdb=" C   ALA A1722 "   -0.056 2.00e-02 2.50e+03
        pdb=" O   ALA A1722 "    0.021 2.00e-02 2.50e+03
        pdb=" N   LEU A1723 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A1651 "    0.003 2.00e-02 2.50e+03   2.26e-02 1.02e+01
        pdb=" CG  TYR A1651 "   -0.006 2.00e-02 2.50e+03
        pdb=" CD1 TYR A1651 "    0.034 2.00e-02 2.50e+03
        pdb=" CD2 TYR A1651 "    0.000 2.00e-02 2.50e+03
        pdb=" CE1 TYR A1651 "   -0.032 2.00e-02 2.50e+03
        pdb=" CE2 TYR A1651 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR A1651 "   -0.031 2.00e-02 2.50e+03
        pdb=" OH  TYR A1651 "    0.031 2.00e-02 2.50e+03
  ... (remaining 4149 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.71: 669
        2.71 -     3.26: 23675
        3.26 -     3.81: 34472
        3.81 -     4.35: 44815
        4.35 -     4.90: 74623
  Nonbonded interactions: 178254
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 144 "
            pdb=" OH  TYR A 196 "
     model   vdw
     2.166 3.040
  nonbonded pdb=" O   PHE A2290 "
            pdb=" NH1 ARG A2311 "
     model   vdw
     2.196 3.120
  nonbonded pdb=" OG  SER A1054 "
            pdb=" OD2 ASP A1065 "
     model   vdw
     2.246 3.040
  nonbonded pdb=" OG1 THR A1953 "
            pdb=" OD2 ASP A1966 "
     model   vdw
     2.265 3.040
  nonbonded pdb=" OH  TYR A1137 "
            pdb=" OE2 GLU A1241 "
     model   vdw
     2.268 3.040
  ... (remaining 178249 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=0.97
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:             3.540
  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:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     23.560
  Find NCS groups from input model:        0.100
  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:             0.000
  Load rotamer database and sin/cos tables:1.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5428
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  23225  Z= 0.132
  Angle     :  0.633   7.044  31478  Z= 0.366
  Chirality :  0.042   0.201   3493
  Planarity :  0.008   0.094   4152
  Dihedral  : 13.730  89.711   8518
  Min Nonbonded Distance : 2.166

Molprobity Statistics.
  All-atom Clashscore : 3.44
  Ramachandran Plot:
    Outliers :  0.03 %
    Allowed  :  5.57 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.29 %
    Favored  : 99.71 %
  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 aren not related in a simple way.
  whole: -2.19 (0.14), residues: 2910
  helix: -1.54 (0.13), residues: 1099
  sheet: -0.69 (0.21), residues: 498
  loop : -1.55 (0.16), residues: 1313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.024   0.003   ARG A 817 
 TYR   0.034   0.004   TYR A1651 
 PHE   0.020   0.001   PHE A1808 
 TRP   0.023   0.002   TRP A 556 
 HIS   0.007   0.001   HIS A2211 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 (23225)
  covalent geometry    : angle       0.63336 (31478)
  hydrogen bonds       : bond        0.17692 ( 1077)
  hydrogen bonds       : angle       7.08588 ( 3135)

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

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

  5820 Ramachandran restraints generated.
    2910 Oldfield, 0 Emsley, 2910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5820 Ramachandran restraints generated.
    2910 Oldfield, 0 Emsley, 2910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  376 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 376
  time to evaluate  : 0.637 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 MET cc_start: 0.6979 (ttm) cc_final: 0.6125 (tpt)
REVERT: A  794 LEU cc_start: 0.9029 (mt) cc_final: 0.8826 (mp)
REVERT: A  901 LEU cc_start: 0.8177 (mt) cc_final: 0.7944 (mt)
REVERT: A 1230 TYR cc_start: 0.6604 (t80) cc_final: 0.5617 (t80)
REVERT: A 1478 MET cc_start: 0.7856 (mmt) cc_final: 0.7489 (mmp)
REVERT: A 1561 PRO cc_start: 0.8705 (Cg_exo) cc_final: 0.8499 (Cg_endo)
REVERT: A 1685 MET cc_start: 0.7460 (tpp) cc_final: 0.7162 (mmm)
REVERT: A 2346 SER cc_start: 0.8549 (t) cc_final: 0.8174 (p)
REVERT: A 2825 MET cc_start: 0.7791 (tmm) cc_final: 0.7569 (tmm)
REVERT: A 2852 ASP cc_start: 0.6905 (m-30) cc_final: 0.6533 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 376
  average time/residue: 0.1668
  time to fit residues: 93.2083
Evaluate side-chains
  171 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 171
  time to evaluate  : 0.833 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 291
   random chunks:
   chunk 197 optimal weight:    2.9990
   chunk 215 optimal weight:    3.9990
   chunk 20 optimal weight:    7.9990
   chunk 132 optimal weight:    9.9990
   chunk 261 optimal weight:    0.0870
   chunk 248 optimal weight:    0.8980
   chunk 207 optimal weight:    8.9990
   chunk 155 optimal weight:    5.9990
   chunk 244 optimal weight:    1.9990
   chunk 183 optimal weight:    8.9990
   chunk 111 optimal weight:    7.9990
   overall best weight:    1.9964

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

Flipped N/Q/H residues before XYZ refinement:
A  62 GLN
A  63 HIS
** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 904 GLN
A1052 ASN
A1142 HIS
A1223 GLN
** A1339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1535 HIS
A1684 HIS
A1691 HIS
A1995 HIS
** A2181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2613 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.098645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.075432 restraints weight = 80183.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.076285 restraints weight = 51169.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.076414 restraints weight = 40074.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.076826 restraints weight = 37745.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.076985 restraints weight = 33290.698|
|-----------------------------------------------------------------------------|
r_work (final): 0.3608
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3608
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3608 r_free = 0.3608    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      544 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3579 r_free = 0.3579    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      538 |
|-----------------------------------------------------------------------------|
r_final: 0.3579
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7190
moved from start:          0.2858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.064  23225  Z= 0.207
  Angle     :  0.723  11.639  31478  Z= 0.380
  Chirality :  0.046   0.180   3493
  Planarity :  0.005   0.061   4152
  Dihedral  :  5.996  31.032   3194
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  :  7.22 %
    Favored  : 91.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.04 %

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 aren not related in a simple way.
  whole: -0.63 (0.15), residues: 2910
  helix:  0.41 (0.15), residues: 1103
  sheet: -0.71 (0.21), residues: 523
  loop : -0.92 (0.18), residues: 1284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG A 236 
 TYR   0.028   0.002   TYR A 443 
 PHE   0.028   0.002   PHE A1727 
 TRP   0.030   0.002   TRP A2532 
 HIS   0.007   0.001   HIS A2811 

Details of bonding type rmsd
  covalent geometry    : bond        0.00470 (23225)
  covalent geometry    : angle       0.72276 (31478)
  hydrogen bonds       : bond        0.04660 ( 1077)
  hydrogen bonds       : angle       5.10470 ( 3135)

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

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

  5820 Ramachandran restraints generated.
    2910 Oldfield, 0 Emsley, 2910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5820 Ramachandran restraints generated.
    2910 Oldfield, 0 Emsley, 2910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 182
  time to evaluate  : 0.888 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 MET cc_start: 0.7862 (ttm) cc_final: 0.6698 (tpt)
REVERT: A  443 TYR cc_start: 0.7195 (m-10) cc_final: 0.6944 (m-10)
REVERT: A  532 ASP cc_start: 0.7192 (p0) cc_final: 0.6939 (p0)
REVERT: A  564 LEU cc_start: 0.8787 (tt) cc_final: 0.8561 (tp)
REVERT: A  676 ASN cc_start: 0.8765 (m-40) cc_final: 0.8397 (t0)
REVERT: A  757 PHE cc_start: 0.8153 (m-80) cc_final: 0.7770 (m-10)
REVERT: A 1105 MET cc_start: 0.6286 (tpp) cc_final: 0.5998 (tpp)
REVERT: A 1325 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.7874 (ttp)
REVERT: A 1478 MET cc_start: 0.7757 (mmt) cc_final: 0.7465 (mmm)
REVERT: A 1488 MET cc_start: 0.8087 (mmm) cc_final: 0.7713 (mmt)
REVERT: A 1523 MET cc_start: 0.8885 (mtp) cc_final: 0.8662 (mtm)
REVERT: A 1557 MET cc_start: 0.8172 (tpp) cc_final: 0.7740 (tpp)
REVERT: A 1591 MET cc_start: 0.7395 (tpt) cc_final: 0.6996 (tpt)
REVERT: A 2364 ARG cc_start: 0.6741 (ttt180) cc_final: 0.6188 (tpp80)
  outliers start: 32
  outliers final: 21
  residues processed: 205
  average time/residue: 0.1557
  time to fit residues: 51.8143
Evaluate side-chains
  157 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 135
  time to evaluate  : 0.820 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue  307 ILE
Chi-restraints excluded: chain A residue  415 LEU
Chi-restraints excluded: chain A residue  459 VAL
Chi-restraints excluded: chain A residue  463 HIS
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  525 LEU
Chi-restraints excluded: chain A residue  554 SER
Chi-restraints excluded: chain A residue  675 SER
Chi-restraints excluded: chain A residue  690 LEU
Chi-restraints excluded: chain A residue  696 SER
Chi-restraints excluded: chain A residue  717 ILE
Chi-restraints excluded: chain A residue  766 THR
Chi-restraints excluded: chain A residue 1135 VAL
Chi-restraints excluded: chain A residue 1325 MET
Chi-restraints excluded: chain A residue 1410 SER
Chi-restraints excluded: chain A residue 1688 LEU
Chi-restraints excluded: chain A residue 1807 LEU
Chi-restraints excluded: chain A residue 2204 LEU
Chi-restraints excluded: chain A residue 2382 ILE
Chi-restraints excluded: chain A residue 2920 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 291
   random chunks:
   chunk 147 optimal weight:    9.9990
   chunk 52 optimal weight:    3.9990
   chunk 168 optimal weight:    7.9990
   chunk 3 optimal weight:    0.4980
   chunk 15 optimal weight:    6.9990
   chunk 237 optimal weight:    0.9990
   chunk 26 optimal weight:    6.9990
   chunk 240 optimal weight:    0.4980
   chunk 27 optimal weight:    8.9990
   chunk 146 optimal weight:    0.8980
   chunk 282 optimal weight:    2.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A2181 GLN
A2636 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.096992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.072660 restraints weight = 79390.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.073458 restraints weight = 54296.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.074107 restraints weight = 40140.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.074509 restraints weight = 36762.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.074583 restraints weight = 32001.836|
|-----------------------------------------------------------------------------|
r_work (final): 0.3574
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3574
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3574 r_free = 0.3574    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      538 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3576 r_free = 0.3576    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      557 |
|-----------------------------------------------------------------------------|
r_final: 0.3576
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7212
moved from start:          0.3302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  23225  Z= 0.144
  Angle     :  0.604  10.217  31478  Z= 0.317
  Chirality :  0.042   0.180   3493
  Planarity :  0.004   0.049   4152
  Dihedral  :  5.423  29.369   3194
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  :  8.42 %
    Favored  : 89.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.21 (0.16), residues: 2910
  helix:  0.95 (0.16), residues: 1098
  sheet: -0.55 (0.21), residues: 537
  loop : -0.84 (0.18), residues: 1275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A1240 
 TYR   0.021   0.002   TYR A 443 
 PHE   0.026   0.002   PHE A1244 
 TRP   0.017   0.001   TRP A2570 
 HIS   0.003   0.001   HIS A 119 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 (23225)
  covalent geometry    : angle       0.60419 (31478)
  hydrogen bonds       : bond        0.04133 ( 1077)
  hydrogen bonds       : angle       4.76682 ( 3135)

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

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

  5820 Ramachandran restraints generated.
    2910 Oldfield, 0 Emsley, 2910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5820 Ramachandran restraints generated.
    2910 Oldfield, 0 Emsley, 2910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 154
  time to evaluate  : 0.686 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 ASP cc_start: 0.8752 (m-30) cc_final: 0.8474 (t0)
REVERT: A  130 MET cc_start: 0.7896 (ttm) cc_final: 0.6723 (tpt)
REVERT: A  443 TYR cc_start: 0.7092 (m-10) cc_final: 0.6863 (m-10)
REVERT: A  533 ASN cc_start: 0.8267 (OUTLIER) cc_final: 0.7279 (m110)
REVERT: A  534 MET cc_start: 0.7633 (mtp) cc_final: 0.6960 (mtm)
REVERT: A  564 LEU cc_start: 0.8741 (tt) cc_final: 0.8526 (tp)
REVERT: A  676 ASN cc_start: 0.8701 (m-40) cc_final: 0.8475 (t0)
REVERT: A  757 PHE cc_start: 0.8316 (m-80) cc_final: 0.7936 (m-10)
REVERT: A 1325 MET cc_start: 0.8231 (mtm) cc_final: 0.7927 (ttp)
REVERT: A 1478 MET cc_start: 0.7872 (mmt) cc_final: 0.7563 (mmm)
REVERT: A 2364 ARG cc_start: 0.6658 (ttt180) cc_final: 0.6349 (tpp80)
  outliers start: 44
  outliers final: 28
  residues processed: 187
  average time/residue: 0.1393
  time to fit residues: 42.9160
Evaluate side-chains
  163 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 134
  time to evaluate  : 0.577 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 ASP
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue   59 LEU
Chi-restraints excluded: chain A residue  222 ASP
Chi-restraints excluded: chain A residue  307 ILE
Chi-restraints excluded: chain A residue  459 VAL
Chi-restraints excluded: chain A residue  463 HIS
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  520 THR
Chi-restraints excluded: chain A residue  525 LEU
Chi-restraints excluded: chain A residue  533 ASN
Chi-restraints excluded: chain A residue  554 SER
Chi-restraints excluded: chain A residue  675 SER
Chi-restraints excluded: chain A residue  695 ASP
Chi-restraints excluded: chain A residue  696 SER
Chi-restraints excluded: chain A residue  717 ILE
Chi-restraints excluded: chain A residue  766 THR
Chi-restraints excluded: chain A residue  822 SER
Chi-restraints excluded: chain A residue 1135 VAL
Chi-restraints excluded: chain A residue 1688 LEU
Chi-restraints excluded: chain A residue 1764 VAL
Chi-restraints excluded: chain A residue 1807 LEU
Chi-restraints excluded: chain A residue 1964 VAL
Chi-restraints excluded: chain A residue 2204 LEU
Chi-restraints excluded: chain A residue 2382 ILE
Chi-restraints excluded: chain A residue 2851 VAL
Chi-restraints excluded: chain A residue 2920 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 291
   random chunks:
   chunk 230 optimal weight:    3.9990
   chunk 18 optimal weight:   10.0000
   chunk 76 optimal weight:    3.9990
   chunk 179 optimal weight:    4.9990
   chunk 80 optimal weight:    3.9990
   chunk 173 optimal weight:    3.9990
   chunk 20 optimal weight:    6.9990
   chunk 282 optimal weight:    5.9990
   chunk 107 optimal weight:    9.9990
   chunk 36 optimal weight:    0.0470
   chunk 244 optimal weight:    1.9990
   overall best weight:    2.8086

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

Flipped N/Q/H residues before XYZ refinement:
A 101 GLN
** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 509 GLN
A 945 HIS
** A1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1234 GLN
A1339 GLN
A1567 ASN
A1765 GLN
A1883 GLN
** A2181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2483 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.094671 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.071390 restraints weight = 80446.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.071604 restraints weight = 47674.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.071546 restraints weight = 41143.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.072159 restraints weight = 38769.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.072563 restraints weight = 32761.641|
|-----------------------------------------------------------------------------|
r_work (final): 0.3527
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3527
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3527 r_free = 0.3527    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      557 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3527 r_free = 0.3527    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      565 |
|-----------------------------------------------------------------------------|
r_final: 0.3527
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7331
moved from start:          0.4155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.072  23225  Z= 0.260
  Angle     :  0.702  13.471  31478  Z= 0.368
  Chirality :  0.045   0.167   3493
  Planarity :  0.005   0.077   4152
  Dihedral  :  5.606  31.886   3194
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.03 %
    Allowed  :  4.64 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 10.66 %
    Favored  : 86.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.04 %

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 aren not related in a simple way.
  whole: -0.44 (0.16), residues: 2910
  helix:  0.90 (0.16), residues: 1101
  sheet: -0.81 (0.21), residues: 557
  loop : -1.05 (0.18), residues: 1252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  84 
 TYR   0.025   0.002   TYR A2313 
 PHE   0.024   0.002   PHE A2590 
 TRP   0.019   0.002   TRP A 124 
 HIS   0.006   0.001   HIS A1822 

Details of bonding type rmsd
  covalent geometry    : bond        0.00599 (23225)
  covalent geometry    : angle       0.70180 (31478)
  hydrogen bonds       : bond        0.04828 ( 1077)
  hydrogen bonds       : angle       5.00067 ( 3135)

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

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

  5820 Ramachandran restraints generated.
    2910 Oldfield, 0 Emsley, 2910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5820 Ramachandran restraints generated.
    2910 Oldfield, 0 Emsley, 2910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 148
  time to evaluate  : 0.743 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 GLN cc_start: 0.7430 (tm-30) cc_final: 0.7028 (tm-30)
REVERT: A  101 GLN cc_start: 0.8892 (OUTLIER) cc_final: 0.8688 (pp30)
REVERT: A  105 ARG cc_start: 0.8156 (mtm110) cc_final: 0.7883 (mtp180)
REVERT: A  124 TRP cc_start: 0.7207 (t60) cc_final: 0.6915 (t60)
REVERT: A  130 MET cc_start: 0.7905 (ttm) cc_final: 0.6731 (tpt)
REVERT: A  482 LYS cc_start: 0.8641 (mmmt) cc_final: 0.8096 (tppt)
REVERT: A  533 ASN cc_start: 0.8251 (OUTLIER) cc_final: 0.7235 (m110)
REVERT: A  593 GLN cc_start: 0.9110 (tt0) cc_final: 0.8791 (mt0)
REVERT: A  676 ASN cc_start: 0.8772 (m-40) cc_final: 0.8524 (t0)
REVERT: A  677 GLU cc_start: 0.8045 (mp0) cc_final: 0.7672 (tp30)
REVERT: A  731 ASN cc_start: 0.8339 (m-40) cc_final: 0.7976 (m110)
REVERT: A 1325 MET cc_start: 0.8218 (mtm) cc_final: 0.7919 (ttp)
REVERT: A 1478 MET cc_start: 0.7933 (mmt) cc_final: 0.7617 (mmm)
REVERT: A 1557 MET cc_start: 0.8423 (tpp) cc_final: 0.8199 (tpp)
  outliers start: 59
  outliers final: 44
  residues processed: 195
  average time/residue: 0.1396
  time to fit residues: 44.4037
Evaluate side-chains
  168 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 122
  time to evaluate  : 0.643 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 ASP
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue   59 LEU
Chi-restraints excluded: chain A residue  101 GLN
Chi-restraints excluded: chain A residue  222 ASP
Chi-restraints excluded: chain A residue  307 ILE
Chi-restraints excluded: chain A residue  459 VAL
Chi-restraints excluded: chain A residue  463 HIS
Chi-restraints excluded: chain A residue  504 THR
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  520 THR
Chi-restraints excluded: chain A residue  525 LEU
Chi-restraints excluded: chain A residue  533 ASN
Chi-restraints excluded: chain A residue  554 SER
Chi-restraints excluded: chain A residue  598 LEU
Chi-restraints excluded: chain A residue  611 GLU
Chi-restraints excluded: chain A residue  652 LEU
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  695 ASP
Chi-restraints excluded: chain A residue  696 SER
Chi-restraints excluded: chain A residue  717 ILE
Chi-restraints excluded: chain A residue  766 THR
Chi-restraints excluded: chain A residue  792 THR
Chi-restraints excluded: chain A residue  822 SER
Chi-restraints excluded: chain A residue  846 LEU
Chi-restraints excluded: chain A residue 1022 PHE
Chi-restraints excluded: chain A residue 1135 VAL
Chi-restraints excluded: chain A residue 1410 SER
Chi-restraints excluded: chain A residue 1567 ASN
Chi-restraints excluded: chain A residue 1688 LEU
Chi-restraints excluded: chain A residue 1764 VAL
Chi-restraints excluded: chain A residue 1807 LEU
Chi-restraints excluded: chain A residue 1827 VAL
Chi-restraints excluded: chain A residue 1964 VAL
Chi-restraints excluded: chain A residue 2032 ILE
Chi-restraints excluded: chain A residue 2204 LEU
Chi-restraints excluded: chain A residue 2382 ILE
Chi-restraints excluded: chain A residue 2445 VAL
Chi-restraints excluded: chain A residue 2507 VAL
Chi-restraints excluded: chain A residue 2547 THR
Chi-restraints excluded: chain A residue 2800 MET
Chi-restraints excluded: chain A residue 2851 VAL
Chi-restraints excluded: chain A residue 2905 VAL
Chi-restraints excluded: chain A residue 2920 ILE
Chi-restraints excluded: chain A residue 2929 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 291
   random chunks:
   chunk 169 optimal weight:    3.9990
   chunk 80 optimal weight:    0.9990
   chunk 159 optimal weight:    0.5980
   chunk 1 optimal weight:    0.9980
   chunk 105 optimal weight:    7.9990
   chunk 255 optimal weight:    0.9990
   chunk 75 optimal weight:    0.4980
   chunk 168 optimal weight:    0.0170
   chunk 193 optimal weight:    1.9990
   chunk 152 optimal weight:   10.0000
   chunk 243 optimal weight:    1.9990
   overall best weight:    0.6220

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

Flipped N/Q/H residues before XYZ refinement:
A 101 GLN
** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 164 GLN
** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1047 HIS
** A1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1234 GLN
A1252 GLN
** A2059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A2181 GLN
A2366 ASN
A2483 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.096526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.071384 restraints weight = 79663.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.072679 restraints weight = 52125.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.073340 restraints weight = 35686.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.073800 restraints weight = 32822.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.073790 restraints weight = 29092.847|
|-----------------------------------------------------------------------------|
r_work (final): 0.3552
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3552
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3552 r_free = 0.3552    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      565 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3553 r_free = 0.3553    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      567 |
|-----------------------------------------------------------------------------|
r_final: 0.3553
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7296
moved from start:          0.4260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  23225  Z= 0.111
  Angle     :  0.565  10.619  31478  Z= 0.298
  Chirality :  0.042   0.166   3493
  Planarity :  0.004   0.051   4152
  Dihedral  :  5.078  28.406   3194
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.03 %
    Allowed  :  3.78 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 11.86 %
    Favored  : 86.48 %
  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 aren not related in a simple way.
  whole: -0.15 (0.16), residues: 2910
  helix:  1.19 (0.16), residues: 1106
  sheet: -0.64 (0.21), residues: 543
  loop : -0.97 (0.18), residues: 1261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 925 
 TYR   0.025   0.001   TYR A 196 
 PHE   0.017   0.001   PHE A 479 
 TRP   0.014   0.001   TRP A2570 
 HIS   0.005   0.001   HIS A  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 (23225)
  covalent geometry    : angle       0.56515 (31478)
  hydrogen bonds       : bond        0.03964 ( 1077)
  hydrogen bonds       : angle       4.63574 ( 3135)

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

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

  5820 Ramachandran restraints generated.
    2910 Oldfield, 0 Emsley, 2910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5820 Ramachandran restraints generated.
    2910 Oldfield, 0 Emsley, 2910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 131
  time to evaluate  : 0.873 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 GLN cc_start: 0.7390 (tm-30) cc_final: 0.7063 (tm-30)
REVERT: A  124 TRP cc_start: 0.7325 (t60) cc_final: 0.6986 (t60)
REVERT: A  130 MET cc_start: 0.7911 (ttm) cc_final: 0.6752 (tpt)
REVERT: A  233 MET cc_start: 0.7572 (mpp) cc_final: 0.7367 (mpp)
REVERT: A  482 LYS cc_start: 0.8606 (mmmt) cc_final: 0.8115 (mmtt)
REVERT: A  533 ASN cc_start: 0.8149 (OUTLIER) cc_final: 0.7256 (m110)
REVERT: A  593 GLN cc_start: 0.9099 (tt0) cc_final: 0.8740 (mt0)
REVERT: A  676 ASN cc_start: 0.8772 (m-40) cc_final: 0.8519 (t0)
REVERT: A  677 GLU cc_start: 0.8117 (mp0) cc_final: 0.7725 (tp30)
REVERT: A  731 ASN cc_start: 0.8390 (m-40) cc_final: 0.7953 (m110)
REVERT: A  809 MET cc_start: 0.8151 (ttp) cc_final: 0.7911 (mtp)
REVERT: A 1062 MET cc_start: 0.7143 (mtt) cc_final: 0.6925 (mmt)
REVERT: A 1325 MET cc_start: 0.8204 (mtm) cc_final: 0.7917 (ttp)
REVERT: A 1478 MET cc_start: 0.7900 (mmt) cc_final: 0.7593 (mmm)
REVERT: A 1557 MET cc_start: 0.8385 (tpp) cc_final: 0.8147 (tpp)
REVERT: A 1574 PHE cc_start: 0.7639 (m-80) cc_final: 0.7205 (m-80)
REVERT: A 2133 ILE cc_start: 0.7942 (OUTLIER) cc_final: 0.7651 (mt)
  outliers start: 40
  outliers final: 28
  residues processed: 162
  average time/residue: 0.1340
  time to fit residues: 35.9710
Evaluate side-chains
  151 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 121
  time to evaluate  : 0.873 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 ASP
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue   59 LEU
Chi-restraints excluded: chain A residue  222 ASP
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  307 ILE
Chi-restraints excluded: chain A residue  459 VAL
Chi-restraints excluded: chain A residue  463 HIS
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  520 THR
Chi-restraints excluded: chain A residue  525 LEU
Chi-restraints excluded: chain A residue  533 ASN
Chi-restraints excluded: chain A residue  554 SER
Chi-restraints excluded: chain A residue  611 GLU
Chi-restraints excluded: chain A residue  652 LEU
Chi-restraints excluded: chain A residue  695 ASP
Chi-restraints excluded: chain A residue  766 THR
Chi-restraints excluded: chain A residue  792 THR
Chi-restraints excluded: chain A residue 1022 PHE
Chi-restraints excluded: chain A residue 1135 VAL
Chi-restraints excluded: chain A residue 1567 ASN
Chi-restraints excluded: chain A residue 1688 LEU
Chi-restraints excluded: chain A residue 1764 VAL
Chi-restraints excluded: chain A residue 1807 LEU
Chi-restraints excluded: chain A residue 2133 ILE
Chi-restraints excluded: chain A residue 2204 LEU
Chi-restraints excluded: chain A residue 2547 THR
Chi-restraints excluded: chain A residue 2800 MET
Chi-restraints excluded: chain A residue 2920 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 291
   random chunks:
   chunk 269 optimal weight:    2.9990
   chunk 152 optimal weight:    0.6980
   chunk 146 optimal weight:    7.9990
   chunk 241 optimal weight:    0.4980
   chunk 179 optimal weight:    1.9990
   chunk 176 optimal weight:    9.9990
   chunk 40 optimal weight:    0.7980
   chunk 33 optimal weight:   10.0000
   chunk 129 optimal weight:    0.0970
   chunk 41 optimal weight:    2.9990
   chunk 254 optimal weight:    0.5980
   overall best weight:    0.5378

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

Flipped N/Q/H residues before XYZ refinement:
** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 518 HIS
** A1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1765 GLN
** A2059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A2538 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.097042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.071425 restraints weight = 80111.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.073547 restraints weight = 50708.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.073975 restraints weight = 32757.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.074348 restraints weight = 29806.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.074653 restraints weight = 27775.665|
|-----------------------------------------------------------------------------|
r_work (final): 0.3589
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3589
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3589 r_free = 0.3589    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      567 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3590 r_free = 0.3590    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      575 |
|-----------------------------------------------------------------------------|
r_final: 0.3590
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7256
moved from start:          0.4416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  23225  Z= 0.103
  Angle     :  0.538  10.345  31478  Z= 0.283
  Chirality :  0.041   0.162   3493
  Planarity :  0.004   0.049   4152
  Dihedral  :  4.752  25.861   3194
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.03 %
    Allowed  :  3.57 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 11.99 %
    Favored  : 86.15 %
  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 aren not related in a simple way.
  whole:  0.04 (0.16), residues: 2910
  helix:  1.40 (0.16), residues: 1103
  sheet: -0.51 (0.22), residues: 543
  loop : -0.93 (0.18), residues: 1264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 195 
 TYR   0.015   0.001   TYR A 443 
 PHE   0.018   0.001   PHE A  64 
 TRP   0.026   0.001   TRP A 556 
 HIS   0.017   0.001   HIS A 119 

Details of bonding type rmsd
  covalent geometry    : bond        0.00216 (23225)
  covalent geometry    : angle       0.53792 (31478)
  hydrogen bonds       : bond        0.03672 ( 1077)
  hydrogen bonds       : angle       4.46697 ( 3135)

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

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

  5820 Ramachandran restraints generated.
    2910 Oldfield, 0 Emsley, 2910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5820 Ramachandran restraints generated.
    2910 Oldfield, 0 Emsley, 2910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 132
  time to evaluate  : 0.892 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 GLN cc_start: 0.7347 (tm-30) cc_final: 0.7007 (tm-30)
REVERT: A   87 MET cc_start: 0.8060 (tmm) cc_final: 0.7839 (tmm)
REVERT: A  124 TRP cc_start: 0.7398 (t60) cc_final: 0.6905 (t60)
REVERT: A  130 MET cc_start: 0.7865 (ttm) cc_final: 0.6733 (tpt)
REVERT: A  233 MET cc_start: 0.7611 (mpp) cc_final: 0.7374 (mpp)
REVERT: A  482 LYS cc_start: 0.8577 (mmmt) cc_final: 0.8089 (mmtt)
REVERT: A  534 MET cc_start: 0.7621 (OUTLIER) cc_final: 0.7401 (ttm)
REVERT: A  564 LEU cc_start: 0.8761 (tt) cc_final: 0.8530 (tp)
REVERT: A  676 ASN cc_start: 0.8777 (m-40) cc_final: 0.8480 (t0)
REVERT: A  677 GLU cc_start: 0.8137 (mp0) cc_final: 0.7738 (tp30)
REVERT: A  725 ASP cc_start: 0.8616 (t70) cc_final: 0.8293 (t0)
REVERT: A  731 ASN cc_start: 0.8424 (m-40) cc_final: 0.8132 (m110)
REVERT: A  809 MET cc_start: 0.8132 (ttp) cc_final: 0.7873 (mtp)
REVERT: A 1062 MET cc_start: 0.7077 (mtt) cc_final: 0.6859 (mmt)
REVERT: A 1325 MET cc_start: 0.8191 (mtm) cc_final: 0.7906 (ttp)
REVERT: A 1478 MET cc_start: 0.7911 (mmt) cc_final: 0.7612 (mmm)
REVERT: A 1488 MET cc_start: 0.7989 (mmt) cc_final: 0.7744 (mmm)
REVERT: A 2133 ILE cc_start: 0.7917 (OUTLIER) cc_final: 0.7650 (mt)
REVERT: A 2311 ARG cc_start: 0.6651 (OUTLIER) cc_final: 0.6057 (ttt90)
  outliers start: 45
  outliers final: 31
  residues processed: 165
  average time/residue: 0.1421
  time to fit residues: 38.7176
Evaluate side-chains
  155 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 121
  time to evaluate  : 0.731 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 ASP
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue   59 LEU
Chi-restraints excluded: chain A residue  222 ASP
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  307 ILE
Chi-restraints excluded: chain A residue  459 VAL
Chi-restraints excluded: chain A residue  463 HIS
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  520 THR
Chi-restraints excluded: chain A residue  534 MET
Chi-restraints excluded: chain A residue  554 SER
Chi-restraints excluded: chain A residue  598 LEU
Chi-restraints excluded: chain A residue  611 GLU
Chi-restraints excluded: chain A residue  643 LEU
Chi-restraints excluded: chain A residue  652 LEU
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  695 ASP
Chi-restraints excluded: chain A residue  696 SER
Chi-restraints excluded: chain A residue  766 THR
Chi-restraints excluded: chain A residue  792 THR
Chi-restraints excluded: chain A residue 1022 PHE
Chi-restraints excluded: chain A residue 1135 VAL
Chi-restraints excluded: chain A residue 1410 SER
Chi-restraints excluded: chain A residue 1688 LEU
Chi-restraints excluded: chain A residue 1764 VAL
Chi-restraints excluded: chain A residue 1765 GLN
Chi-restraints excluded: chain A residue 1807 LEU
Chi-restraints excluded: chain A residue 2133 ILE
Chi-restraints excluded: chain A residue 2204 LEU
Chi-restraints excluded: chain A residue 2311 ARG
Chi-restraints excluded: chain A residue 2547 THR
Chi-restraints excluded: chain A residue 2800 MET
Chi-restraints excluded: chain A residue 2920 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 291
   random chunks:
   chunk 288 optimal weight:   10.0000
   chunk 257 optimal weight:    0.0470
   chunk 116 optimal weight:    0.8980
   chunk 120 optimal weight:    0.7980
   chunk 131 optimal weight:   10.0000
   chunk 275 optimal weight:    5.9990
   chunk 266 optimal weight:    0.9980
   chunk 187 optimal weight:    3.9990
   chunk 225 optimal weight:    1.9990
   chunk 252 optimal weight:    1.9990
   chunk 231 optimal weight:    3.9990
   overall best weight:    0.9480

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

Flipped N/Q/H residues before XYZ refinement:
** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 821 HIS
** A1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1765 GLN
** A2059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.096671 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.071619 restraints weight = 80197.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.073099 restraints weight = 48385.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.073777 restraints weight = 33602.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.074085 restraints weight = 33955.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.073990 restraints weight = 29545.234|
|-----------------------------------------------------------------------------|
r_work (final): 0.3568
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3568
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3568 r_free = 0.3568    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      575 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3568 r_free = 0.3568    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      576 |
|-----------------------------------------------------------------------------|
r_final: 0.3568
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7279
moved from start:          0.4566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  23225  Z= 0.118
  Angle     :  0.542  10.051  31478  Z= 0.285
  Chirality :  0.041   0.262   3493
  Planarity :  0.004   0.049   4152
  Dihedral  :  4.686  25.670   3194
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.03 %
    Allowed  :  3.75 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 12.69 %
    Favored  : 85.52 %
  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 aren not related in a simple way.
  whole:  0.07 (0.16), residues: 2910
  helix:  1.46 (0.16), residues: 1103
  sheet: -0.51 (0.22), residues: 551
  loop : -0.93 (0.18), residues: 1256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A2055 
 TYR   0.013   0.001   TYR A 443 
 PHE   0.011   0.001   PHE A 479 
 TRP   0.015   0.001   TRP A 556 
 HIS   0.020   0.001   HIS A 119 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 (23225)
  covalent geometry    : angle       0.54191 (31478)
  hydrogen bonds       : bond        0.03706 ( 1077)
  hydrogen bonds       : angle       4.45084 ( 3135)

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

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

  5820 Ramachandran restraints generated.
    2910 Oldfield, 0 Emsley, 2910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5820 Ramachandran restraints generated.
    2910 Oldfield, 0 Emsley, 2910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 133
  time to evaluate  : 1.025 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 GLN cc_start: 0.7448 (tm-30) cc_final: 0.7158 (tm-30)
REVERT: A   87 MET cc_start: 0.8089 (tmm) cc_final: 0.7853 (tmm)
REVERT: A  128 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8570 (mm)
REVERT: A  130 MET cc_start: 0.7869 (ttm) cc_final: 0.6736 (tpt)
REVERT: A  233 MET cc_start: 0.7628 (mpp) cc_final: 0.7402 (mpp)
REVERT: A  482 LYS cc_start: 0.8600 (mmmt) cc_final: 0.8126 (mmtt)
REVERT: A  534 MET cc_start: 0.7659 (OUTLIER) cc_final: 0.7435 (ttm)
REVERT: A  564 LEU cc_start: 0.8776 (tt) cc_final: 0.8547 (tp)
REVERT: A  676 ASN cc_start: 0.8789 (m-40) cc_final: 0.8487 (t0)
REVERT: A  677 GLU cc_start: 0.8171 (mp0) cc_final: 0.7663 (tp30)
REVERT: A  725 ASP cc_start: 0.8607 (t70) cc_final: 0.8051 (t0)
REVERT: A  731 ASN cc_start: 0.8418 (m-40) cc_final: 0.8120 (m110)
REVERT: A  809 MET cc_start: 0.8174 (ttp) cc_final: 0.7916 (mtp)
REVERT: A 1062 MET cc_start: 0.7118 (mtt) cc_final: 0.6906 (mmt)
REVERT: A 1325 MET cc_start: 0.8199 (mtm) cc_final: 0.7910 (ttp)
REVERT: A 1478 MET cc_start: 0.7932 (mmt) cc_final: 0.7610 (mmm)
REVERT: A 1574 PHE cc_start: 0.7403 (m-80) cc_final: 0.7145 (m-80)
REVERT: A 2133 ILE cc_start: 0.7983 (OUTLIER) cc_final: 0.7718 (mt)
REVERT: A 2311 ARG cc_start: 0.6763 (OUTLIER) cc_final: 0.6136 (ttt90)
  outliers start: 43
  outliers final: 32
  residues processed: 165
  average time/residue: 0.1561
  time to fit residues: 42.2981
Evaluate side-chains
  160 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 124
  time to evaluate  : 0.962 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 ASP
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  181 THR
Chi-restraints excluded: chain A residue  222 ASP
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  307 ILE
Chi-restraints excluded: chain A residue  459 VAL
Chi-restraints excluded: chain A residue  463 HIS
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  520 THR
Chi-restraints excluded: chain A residue  534 MET
Chi-restraints excluded: chain A residue  554 SER
Chi-restraints excluded: chain A residue  598 LEU
Chi-restraints excluded: chain A residue  611 GLU
Chi-restraints excluded: chain A residue  652 LEU
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  695 ASP
Chi-restraints excluded: chain A residue  717 ILE
Chi-restraints excluded: chain A residue  766 THR
Chi-restraints excluded: chain A residue 1022 PHE
Chi-restraints excluded: chain A residue 1034 VAL
Chi-restraints excluded: chain A residue 1135 VAL
Chi-restraints excluded: chain A residue 1681 VAL
Chi-restraints excluded: chain A residue 1688 LEU
Chi-restraints excluded: chain A residue 1807 LEU
Chi-restraints excluded: chain A residue 1978 ILE
Chi-restraints excluded: chain A residue 2133 ILE
Chi-restraints excluded: chain A residue 2191 GLN
Chi-restraints excluded: chain A residue 2204 LEU
Chi-restraints excluded: chain A residue 2291 ASN
Chi-restraints excluded: chain A residue 2311 ARG
Chi-restraints excluded: chain A residue 2547 THR
Chi-restraints excluded: chain A residue 2655 VAL
Chi-restraints excluded: chain A residue 2800 MET
Chi-restraints excluded: chain A residue 2920 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 291
   random chunks:
   chunk 236 optimal weight:    0.9980
   chunk 217 optimal weight:   20.0000
   chunk 107 optimal weight:   10.0000
   chunk 92 optimal weight:    8.9990
   chunk 144 optimal weight:    8.9990
   chunk 227 optimal weight:    2.9990
   chunk 133 optimal weight:    0.9980
   chunk 192 optimal weight:    2.9990
   chunk 101 optimal weight:    4.9990
   chunk 136 optimal weight:    0.0980
   chunk 119 optimal weight:    4.9990
   overall best weight:    1.6184

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

Flipped N/Q/H residues before XYZ refinement:
** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1765 GLN
A2058 HIS
** A2059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2483 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.095183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.071365 restraints weight = 79372.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.072172 restraints weight = 49772.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.072759 restraints weight = 38606.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.072942 restraints weight = 38925.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.073061 restraints weight = 32805.384|
|-----------------------------------------------------------------------------|
r_work (final): 0.3554
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3554
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3554 r_free = 0.3554    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      576 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3554 r_free = 0.3554    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      580 |
|-----------------------------------------------------------------------------|
r_final: 0.3554
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7305
moved from start:          0.4929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  23225  Z= 0.164
  Angle     :  0.593  12.171  31478  Z= 0.309
  Chirality :  0.042   0.198   3493
  Planarity :  0.004   0.051   4152
  Dihedral  :  4.843  27.548   3194
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.03 %
    Allowed  :  4.54 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 13.23 %
    Favored  : 84.74 %
  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 aren not related in a simple way.
  whole: -0.05 (0.16), residues: 2910
  helix:  1.36 (0.16), residues: 1105
  sheet: -0.60 (0.22), residues: 551
  loop : -1.00 (0.18), residues: 1254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1596 
 TYR   0.023   0.002   TYR A 602 
 PHE   0.016   0.002   PHE A1789 
 TRP   0.028   0.002   TRP A 124 
 HIS   0.022   0.001   HIS A 119 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 (23225)
  covalent geometry    : angle       0.59303 (31478)
  hydrogen bonds       : bond        0.04094 ( 1077)
  hydrogen bonds       : angle       4.57211 ( 3135)

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

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

  5820 Ramachandran restraints generated.
    2910 Oldfield, 0 Emsley, 2910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5820 Ramachandran restraints generated.
    2910 Oldfield, 0 Emsley, 2910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 134
  time to evaluate  : 0.995 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 GLN cc_start: 0.7619 (tm-30) cc_final: 0.7343 (tm-30)
REVERT: A   87 MET cc_start: 0.8179 (tmm) cc_final: 0.7875 (tmm)
REVERT: A  128 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8589 (mm)
REVERT: A  130 MET cc_start: 0.7964 (ttm) cc_final: 0.6844 (tpt)
REVERT: A  482 LYS cc_start: 0.8515 (mmmt) cc_final: 0.8074 (mmtt)
REVERT: A  533 ASN cc_start: 0.8251 (OUTLIER) cc_final: 0.7271 (m110)
REVERT: A  534 MET cc_start: 0.7850 (OUTLIER) cc_final: 0.7300 (ttm)
REVERT: A  564 LEU cc_start: 0.8775 (tt) cc_final: 0.8553 (tp)
REVERT: A  676 ASN cc_start: 0.8766 (m-40) cc_final: 0.8553 (t0)
REVERT: A  677 GLU cc_start: 0.8243 (mp0) cc_final: 0.7766 (tp30)
REVERT: A  725 ASP cc_start: 0.8567 (t70) cc_final: 0.8219 (t0)
REVERT: A 1105 MET cc_start: 0.6567 (tpp) cc_final: 0.5769 (ttp)
REVERT: A 1325 MET cc_start: 0.8051 (mtm) cc_final: 0.7793 (ttp)
REVERT: A 1478 MET cc_start: 0.8009 (mmt) cc_final: 0.7675 (mmm)
REVERT: A 1574 PHE cc_start: 0.7451 (m-80) cc_final: 0.7186 (m-80)
REVERT: A 2133 ILE cc_start: 0.8066 (OUTLIER) cc_final: 0.7794 (mt)
REVERT: A 2311 ARG cc_start: 0.7047 (OUTLIER) cc_final: 0.6416 (ttt90)
  outliers start: 49
  outliers final: 38
  residues processed: 174
  average time/residue: 0.1637
  time to fit residues: 46.1937
Evaluate side-chains
  164 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 121
  time to evaluate  : 0.932 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 ASP
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue   59 LEU
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  181 THR
Chi-restraints excluded: chain A residue  222 ASP
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  307 ILE
Chi-restraints excluded: chain A residue  459 VAL
Chi-restraints excluded: chain A residue  463 HIS
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  520 THR
Chi-restraints excluded: chain A residue  533 ASN
Chi-restraints excluded: chain A residue  534 MET
Chi-restraints excluded: chain A residue  554 SER
Chi-restraints excluded: chain A residue  598 LEU
Chi-restraints excluded: chain A residue  611 GLU
Chi-restraints excluded: chain A residue  652 LEU
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  695 ASP
Chi-restraints excluded: chain A residue  717 ILE
Chi-restraints excluded: chain A residue  766 THR
Chi-restraints excluded: chain A residue 1022 PHE
Chi-restraints excluded: chain A residue 1034 VAL
Chi-restraints excluded: chain A residue 1135 VAL
Chi-restraints excluded: chain A residue 1568 VAL
Chi-restraints excluded: chain A residue 1681 VAL
Chi-restraints excluded: chain A residue 1688 LEU
Chi-restraints excluded: chain A residue 1807 LEU
Chi-restraints excluded: chain A residue 1825 ASN
Chi-restraints excluded: chain A residue 1827 VAL
Chi-restraints excluded: chain A residue 1978 ILE
Chi-restraints excluded: chain A residue 2133 ILE
Chi-restraints excluded: chain A residue 2191 GLN
Chi-restraints excluded: chain A residue 2204 LEU
Chi-restraints excluded: chain A residue 2291 ASN
Chi-restraints excluded: chain A residue 2311 ARG
Chi-restraints excluded: chain A residue 2547 THR
Chi-restraints excluded: chain A residue 2655 VAL
Chi-restraints excluded: chain A residue 2800 MET
Chi-restraints excluded: chain A residue 2861 HIS
Chi-restraints excluded: chain A residue 2920 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 291
   random chunks:
   chunk 249 optimal weight:    0.9990
   chunk 188 optimal weight:    0.9980
   chunk 151 optimal weight:    4.9990
   chunk 71 optimal weight:    6.9990
   chunk 236 optimal weight:    2.9990
   chunk 224 optimal weight:    0.8980
   chunk 97 optimal weight:    4.9990
   chunk 222 optimal weight:    0.6980
   chunk 64 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9980
   chunk 218 optimal weight:    7.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 517 ASN
** A1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1765 GLN
** A2059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.095875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.072020 restraints weight = 79809.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.072623 restraints weight = 54385.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.074176 restraints weight = 38834.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.074321 restraints weight = 32735.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.074443 restraints weight = 29966.584|
|-----------------------------------------------------------------------------|
r_work (final): 0.3585
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3585
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3585 r_free = 0.3585    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      580 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3585 r_free = 0.3585    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      578 |
|-----------------------------------------------------------------------------|
r_final: 0.3585
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7248
moved from start:          0.5033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  23225  Z= 0.119
  Angle     :  0.564  12.043  31478  Z= 0.294
  Chirality :  0.041   0.288   3493
  Planarity :  0.004   0.048   4152
  Dihedral  :  4.672  25.703   3194
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.03 %
    Allowed  :  3.81 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 13.52 %
    Favored  : 84.57 %
  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 aren not related in a simple way.
  whole:  0.01 (0.16), residues: 2910
  helix:  1.40 (0.16), residues: 1104
  sheet: -0.52 (0.22), residues: 551
  loop : -0.97 (0.18), residues: 1255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 758 
 TYR   0.027   0.001   TYR A 602 
 PHE   0.010   0.001   PHE A 480 
 TRP   0.057   0.002   TRP A 124 
 HIS   0.025   0.001   HIS A 119 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 (23225)
  covalent geometry    : angle       0.56354 (31478)
  hydrogen bonds       : bond        0.03788 ( 1077)
  hydrogen bonds       : angle       4.48660 ( 3135)

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

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

  5820 Ramachandran restraints generated.
    2910 Oldfield, 0 Emsley, 2910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5820 Ramachandran restraints generated.
    2910 Oldfield, 0 Emsley, 2910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 134
  time to evaluate  : 0.888 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 GLN cc_start: 0.7613 (tm-30) cc_final: 0.7335 (tm-30)
REVERT: A  130 MET cc_start: 0.7932 (ttm) cc_final: 0.6806 (tpt)
REVERT: A  482 LYS cc_start: 0.8363 (mmmt) cc_final: 0.7987 (mmtt)
REVERT: A  491 MET cc_start: 0.5268 (tpt) cc_final: 0.5004 (tpt)
REVERT: A  533 ASN cc_start: 0.8224 (OUTLIER) cc_final: 0.7280 (m110)
REVERT: A  534 MET cc_start: 0.7803 (OUTLIER) cc_final: 0.7305 (ttm)
REVERT: A  564 LEU cc_start: 0.8765 (tt) cc_final: 0.8554 (tp)
REVERT: A  677 GLU cc_start: 0.8204 (mp0) cc_final: 0.7716 (tp30)
REVERT: A  725 ASP cc_start: 0.8545 (t70) cc_final: 0.8011 (t0)
REVERT: A  809 MET cc_start: 0.8187 (ttp) cc_final: 0.7917 (mtp)
REVERT: A  815 MET cc_start: 0.8806 (mmt) cc_final: 0.8173 (mmt)
REVERT: A 1105 MET cc_start: 0.6497 (tpp) cc_final: 0.5744 (ttp)
REVERT: A 1325 MET cc_start: 0.8014 (mtm) cc_final: 0.7763 (ttp)
REVERT: A 1478 MET cc_start: 0.7972 (mmt) cc_final: 0.7638 (mmm)
REVERT: A 2133 ILE cc_start: 0.8030 (OUTLIER) cc_final: 0.7787 (mt)
REVERT: A 2311 ARG cc_start: 0.6878 (OUTLIER) cc_final: 0.6203 (ttt90)
  outliers start: 46
  outliers final: 40
  residues processed: 169
  average time/residue: 0.1505
  time to fit residues: 42.0447
Evaluate side-chains
  171 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 127
  time to evaluate  : 0.883 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 ASP
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue  181 THR
Chi-restraints excluded: chain A residue  222 ASP
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  307 ILE
Chi-restraints excluded: chain A residue  415 LEU
Chi-restraints excluded: chain A residue  459 VAL
Chi-restraints excluded: chain A residue  463 HIS
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  520 THR
Chi-restraints excluded: chain A residue  533 ASN
Chi-restraints excluded: chain A residue  534 MET
Chi-restraints excluded: chain A residue  554 SER
Chi-restraints excluded: chain A residue  611 GLU
Chi-restraints excluded: chain A residue  652 LEU
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  695 ASP
Chi-restraints excluded: chain A residue  696 SER
Chi-restraints excluded: chain A residue  712 VAL
Chi-restraints excluded: chain A residue  717 ILE
Chi-restraints excluded: chain A residue  766 THR
Chi-restraints excluded: chain A residue 1022 PHE
Chi-restraints excluded: chain A residue 1034 VAL
Chi-restraints excluded: chain A residue 1135 VAL
Chi-restraints excluded: chain A residue 1452 VAL
Chi-restraints excluded: chain A residue 1568 VAL
Chi-restraints excluded: chain A residue 1688 LEU
Chi-restraints excluded: chain A residue 1765 GLN
Chi-restraints excluded: chain A residue 1807 LEU
Chi-restraints excluded: chain A residue 1825 ASN
Chi-restraints excluded: chain A residue 1827 VAL
Chi-restraints excluded: chain A residue 1964 VAL
Chi-restraints excluded: chain A residue 1978 ILE
Chi-restraints excluded: chain A residue 2133 ILE
Chi-restraints excluded: chain A residue 2191 GLN
Chi-restraints excluded: chain A residue 2204 LEU
Chi-restraints excluded: chain A residue 2291 ASN
Chi-restraints excluded: chain A residue 2311 ARG
Chi-restraints excluded: chain A residue 2547 THR
Chi-restraints excluded: chain A residue 2655 VAL
Chi-restraints excluded: chain A residue 2800 MET
Chi-restraints excluded: chain A residue 2861 HIS
Chi-restraints excluded: chain A residue 2920 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 291
   random chunks:
   chunk 157 optimal weight:    0.5980
   chunk 43 optimal weight:    0.0010
   chunk 137 optimal weight:   10.0000
   chunk 134 optimal weight:    0.0370
   chunk 215 optimal weight:    3.9990
   chunk 96 optimal weight:    9.9990
   chunk 149 optimal weight:    1.9990
   chunk 17 optimal weight:    7.9990
   chunk 270 optimal weight:    1.9990
   chunk 143 optimal weight:    5.9990
   chunk 243 optimal weight:    4.9990
   overall best weight:    0.9268

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

Flipped N/Q/H residues before XYZ refinement:
** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 409 HIS
A 676 ASN
** A1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1765 GLN
** A2059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.095745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.070928 restraints weight = 79283.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.071863 restraints weight = 51808.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.073298 restraints weight = 36610.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.073207 restraints weight = 33341.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.073327 restraints weight = 29010.393|
|-----------------------------------------------------------------------------|
r_work (final): 0.3561
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3561
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3561 r_free = 0.3561    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      578 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3561 r_free = 0.3561    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      578 |
|-----------------------------------------------------------------------------|
r_final: 0.3561
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7298
moved from start:          0.5132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058  23225  Z= 0.123
  Angle     :  0.569  12.108  31478  Z= 0.295
  Chirality :  0.042   0.236   3493
  Planarity :  0.004   0.047   4152
  Dihedral  :  4.606  25.037   3194
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.03 %
    Allowed  :  4.26 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 13.73 %
    Favored  : 84.32 %
  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 aren not related in a simple way.
  whole:  0.05 (0.16), residues: 2910
  helix:  1.44 (0.16), residues: 1099
  sheet: -0.51 (0.22), residues: 546
  loop : -0.93 (0.18), residues: 1265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 758 
 TYR   0.027   0.001   TYR A 602 
 PHE   0.010   0.001   PHE A1789 
 TRP   0.043   0.001   TRP A 124 
 HIS   0.026   0.001   HIS A 119 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 (23225)
  covalent geometry    : angle       0.56912 (31478)
  hydrogen bonds       : bond        0.03757 ( 1077)
  hydrogen bonds       : angle       4.45865 ( 3135)

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

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

  5820 Ramachandran restraints generated.
    2910 Oldfield, 0 Emsley, 2910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5820 Ramachandran restraints generated.
    2910 Oldfield, 0 Emsley, 2910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 133
  time to evaluate  : 0.990 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 GLN cc_start: 0.7619 (tm-30) cc_final: 0.7352 (tm-30)
REVERT: A  130 MET cc_start: 0.7964 (ttm) cc_final: 0.6844 (tpt)
REVERT: A  195 ARG cc_start: 0.8522 (mmp80) cc_final: 0.7859 (mmm160)
REVERT: A  225 PRO cc_start: 0.7307 (Cg_exo) cc_final: 0.7071 (Cg_endo)
REVERT: A  482 LYS cc_start: 0.8379 (mmmt) cc_final: 0.8042 (mmtt)
REVERT: A  533 ASN cc_start: 0.8210 (OUTLIER) cc_final: 0.7291 (m110)
REVERT: A  534 MET cc_start: 0.7855 (OUTLIER) cc_final: 0.7393 (ttm)
REVERT: A  564 LEU cc_start: 0.8756 (tt) cc_final: 0.8548 (tp)
REVERT: A  677 GLU cc_start: 0.8227 (mp0) cc_final: 0.7792 (tp30)
REVERT: A  725 ASP cc_start: 0.8543 (t70) cc_final: 0.7933 (t0)
REVERT: A  809 MET cc_start: 0.8248 (ttp) cc_final: 0.7968 (mtp)
REVERT: A 1105 MET cc_start: 0.6470 (tpp) cc_final: 0.5704 (ttp)
REVERT: A 1325 MET cc_start: 0.8028 (mtm) cc_final: 0.7764 (ttp)
REVERT: A 1478 MET cc_start: 0.7987 (mmt) cc_final: 0.7656 (mmm)
REVERT: A 2133 ILE cc_start: 0.8023 (OUTLIER) cc_final: 0.7798 (mt)
REVERT: A 2311 ARG cc_start: 0.6773 (OUTLIER) cc_final: 0.6098 (ttt90)
  outliers start: 47
  outliers final: 40
  residues processed: 169
  average time/residue: 0.1495
  time to fit residues: 41.9261
Evaluate side-chains
  171 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 127
  time to evaluate  : 0.889 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 ASP
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue  181 THR
Chi-restraints excluded: chain A residue  222 ASP
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  307 ILE
Chi-restraints excluded: chain A residue  409 HIS
Chi-restraints excluded: chain A residue  415 LEU
Chi-restraints excluded: chain A residue  459 VAL
Chi-restraints excluded: chain A residue  463 HIS
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  520 THR
Chi-restraints excluded: chain A residue  533 ASN
Chi-restraints excluded: chain A residue  534 MET
Chi-restraints excluded: chain A residue  554 SER
Chi-restraints excluded: chain A residue  611 GLU
Chi-restraints excluded: chain A residue  652 LEU
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  695 ASP
Chi-restraints excluded: chain A residue  712 VAL
Chi-restraints excluded: chain A residue  766 THR
Chi-restraints excluded: chain A residue 1022 PHE
Chi-restraints excluded: chain A residue 1034 VAL
Chi-restraints excluded: chain A residue 1135 VAL
Chi-restraints excluded: chain A residue 1452 VAL
Chi-restraints excluded: chain A residue 1568 VAL
Chi-restraints excluded: chain A residue 1688 LEU
Chi-restraints excluded: chain A residue 1765 GLN
Chi-restraints excluded: chain A residue 1807 LEU
Chi-restraints excluded: chain A residue 1825 ASN
Chi-restraints excluded: chain A residue 1827 VAL
Chi-restraints excluded: chain A residue 1964 VAL
Chi-restraints excluded: chain A residue 1978 ILE
Chi-restraints excluded: chain A residue 2133 ILE
Chi-restraints excluded: chain A residue 2191 GLN
Chi-restraints excluded: chain A residue 2204 LEU
Chi-restraints excluded: chain A residue 2291 ASN
Chi-restraints excluded: chain A residue 2311 ARG
Chi-restraints excluded: chain A residue 2547 THR
Chi-restraints excluded: chain A residue 2558 VAL
Chi-restraints excluded: chain A residue 2655 VAL
Chi-restraints excluded: chain A residue 2800 MET
Chi-restraints excluded: chain A residue 2861 HIS
Chi-restraints excluded: chain A residue 2920 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 291
   random chunks:
   chunk 30 optimal weight:    0.0980
   chunk 194 optimal weight:    2.9990
   chunk 107 optimal weight:    7.9990
   chunk 167 optimal weight:    1.9990
   chunk 254 optimal weight:    0.3980
   chunk 101 optimal weight:    9.9990
   chunk 125 optimal weight:    8.9990
   chunk 118 optimal weight:    0.9980
   chunk 273 optimal weight:    1.9990
   chunk 124 optimal weight:    0.9980
   chunk 209 optimal weight:    5.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 409 HIS
** A 707 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1765 GLN
** A2059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.095817 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.071999 restraints weight = 79174.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.072972 restraints weight = 49963.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.074028 restraints weight = 36733.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.074271 restraints weight = 33657.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.074313 restraints weight = 28960.369|
|-----------------------------------------------------------------------------|
r_work (final): 0.3581
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3581
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3581 r_free = 0.3581    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      578 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3581 r_free = 0.3581    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      579 |
|-----------------------------------------------------------------------------|
r_final: 0.3581
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7254
moved from start:          0.5185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  23225  Z= 0.118
  Angle     :  0.564  12.070  31478  Z= 0.291
  Chirality :  0.041   0.191   3493
  Planarity :  0.004   0.047   4152
  Dihedral  :  4.567  24.694   3194
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.03 %
    Allowed  :  4.12 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 13.81 %
    Favored  : 84.24 %
  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 aren not related in a simple way.
  whole:  0.09 (0.16), residues: 2910
  helix:  1.47 (0.16), residues: 1098
  sheet: -0.47 (0.22), residues: 545
  loop : -0.92 (0.18), residues: 1267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 758 
 TYR   0.026   0.001   TYR A 602 
 PHE   0.012   0.001   PHE A 480 
 TRP   0.035   0.001   TRP A 124 
 HIS   0.028   0.001   HIS A 119 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 (23225)
  covalent geometry    : angle       0.56428 (31478)
  hydrogen bonds       : bond        0.03709 ( 1077)
  hydrogen bonds       : angle       4.40769 ( 3135)

===============================================================================
Job complete
usr+sys time: 4539.60 seconds
wall clock time: 78 minutes 44.36 seconds (4724.36 seconds total)