Starting phenix.real_space_refine
on Wed Mar  4 19:24:16 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ojk_12954/03_2026/7ojk_12954.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ojk_12954/03_2026/7ojk_12954.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.89
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ojk_12954/03_2026/7ojk_12954.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ojk_12954/03_2026/7ojk_12954.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ojk_12954/03_2026/7ojk_12954.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ojk_12954/03_2026/7ojk_12954.cif"
  }
  resolution = 3.89
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.011
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: 6
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     P      20      5.49       5
     S      91      5.16       5
     C    9691      2.51       5
     N    2584      2.21       5
     O    2929      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 15316
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "L"
      Number of atoms: 14866
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1843, 14866
          Classifications: {'peptide': 1843}
          Incomplete info: {'backbone_only': 1}
          Link IDs: {'PTRANS': 62, 'TRANS': 1780}
          Chain breaks: 12
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "E"
      Number of atoms: 193
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 193
          Classifications: {'RNA': 9}
          Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 4}
          Link IDs: {'rna3p': 8}
    Chain: "D"
      Number of atoms: 256
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 256
          Classifications: {'RNA': 12}
          Modifications used: {'5*END': 1, 'rna2p_pur': 2, 'rna3p_pur': 5, 'rna3p_pyr': 5}
          Link IDs: {'rna2p': 2, 'rna3p': 9}
    Chain: "L"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   2531  SG  CYS L 321      44.699 105.525  90.938  1.00135.50           S
  ATOM   2916  SG  CYS L 366      42.614 104.378  93.658  1.00140.11           S

  Time building chain proxies: 3.57, per 1000 atoms: 0.23
  Number of scatterers: 15316
  At special positions: 0
  Unit cell: (113.97, 126.15, 147.03, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      1     29.99
     S      91     16.00
     P      20     15.00
     O    2929      8.00
     N    2584      7.00
     C    9691      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: 1.48
  Conformation dependent library (CDL) restraints added in 664.8 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN L2301 "
        pdb="ZN    ZN L2301 " - pdb=" NE2 HIS L 364 "
        pdb="ZN    ZN L2301 " - pdb=" SG  CYS L 366 "
        pdb="ZN    ZN L2301 " - pdb=" SG  CYS L 321 "


  3634 Ramachandran restraints generated.
    1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3528

  Finding SS restraints...
    Secondary structure from input PDB file:
      85 helices and 9 sheets defined
      55.3% alpha, 3.7% beta
      3 base pairs and 8 stacking pairs defined.
    Time for finding SS restraints: 1.83
  Creating SS restraints...
    Processing helix  chain 'L' and resid 1 through 15
      removed outlier: 3.578A  pdb=" N   MET L   5 " --> pdb=" O   MET L   1 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 19 through 21
      No H-bonds generated for 'chain 'L' and resid 19 through 21'
    Processing helix  chain 'L' and resid 22 through 30
    Processing helix  chain 'L' and resid 34 through 59
    Processing helix  chain 'L' and resid 68 through 75
    Processing helix  chain 'L' and resid 112 through 131
      removed outlier: 3.636A  pdb=" N   TYR L 116 " --> pdb=" O   PHE L 112 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   LEU L 126 " --> pdb=" O   LYS L 122 " (cutoff:3.500A)
      removed outlier: 4.595A  pdb=" N   ASP L 129 " --> pdb=" O   GLN L 125 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 132 through 134
      No H-bonds generated for 'chain 'L' and resid 132 through 134'
    Processing helix  chain 'L' and resid 153 through 169
      removed outlier: 3.726A  pdb=" N   THR L 163 " --> pdb=" O   LYS L 159 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 170 through 176
    Processing helix  chain 'L' and resid 179 through 188
      removed outlier: 3.532A  pdb=" N   GLU L 188 " --> pdb=" O   SER L 184 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 200 through 206
    Processing helix  chain 'L' and resid 214 through 224
      removed outlier: 3.864A  pdb=" N   ILE L 218 " --> pdb=" O   TYR L 214 " (cutoff:3.500A)
      removed outlier: 4.531A  pdb=" N   GLY L 224 " --> pdb=" O   SER L 220 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 232 through 251
      removed outlier: 4.140A  pdb=" N   LEU L 236 " --> pdb=" O   HIS L 232 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   GLN L 237 " --> pdb=" O   GLU L 233 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   LYS L 251 " --> pdb=" O   ASN L 247 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 262 through 272
    Processing helix  chain 'L' and resid 284 through 293
      removed outlier: 3.882A  pdb=" N   LYS L 293 " --> pdb=" O   ILE L 289 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 296 through 303
      removed outlier: 3.534A  pdb=" N   TYR L 303 " --> pdb=" O   LEU L 299 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 324 through 336
      removed outlier: 3.628A  pdb=" N   LEU L 336 " --> pdb=" O   LYS L 332 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 345 through 365
      removed outlier: 3.738A  pdb=" N   PHE L 349 " --> pdb=" O   LEU L 345 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   ILE L 353 " --> pdb=" O   PHE L 349 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   THR L 362 " --> pdb=" O   ILE L 358 " (cutoff:3.500A)
      removed outlier: 4.470A  pdb=" N   ARG L 363 " --> pdb=" O   HIS L 359 " (cutoff:3.500A)
      removed outlier: 4.176A  pdb=" N   HIS L 364 " --> pdb=" O   ASP L 360 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 385 through 405
    Processing helix  chain 'L' and resid 412 through 433
    Processing helix  chain 'L' and resid 453 through 459
    Processing helix  chain 'L' and resid 491 through 506
      removed outlier: 4.129A  pdb=" N   GLU L 495 " --> pdb=" O   SER L 491 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 507 through 509
      No H-bonds generated for 'chain 'L' and resid 507 through 509'
    Processing helix  chain 'L' and resid 522 through 527
      removed outlier: 3.939A  pdb=" N   TYR L 526 " --> pdb=" O   PRO L 523 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 589 through 600
      removed outlier: 3.816A  pdb=" N   TRP L 600 " --> pdb=" O   THR L 596 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 604 through 609
      removed outlier: 6.017A  pdb=" N   GLU L 609 " --> pdb=" O   GLU L 606 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 610 through 628
      removed outlier: 3.512A  pdb=" N   ILE L 614 " --> pdb=" O   GLN L 610 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 630 through 632
      No H-bonds generated for 'chain 'L' and resid 630 through 632'
    Processing helix  chain 'L' and resid 633 through 648
      removed outlier: 3.845A  pdb=" N   LEU L 637 " --> pdb=" O   SER L 633 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   LEU L 640 " --> pdb=" O   LEU L 636 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   ARG L 641 " --> pdb=" O   LEU L 637 " (cutoff:3.500A)
      removed outlier: 4.421A  pdb=" N   TYR L 642 " --> pdb=" O   GLN L 638 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   PHE L 643 " --> pdb=" O   ASN L 639 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 656 through 660
    Processing helix  chain 'L' and resid 667 through 685
    Processing helix  chain 'L' and resid 691 through 704
      removed outlier: 3.985A  pdb=" N   ARG L 695 " --> pdb=" O   MET L 691 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 716 through 729
      removed outlier: 3.991A  pdb=" N   LYS L 722 " --> pdb=" O   THR L 718 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   CYS L 723 " --> pdb=" O   ASP L 719 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 729 through 734
      removed outlier: 4.314A  pdb=" N   GLU L 733 " --> pdb=" O   GLU L 729 " (cutoff:3.500A)
      removed outlier: 4.392A  pdb=" N   PHE L 734 " --> pdb=" O   PRO L 730 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 729 through 734'
    Processing helix  chain 'L' and resid 746 through 761
      removed outlier: 3.678A  pdb=" N   LEU L 750 " --> pdb=" O   THR L 746 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   LEU L 761 " --> pdb=" O   ALA L 757 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 780 through 793
    Processing helix  chain 'L' and resid 798 through 803
    Processing helix  chain 'L' and resid 842 through 861
      removed outlier: 3.651A  pdb=" N   LEU L 846 " --> pdb=" O   ASP L 842 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 862 through 865
    Processing helix  chain 'L' and resid 870 through 884
    Processing helix  chain 'L' and resid 897 through 905
    Processing helix  chain 'L' and resid 908 through 925
      removed outlier: 3.607A  pdb=" N   ASP L 912 " --> pdb=" O   SER L 908 " (cutoff:3.500A)
      removed outlier: 4.309A  pdb=" N   GLU L 916 " --> pdb=" O   ASP L 912 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   TYR L 925 " --> pdb=" O   ILE L 921 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 943 through 949
    Processing helix  chain 'L' and resid 952 through 964
      removed outlier: 4.100A  pdb=" N   ILE L 956 " --> pdb=" O   ASN L 952 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 977 through 991
      removed outlier: 3.953A  pdb=" N   TYR L 981 " --> pdb=" O   PRO L 977 " (cutoff:3.500A)
      removed outlier: 4.068A  pdb=" N   GLU L 982 " --> pdb=" O   GLY L 978 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   ASN L 991 " --> pdb=" O   ALA L 987 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 991 through 999
    Processing helix  chain 'L' and resid 1014 through 1024
      removed outlier: 3.821A  pdb=" N   PHE L1022 " --> pdb=" O   THR L1018 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ASP L1023 " --> pdb=" O   ARG L1019 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1025 through 1038
    Processing helix  chain 'L' and resid 1059 through 1067
      removed outlier: 3.841A  pdb=" N   LEU L1063 " --> pdb=" O   ASP L1059 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1075 through 1084
      removed outlier: 3.553A  pdb=" N   LEU L1079 " --> pdb=" O   ASN L1075 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   LYS L1081 " --> pdb=" O   GLU L1077 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1092 through 1096
      removed outlier: 3.532A  pdb=" N   LEU L1096 " --> pdb=" O   LEU L1093 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1137 through 1156
      removed outlier: 3.940A  pdb=" N   LEU L1146 " --> pdb=" O   MET L1142 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   ILE L1147 " --> pdb=" O   PHE L1143 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1168 through 1180
    Processing helix  chain 'L' and resid 1199 through 1209
      removed outlier: 3.613A  pdb=" N   PHE L1203 " --> pdb=" O   CYS L1199 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   ASN L1209 " --> pdb=" O   ALA L1205 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1218 through 1235
    Processing helix  chain 'L' and resid 1242 through 1259
      removed outlier: 3.698A  pdb=" N   VAL L1246 " --> pdb=" O   PRO L1242 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   LEU L1258 " --> pdb=" O   ILE L1254 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1267 through 1278
      removed outlier: 3.814A  pdb=" N   ASP L1271 " --> pdb=" O   SER L1267 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   ASN L1276 " --> pdb=" O   PHE L1272 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1297 through 1320
    Processing helix  chain 'L' and resid 1338 through 1345
      removed outlier: 3.787A  pdb=" N   MET L1345 " --> pdb=" O   LEU L1341 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1348 through 1366
    Processing helix  chain 'L' and resid 1396 through 1406
      removed outlier: 3.774A  pdb=" N   PHE L1400 " --> pdb=" O   LEU L1396 " (cutoff:3.500A)
      removed outlier: 4.166A  pdb=" N   HIS L1406 " --> pdb=" O   ALA L1402 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1414 through 1429
      removed outlier: 4.396A  pdb=" N   GLU L1418 " --> pdb=" O   HIS L1414 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   ALA L1429 " --> pdb=" O   ASP L1425 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1433 through 1450
      removed outlier: 3.704A  pdb=" N   CYS L1437 " --> pdb=" O   PRO L1433 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1466 through 1471
      removed outlier: 4.080A  pdb=" N   VAL L1470 " --> pdb=" O   VAL L1466 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   ASP L1471 " --> pdb=" O   ARG L1467 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 1466 through 1471'
    Processing helix  chain 'L' and resid 1475 through 1486
    Processing helix  chain 'L' and resid 1489 through 1506
      removed outlier: 3.531A  pdb=" N   ILE L1493 " --> pdb=" O   ALA L1489 " (cutoff:3.500A)
      removed outlier: 5.144A  pdb=" N   SER L1495 " --> pdb=" O   GLY L1491 " (cutoff:3.500A)
      removed outlier: 4.091A  pdb=" N   THR L1506 " --> pdb=" O   ASN L1502 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1524 through 1534
    Processing helix  chain 'L' and resid 1613 through 1624
      removed outlier: 3.934A  pdb=" N   LEU L1624 " --> pdb=" O   LEU L1620 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1639 through 1649
      removed outlier: 4.191A  pdb=" N   ILE L1649 " --> pdb=" O   LEU L1645 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1667 through 1671
    Processing helix  chain 'L' and resid 1684 through 1699
    Processing helix  chain 'L' and resid 1700 through 1705
      removed outlier: 3.500A  pdb=" N   VAL L1703 " --> pdb=" O   GLY L1700 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   LEU L1704 " --> pdb=" O   ALA L1701 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   GLY L1705 " --> pdb=" O   TRP L1702 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 1700 through 1705'
    Processing helix  chain 'L' and resid 1740 through 1751
    Processing helix  chain 'L' and resid 1751 through 1757
      removed outlier: 3.691A  pdb=" N   LYS L1757 " --> pdb=" O   SER L1753 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1759 through 1764
    Processing helix  chain 'L' and resid 1777 through 1790
    Processing helix  chain 'L' and resid 1835 through 1852
      removed outlier: 3.830A  pdb=" N   TYR L1850 " --> pdb=" O   TYR L1846 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   VAL L1851 " --> pdb=" O   PHE L1847 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ARG L1852 " --> pdb=" O   GLU L1848 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1878 through 1884
      removed outlier: 3.834A  pdb=" N   LEU L1882 " --> pdb=" O   LEU L1879 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   GLY L1883 " --> pdb=" O   GLN L1880 " (cutoff:3.500A)
      Proline residue:  L1884  - end of helix
    Processing helix  chain 'L' and resid 1885 through 1892
      removed outlier: 3.632A  pdb=" N   VAL L1889 " --> pdb=" O   PHE L1885 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1893 through 1896
    Processing helix  chain 'L' and resid 1902 through 1906
      removed outlier: 3.661A  pdb=" N   LEU L1906 " --> pdb=" O   LYS L1903 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 2102 through 2114
    Processing helix  chain 'L' and resid 2118 through 2134
    Processing helix  chain 'L' and resid 2144 through 2152
    Processing helix  chain 'L' and resid 2155 through 2165
      removed outlier: 3.838A  pdb=" N   VAL L2159 " --> pdb=" O   ASN L2155 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'L' and resid 91 through 94
      removed outlier: 3.676A  pdb=" N   LEU L 100 " --> pdb=" O   ILE L 138 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'L' and resid 258 through 260
      removed outlier: 3.788A  pdb=" N   TYR L 651 " --> pdb=" O   ILE L1376 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   ILE L1376 " --> pdb=" O   TYR L 651 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   MET L1189 " --> pdb=" O   GLN L1333 " (cutoff:3.500A)
      removed outlier: 4.478A  pdb=" N   GLN L1333 " --> pdb=" O   MET L1189 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   ASP L1325 " --> pdb=" O   LEU L1336 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'L' and resid 375 through 376
      removed outlier: 3.679A  pdb=" N   PHE L 375 " --> pdb=" O   VAL L 383 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   VAL L 383 " --> pdb=" O   PHE L 375 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'L' and resid 536 through 540
    Processing sheet with id=AA5, first strand: chain 'L' and resid 826 through 829
    Processing sheet with id=AA6, first strand: chain 'L' and resid 1120 through 1125
    Processing sheet with id=AA7, first strand: chain 'L' and resid 1653 through 1655
      removed outlier: 3.564A  pdb=" N   TRP L1664 " --> pdb=" O   SER L1546 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   SER L1546 " --> pdb=" O   TRP L1664 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 1724 through 1726
      removed outlier: 4.063A  pdb=" N   VAL L1810 " --> pdb=" O   PHE L1724 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 1854 through 1855
      removed outlier: 3.805A  pdb=" N   PHE L1854 " --> pdb=" O   VAL L2082 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   LYS L2092 " --> pdb=" O   GLU L2089 " (cutoff:3.500A)

    657 hydrogen bonds defined for protein.
    1875 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      8 hydrogen bonds
      16 hydrogen bond angles
      0 basepair planarities
      3 basepair parallelities
      8 stacking parallelities
  Total time for adding SS restraints: 2.85

  Time building geometry restraints manager: 1.93 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: 4753
        1.34 -     1.46: 2456
        1.46 -     1.58: 8271
        1.58 -     1.70: 39
        1.70 -     1.81: 139
  Bond restraints: 15658
  Sorted by residual:
  bond pdb=" CA  ARG L 342 "
       pdb=" C   ARG L 342 "
    ideal  model  delta    sigma   weight residual
    1.523  1.542 -0.019 1.34e-02 5.57e+03 2.03e+00
  bond pdb=" C   SER L 296 "
       pdb=" N   PRO L 297 "
    ideal  model  delta    sigma   weight residual
    1.334  1.361 -0.027 2.34e-02 1.83e+03 1.35e+00
  bond pdb=" CA  THR L 710 "
       pdb=" CB  THR L 710 "
    ideal  model  delta    sigma   weight residual
    1.530  1.548 -0.018 1.93e-02 2.68e+03 8.72e-01
  bond pdb=" CA  ARG L 342 "
       pdb=" CB  ARG L 342 "
    ideal  model  delta    sigma   weight residual
    1.530  1.546 -0.016 1.69e-02 3.50e+03 8.53e-01
  bond pdb=" N   ARG L 342 "
       pdb=" CA  ARG L 342 "
    ideal  model  delta    sigma   weight residual
    1.457  1.469 -0.011 1.29e-02 6.01e+03 7.57e-01
  ... (remaining 15653 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.35: 20970
        2.35 -     4.70: 223
        4.70 -     7.04: 27
        7.04 -     9.39: 4
        9.39 -    11.74: 2
  Bond angle restraints: 21226
  Sorted by residual:
  angle pdb=" C   THR L 341 "
        pdb=" N   ARG L 342 "
        pdb=" CA  ARG L 342 "
      ideal   model   delta    sigma   weight residual
     121.54  132.71  -11.17 1.91e+00 2.74e-01 3.42e+01
  angle pdb=" N   ARG L 342 "
        pdb=" CA  ARG L 342 "
        pdb=" CB  ARG L 342 "
      ideal   model   delta    sigma   weight residual
     110.49  104.01    6.48 1.69e+00 3.50e-01 1.47e+01
  angle pdb=" CA  ARG L 342 "
        pdb=" CB  ARG L 342 "
        pdb=" CG  ARG L 342 "
      ideal   model   delta    sigma   weight residual
     114.10  121.61   -7.51 2.00e+00 2.50e-01 1.41e+01
  angle pdb=" C   MET L1189 "
        pdb=" N   ASP L1190 "
        pdb=" CA  ASP L1190 "
      ideal   model   delta    sigma   weight residual
     122.45  129.11   -6.66 1.78e+00 3.16e-01 1.40e+01
  angle pdb=" N   ARG L 342 "
        pdb=" CA  ARG L 342 "
        pdb=" C   ARG L 342 "
      ideal   model   delta    sigma   weight residual
     110.80  118.58   -7.78 2.13e+00 2.20e-01 1.33e+01
  ... (remaining 21221 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.21: 8854
       22.21 -    44.42: 587
       44.42 -    66.63: 84
       66.63 -    88.84: 25
       88.84 -   111.04: 2
  Dihedral angle restraints: 9552
    sinusoidal: 4124
      harmonic: 5428
  Sorted by residual:
  dihedral pdb=" CA  PHE L 581 "
           pdb=" C   PHE L 581 "
           pdb=" N   PRO L 582 "
           pdb=" CA  PRO L 582 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.84  -26.16     0      5.00e+00 4.00e-02 2.74e+01
  dihedral pdb=" CA  TYR L1663 "
           pdb=" C   TYR L1663 "
           pdb=" N   TRP L1664 "
           pdb=" CA  TRP L1664 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.02  -23.98     0      5.00e+00 4.00e-02 2.30e+01
  dihedral pdb=" CA  ARG L 210 "
           pdb=" C   ARG L 210 "
           pdb=" N   SER L 211 "
           pdb=" CA  SER L 211 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -157.34  -22.66     0      5.00e+00 4.00e-02 2.05e+01
  ... (remaining 9549 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 1696
       0.036 -    0.073: 521
       0.073 -    0.109: 145
       0.109 -    0.146: 37
       0.146 -    0.182: 4
  Chirality restraints: 2403
  Sorted by residual:
  chirality pdb=" CA  ILE L1376 "
            pdb=" N   ILE L1376 "
            pdb=" C   ILE L1376 "
            pdb=" CB  ILE L1376 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.62   -0.18 2.00e-01 2.50e+01 8.29e-01
  chirality pdb=" CA  ARG L 343 "
            pdb=" N   ARG L 343 "
            pdb=" C   ARG L 343 "
            pdb=" CB  ARG L 343 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.38e-01
  chirality pdb=" CB  ILE L2144 "
            pdb=" CA  ILE L2144 "
            pdb=" CG1 ILE L2144 "
            pdb=" CG2 ILE L2144 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.49    0.16 2.00e-01 2.50e+01 6.08e-01
  ... (remaining 2400 not shown)

  Planarity restraints: 2618
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER L 616 "   -0.014 2.00e-02 2.50e+03   2.86e-02 8.20e+00
        pdb=" C   SER L 616 "    0.050 2.00e-02 2.50e+03
        pdb=" O   SER L 616 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   LEU L 617 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET L 620 "   -0.014 2.00e-02 2.50e+03   2.77e-02 7.67e+00
        pdb=" C   MET L 620 "    0.048 2.00e-02 2.50e+03
        pdb=" O   MET L 620 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   ILE L 621 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL L1016 "    0.014 2.00e-02 2.50e+03   2.71e-02 7.36e+00
        pdb=" C   VAL L1016 "   -0.047 2.00e-02 2.50e+03
        pdb=" O   VAL L1016 "    0.018 2.00e-02 2.50e+03
        pdb=" N   ALA L1017 "    0.016 2.00e-02 2.50e+03
  ... (remaining 2615 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 704
        2.72 -     3.26: 16229
        3.26 -     3.81: 23034
        3.81 -     4.35: 27761
        4.35 -     4.90: 45356
  Nonbonded interactions: 113084
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP L2143 "
            pdb=" OG  SER L2146 "
     model   vdw
     2.174 3.040
  nonbonded pdb=" OG  SER L 384 "
            pdb=" OE1 GLU L 386 "
     model   vdw
     2.182 3.040
  nonbonded pdb=" OD1 ASP L 350 "
            pdb=" OG  SER L 377 "
     model   vdw
     2.184 3.040
  nonbonded pdb=" O   LEU L 385 "
            pdb=" OG1 THR L 388 "
     model   vdw
     2.184 3.040
  nonbonded pdb=" OH  TYR L1476 "
            pdb=" NH2 ARG L1480 "
     model   vdw
     2.187 3.120
  ... (remaining 113079 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             7.090
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.040
  Process input model:                     17.980
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.990
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8120
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   0.027  15661  Z= 0.112
  Angle     :  0.614  11.741  21226  Z= 0.328
  Chirality :  0.040   0.182   2403
  Planarity :  0.005   0.053   2618
  Dihedral  : 15.072 111.045   6024
  Min Nonbonded Distance : 2.174

Molprobity Statistics.
  All-atom Clashscore : 10.15
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  : 15.24 %
    Favored  : 84.53 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  :  1.72 %
    Favored  : 98.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.19 (0.16), residues: 1817
  helix: -1.57 (0.15), residues: 921
  sheet: -3.65 (0.44), residues: 90
  loop : -4.24 (0.17), residues: 806

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG L 860 
 TYR   0.013   0.001   TYR L1476 
 PHE   0.032   0.001   PHE L1458 
 TRP   0.015   0.002   TRP L1233 
 HIS   0.008   0.001   HIS L1819 

Details of bonding type rmsd
  covalent geometry    : bond        0.00216 (15658)
  covalent geometry    : angle       0.61383 (21226)
  hydrogen bonds       : bond        0.13093 (  665)
  hydrogen bonds       : angle       6.14446 ( 1891)
  metal coordination   : bond        0.00192 (    3)

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

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

  3634 Ramachandran restraints generated.
    1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3634 Ramachandran restraints generated.
    1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 204
  time to evaluate  : 0.570 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L  393 GLU cc_start: 0.8657 (tt0) cc_final: 0.8445 (tp30)
REVERT: L  394 LYS cc_start: 0.9263 (tppt) cc_final: 0.8984 (tppt)
REVERT: L  442 TYR cc_start: 0.7880 (m-80) cc_final: 0.7632 (m-10)
REVERT: L  483 MET cc_start: 0.9032 (mmt) cc_final: 0.8771 (mmm)
REVERT: L  692 MET cc_start: 0.7848 (mmm) cc_final: 0.7629 (tpp)
REVERT: L  753 MET cc_start: 0.8850 (tpp) cc_final: 0.8583 (tpp)
REVERT: L  956 ILE cc_start: 0.9657 (mt) cc_final: 0.9449 (mp)
REVERT: L 1060 MET cc_start: 0.7631 (mmm) cc_final: 0.7343 (mmm)
REVERT: L 1077 GLU cc_start: 0.8331 (mt-10) cc_final: 0.8102 (mt-10)
REVERT: L 1842 MET cc_start: 0.9058 (mmp) cc_final: 0.8720 (mmm)
  outliers start: 1
  outliers final: 0
  residues processed: 204
  average time/residue: 0.1611
  time to fit residues: 45.3537
Evaluate side-chains
  121 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 98 optimal weight:    9.9990
   chunk 107 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9980
   chunk 66 optimal weight:    0.9990
   chunk 130 optimal weight:    1.9990
   chunk 124 optimal weight:    3.9990
   chunk 103 optimal weight:    5.9990
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    3.9990
   chunk 91 optimal weight:    0.8980
   chunk 149 optimal weight:    0.6980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
L  76 HIS
** L 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L 694 ASN
** L 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L1208 GLN
L1435 HIS
L1438 ASN
L1461 ASN
** L1844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.081636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.057676 restraints weight = 63763.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.059542 restraints weight = 35928.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.060177 restraints weight = 20289.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.060264 restraints weight = 18493.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.060295 restraints weight = 16617.461|
|-----------------------------------------------------------------------------|
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8186
moved from start:          0.1823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  15661  Z= 0.139
  Angle     :  0.653  12.127  21226  Z= 0.329
  Chirality :  0.040   0.160   2403
  Planarity :  0.004   0.081   2618
  Dihedral  : 10.950 109.192   2320
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 9.13
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  : 10.02 %
    Favored  : 89.93 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  :  8.96 %
    Favored  : 90.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.44 (0.19), residues: 1817
  helix: -0.04 (0.17), residues: 927
  sheet: -2.98 (0.44), residues: 102
  loop : -3.51 (0.20), residues: 788

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG L  71 
 TYR   0.013   0.001   TYR L1187 
 PHE   0.025   0.002   PHE L1885 
 TRP   0.025   0.002   TRP L2088 
 HIS   0.010   0.001   HIS L  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 (15658)
  covalent geometry    : angle       0.65283 (21226)
  hydrogen bonds       : bond        0.04304 (  665)
  hydrogen bonds       : angle       4.48532 ( 1891)
  metal coordination   : bond        0.00271 (    3)

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

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

  3634 Ramachandran restraints generated.
    1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3634 Ramachandran restraints generated.
    1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 133
  time to evaluate  : 0.680 
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: L  393 GLU cc_start: 0.8902 (tt0) cc_final: 0.8580 (tp30)
REVERT: L  394 LYS cc_start: 0.9344 (tppt) cc_final: 0.9055 (tppt)
REVERT: L  442 TYR cc_start: 0.8137 (m-80) cc_final: 0.7856 (m-10)
REVERT: L  483 MET cc_start: 0.8993 (mmt) cc_final: 0.8594 (mmm)
REVERT: L  684 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8791 (mm)
REVERT: L  753 MET cc_start: 0.8958 (tpp) cc_final: 0.8616 (tpp)
REVERT: L  971 PHE cc_start: 0.8132 (t80) cc_final: 0.7869 (t80)
REVERT: L 1032 SER cc_start: 0.9490 (m) cc_final: 0.9144 (p)
REVERT: L 1077 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8129 (mt-10)
REVERT: L 1885 PHE cc_start: 0.8221 (t80) cc_final: 0.7926 (t80)
REVERT: L 1901 MET cc_start: 0.5697 (mmm) cc_final: 0.5276 (mmp)
  outliers start: 15
  outliers final: 7
  residues processed: 144
  average time/residue: 0.1406
  time to fit residues: 29.3257
Evaluate side-chains
  113 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 105
  time to evaluate  : 0.512 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   38 LEU
Chi-restraints excluded: chain L residue  513 THR
Chi-restraints excluded: chain L residue  540 LEU
Chi-restraints excluded: chain L residue  684 LEU
Chi-restraints excluded: chain L residue  833 THR
Chi-restraints excluded: chain L residue 1084 SER
Chi-restraints excluded: chain L residue 1458 PHE
Chi-restraints excluded: chain L residue 1481 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 3 optimal weight:    5.9990
   chunk 112 optimal weight:    2.9990
   chunk 137 optimal weight:    1.9990
   chunk 100 optimal weight:    0.7980
   chunk 181 optimal weight:    7.9990
   chunk 147 optimal weight:    3.9990
   chunk 81 optimal weight:    0.9980
   chunk 68 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 102 optimal weight:    5.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
** L 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L 401 GLN
** L 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L1028 GLN
L1407 ASN
L1742 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.079467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.055241 restraints weight = 64419.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.056714 restraints weight = 37915.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.057347 restraints weight = 23060.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.057654 restraints weight = 18912.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.057656 restraints weight = 17507.233|
|-----------------------------------------------------------------------------|
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8265
moved from start:          0.2489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  15661  Z= 0.185
  Angle     :  0.642  10.973  21226  Z= 0.327
  Chirality :  0.040   0.152   2403
  Planarity :  0.004   0.051   2618
  Dihedral  : 10.802 110.286   2320
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.35 %
    Favored  : 89.65 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 11.45 %
    Favored  : 86.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.97 (0.20), residues: 1817
  helix:  0.30 (0.17), residues: 935
  sheet: -2.61 (0.46), residues: 102
  loop : -3.26 (0.21), residues: 780

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG L 920 
 TYR   0.016   0.001   TYR L1026 
 PHE   0.024   0.002   PHE L1058 
 TRP   0.012   0.002   TRP L1233 
 HIS   0.008   0.001   HIS L1819 

Details of bonding type rmsd
  covalent geometry    : bond        0.00418 (15658)
  covalent geometry    : angle       0.64240 (21226)
  hydrogen bonds       : bond        0.04455 (  665)
  hydrogen bonds       : angle       4.42125 ( 1891)
  metal coordination   : bond        0.00360 (    3)

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

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

  3634 Ramachandran restraints generated.
    1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3634 Ramachandran restraints generated.
    1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 116
  time to evaluate  : 0.569 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L    1 MET cc_start: 0.8908 (ppp) cc_final: 0.8522 (tmm)
REVERT: L  154 ASP cc_start: 0.8785 (m-30) cc_final: 0.8289 (m-30)
REVERT: L  393 GLU cc_start: 0.8920 (tt0) cc_final: 0.8606 (tp30)
REVERT: L  394 LYS cc_start: 0.9343 (tppt) cc_final: 0.9069 (tppt)
REVERT: L  483 MET cc_start: 0.8894 (mmt) cc_final: 0.8544 (mmm)
REVERT: L  513 THR cc_start: 0.8714 (OUTLIER) cc_final: 0.8512 (p)
REVERT: L  684 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8871 (mm)
REVERT: L  691 MET cc_start: 0.7809 (mtt) cc_final: 0.7607 (mtt)
REVERT: L  753 MET cc_start: 0.9010 (tpp) cc_final: 0.8662 (tpp)
REVERT: L 1060 MET cc_start: 0.8232 (mmm) cc_final: 0.7932 (mmp)
REVERT: L 1077 GLU cc_start: 0.8291 (mt-10) cc_final: 0.8020 (mt-10)
REVERT: L 1770 LYS cc_start: 0.7407 (OUTLIER) cc_final: 0.7097 (tmtt)
REVERT: L 1871 THR cc_start: 0.7657 (OUTLIER) cc_final: 0.7209 (t)
REVERT: L 1885 PHE cc_start: 0.8440 (t80) cc_final: 0.8159 (t80)
  outliers start: 32
  outliers final: 15
  residues processed: 139
  average time/residue: 0.1229
  time to fit residues: 25.7455
Evaluate side-chains
  115 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 96
  time to evaluate  : 0.679 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   38 LEU
Chi-restraints excluded: chain L residue   45 LEU
Chi-restraints excluded: chain L residue  160 LEU
Chi-restraints excluded: chain L residue  259 LEU
Chi-restraints excluded: chain L residue  435 VAL
Chi-restraints excluded: chain L residue  502 LEU
Chi-restraints excluded: chain L residue  513 THR
Chi-restraints excluded: chain L residue  684 LEU
Chi-restraints excluded: chain L residue  833 THR
Chi-restraints excluded: chain L residue 1084 SER
Chi-restraints excluded: chain L residue 1300 THR
Chi-restraints excluded: chain L residue 1458 PHE
Chi-restraints excluded: chain L residue 1481 GLN
Chi-restraints excluded: chain L residue 1513 PHE
Chi-restraints excluded: chain L residue 1693 LEU
Chi-restraints excluded: chain L residue 1697 ILE
Chi-restraints excluded: chain L residue 1770 LYS
Chi-restraints excluded: chain L residue 1780 LEU
Chi-restraints excluded: chain L residue 1871 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 179 optimal weight:    5.9990
   chunk 106 optimal weight:    1.9990
   chunk 95 optimal weight:    5.9990
   chunk 119 optimal weight:    0.9990
   chunk 19 optimal weight:    8.9990
   chunk 14 optimal weight:    4.9990
   chunk 137 optimal weight:    0.3980
   chunk 112 optimal weight:    2.9990
   chunk 139 optimal weight:    1.9990
   chunk 86 optimal weight:    0.5980
   chunk 100 optimal weight:    1.9990
   overall best weight:    1.1986

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

Flipped N/Q/H residues before XYZ refinement:
** L 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L1407 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.079833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.055655 restraints weight = 64002.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.057586 restraints weight = 36285.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.057914 restraints weight = 20875.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.058161 restraints weight = 18687.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.058108 restraints weight = 16971.792|
|-----------------------------------------------------------------------------|
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8255
moved from start:          0.2811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  15661  Z= 0.148
  Angle     :  0.608  13.292  21226  Z= 0.306
  Chirality :  0.039   0.159   2403
  Planarity :  0.004   0.046   2618
  Dihedral  : 10.621 110.724   2320
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.41 %
    Favored  : 90.59 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 13.58 %
    Favored  : 84.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.61 (0.20), residues: 1817
  helix:  0.53 (0.17), residues: 944
  sheet: -2.29 (0.48), residues: 102
  loop : -3.06 (0.22), residues: 771

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L 920 
 TYR   0.016   0.001   TYR L  91 
 PHE   0.025   0.001   PHE L 954 
 TRP   0.009   0.001   TRP L1194 
 HIS   0.006   0.001   HIS L1819 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 (15658)
  covalent geometry    : angle       0.60802 (21226)
  hydrogen bonds       : bond        0.03963 (  665)
  hydrogen bonds       : angle       4.23686 ( 1891)
  metal coordination   : bond        0.00319 (    3)

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

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

  3634 Ramachandran restraints generated.
    1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3634 Ramachandran restraints generated.
    1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 109
  time to evaluate  : 0.584 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   38 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8422 (mm)
REVERT: L  154 ASP cc_start: 0.8773 (m-30) cc_final: 0.8277 (m-30)
REVERT: L  393 GLU cc_start: 0.8966 (tt0) cc_final: 0.8616 (tp30)
REVERT: L  394 LYS cc_start: 0.9352 (tppt) cc_final: 0.9069 (tppt)
REVERT: L  442 TYR cc_start: 0.8243 (m-80) cc_final: 0.7987 (m-10)
REVERT: L  483 MET cc_start: 0.8846 (mmt) cc_final: 0.8483 (mmm)
REVERT: L  684 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8845 (mm)
REVERT: L  753 MET cc_start: 0.9003 (tpp) cc_final: 0.8691 (tpp)
REVERT: L 1060 MET cc_start: 0.8166 (mmm) cc_final: 0.7642 (mmp)
REVERT: L 1077 GLU cc_start: 0.8311 (mt-10) cc_final: 0.7977 (mt-10)
REVERT: L 1699 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8757 (mt)
REVERT: L 1770 LYS cc_start: 0.7470 (OUTLIER) cc_final: 0.7066 (tmtt)
REVERT: L 1871 THR cc_start: 0.7785 (OUTLIER) cc_final: 0.7352 (t)
REVERT: L 1885 PHE cc_start: 0.8451 (t80) cc_final: 0.8189 (t80)
REVERT: L 1901 MET cc_start: 0.5928 (mmm) cc_final: 0.5492 (mmp)
  outliers start: 30
  outliers final: 16
  residues processed: 131
  average time/residue: 0.1346
  time to fit residues: 26.1770
Evaluate side-chains
  117 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 96
  time to evaluate  : 0.553 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   38 LEU
Chi-restraints excluded: chain L residue  160 LEU
Chi-restraints excluded: chain L residue  254 ILE
Chi-restraints excluded: chain L residue  259 LEU
Chi-restraints excluded: chain L residue  435 VAL
Chi-restraints excluded: chain L residue  465 VAL
Chi-restraints excluded: chain L residue  502 LEU
Chi-restraints excluded: chain L residue  513 THR
Chi-restraints excluded: chain L residue  684 LEU
Chi-restraints excluded: chain L residue  882 LEU
Chi-restraints excluded: chain L residue 1084 SER
Chi-restraints excluded: chain L residue 1328 THR
Chi-restraints excluded: chain L residue 1458 PHE
Chi-restraints excluded: chain L residue 1481 GLN
Chi-restraints excluded: chain L residue 1513 PHE
Chi-restraints excluded: chain L residue 1693 LEU
Chi-restraints excluded: chain L residue 1699 LEU
Chi-restraints excluded: chain L residue 1770 LYS
Chi-restraints excluded: chain L residue 1780 LEU
Chi-restraints excluded: chain L residue 1871 THR
Chi-restraints excluded: chain L residue 2109 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 50 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9990
   chunk 18 optimal weight:    0.7980
   chunk 92 optimal weight:    0.0060
   chunk 101 optimal weight:    0.9990
   chunk 95 optimal weight:    4.9990
   chunk 22 optimal weight:    3.9990
   chunk 0 optimal weight:    9.9990
   chunk 12 optimal weight:    0.9990
   chunk 108 optimal weight:    1.9990
   chunk 7 optimal weight:    3.9990
   overall best weight:    0.7602

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

Flipped N/Q/H residues before XYZ refinement:
L  56 ASN
** L 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L 324 GLN
** L 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.080613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.056968 restraints weight = 64187.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.058169 restraints weight = 36713.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.059033 restraints weight = 22776.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.059031 restraints weight = 19698.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.059255 restraints weight = 17228.797|
|-----------------------------------------------------------------------------|
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8213
moved from start:          0.3084

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  15661  Z= 0.117
  Angle     :  0.583  13.828  21226  Z= 0.292
  Chirality :  0.038   0.164   2403
  Planarity :  0.003   0.047   2618
  Dihedral  : 10.439 111.201   2320
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.47 %
    Favored  : 90.53 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 14.18 %
    Favored  : 84.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.37 (0.20), residues: 1817
  helix:  0.72 (0.17), residues: 954
  sheet: -2.28 (0.47), residues: 109
  loop : -2.95 (0.22), residues: 754

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L 363 
 TYR   0.011   0.001   TYR L  91 
 PHE   0.014   0.001   PHE L 971 
 TRP   0.009   0.001   TRP L1547 
 HIS   0.006   0.001   HIS L 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 (15658)
  covalent geometry    : angle       0.58329 (21226)
  hydrogen bonds       : bond        0.03563 (  665)
  hydrogen bonds       : angle       4.05504 ( 1891)
  metal coordination   : bond        0.00225 (    3)

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

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

  3634 Ramachandran restraints generated.
    1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3634 Ramachandran restraints generated.
    1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 109
  time to evaluate  : 0.587 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   38 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8368 (mm)
REVERT: L  154 ASP cc_start: 0.8838 (m-30) cc_final: 0.8259 (m-30)
REVERT: L  393 GLU cc_start: 0.8925 (tt0) cc_final: 0.8593 (tp30)
REVERT: L  394 LYS cc_start: 0.9333 (tppt) cc_final: 0.9042 (tppt)
REVERT: L  442 TYR cc_start: 0.8187 (m-80) cc_final: 0.7941 (m-10)
REVERT: L  483 MET cc_start: 0.8794 (mmt) cc_final: 0.8466 (mmt)
REVERT: L  753 MET cc_start: 0.8977 (tpp) cc_final: 0.8745 (tpp)
REVERT: L  856 GLU cc_start: 0.8711 (tt0) cc_final: 0.8476 (tt0)
REVERT: L 1030 PHE cc_start: 0.8257 (OUTLIER) cc_final: 0.7907 (m-80)
REVERT: L 1060 MET cc_start: 0.8259 (mmm) cc_final: 0.7710 (mmp)
REVERT: L 1077 GLU cc_start: 0.8284 (mt-10) cc_final: 0.7941 (mt-10)
REVERT: L 1770 LYS cc_start: 0.7349 (OUTLIER) cc_final: 0.7060 (tmtt)
REVERT: L 1871 THR cc_start: 0.7626 (OUTLIER) cc_final: 0.7208 (t)
REVERT: L 1885 PHE cc_start: 0.8438 (t80) cc_final: 0.8182 (t80)
REVERT: L 1901 MET cc_start: 0.6317 (mmm) cc_final: 0.5563 (mmp)
  outliers start: 28
  outliers final: 17
  residues processed: 133
  average time/residue: 0.1228
  time to fit residues: 24.8965
Evaluate side-chains
  119 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 98
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   38 LEU
Chi-restraints excluded: chain L residue  160 LEU
Chi-restraints excluded: chain L residue  205 VAL
Chi-restraints excluded: chain L residue  259 LEU
Chi-restraints excluded: chain L residue  435 VAL
Chi-restraints excluded: chain L residue  465 VAL
Chi-restraints excluded: chain L residue  502 LEU
Chi-restraints excluded: chain L residue  513 THR
Chi-restraints excluded: chain L residue  540 LEU
Chi-restraints excluded: chain L residue  829 VAL
Chi-restraints excluded: chain L residue  882 LEU
Chi-restraints excluded: chain L residue 1030 PHE
Chi-restraints excluded: chain L residue 1084 SER
Chi-restraints excluded: chain L residue 1300 THR
Chi-restraints excluded: chain L residue 1458 PHE
Chi-restraints excluded: chain L residue 1481 GLN
Chi-restraints excluded: chain L residue 1770 LYS
Chi-restraints excluded: chain L residue 1780 LEU
Chi-restraints excluded: chain L residue 1871 THR
Chi-restraints excluded: chain L residue 2118 LEU
Chi-restraints excluded: chain L residue 2157 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 76 optimal weight:    1.9990
   chunk 126 optimal weight:    2.9990
   chunk 49 optimal weight:    0.8980
   chunk 81 optimal weight:    0.0980
   chunk 158 optimal weight:    0.1980
   chunk 53 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 14 optimal weight:    9.9990
   chunk 10 optimal weight:    6.9990
   chunk 150 optimal weight:    0.9980
   chunk 154 optimal weight:    0.0670
   overall best weight:    0.4518

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

Flipped N/Q/H residues before XYZ refinement:
L  63 ASN
** L 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.081438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.056797 restraints weight = 63820.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.058453 restraints weight = 33570.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.059474 restraints weight = 22479.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.060162 restraints weight = 17580.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.060548 restraints weight = 15044.278|
|-----------------------------------------------------------------------------|
r_work (final): 0.3214
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8147
moved from start:          0.3239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  15661  Z= 0.100
  Angle     :  0.553  11.378  21226  Z= 0.279
  Chirality :  0.037   0.175   2403
  Planarity :  0.003   0.047   2618
  Dihedral  : 10.302 111.755   2320
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.37 %
    Favored  : 91.63 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 15.07 %
    Favored  : 83.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.16 (0.20), residues: 1817
  helix:  0.90 (0.17), residues: 951
  sheet: -2.09 (0.47), residues: 109
  loop : -2.89 (0.22), residues: 757

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L1019 
 TYR   0.008   0.001   TYR L  91 
 PHE   0.028   0.001   PHE L 954 
 TRP   0.010   0.001   TRP L 155 
 HIS   0.003   0.000   HIS L1819 

Details of bonding type rmsd
  covalent geometry    : bond        0.00219 (15658)
  covalent geometry    : angle       0.55303 (21226)
  hydrogen bonds       : bond        0.03261 (  665)
  hydrogen bonds       : angle       3.91388 ( 1891)
  metal coordination   : bond        0.00176 (    3)

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

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

  3634 Ramachandran restraints generated.
    1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3634 Ramachandran restraints generated.
    1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 109
  time to evaluate  : 0.589 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   38 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8281 (mm)
REVERT: L  154 ASP cc_start: 0.8772 (m-30) cc_final: 0.8138 (m-30)
REVERT: L  393 GLU cc_start: 0.8725 (tt0) cc_final: 0.8453 (tp30)
REVERT: L  394 LYS cc_start: 0.9269 (tppt) cc_final: 0.9027 (tppt)
REVERT: L  442 TYR cc_start: 0.8070 (m-80) cc_final: 0.7832 (m-10)
REVERT: L  483 MET cc_start: 0.8732 (mmt) cc_final: 0.8469 (mmm)
REVERT: L 1030 PHE cc_start: 0.8260 (OUTLIER) cc_final: 0.8009 (m-80)
REVERT: L 1060 MET cc_start: 0.8207 (mmm) cc_final: 0.7758 (tpp)
REVERT: L 1077 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7890 (mt-10)
REVERT: L 1770 LYS cc_start: 0.7276 (OUTLIER) cc_final: 0.7057 (tmtt)
REVERT: L 1885 PHE cc_start: 0.8419 (t80) cc_final: 0.8187 (t80)
REVERT: L 1901 MET cc_start: 0.6258 (mmm) cc_final: 0.5577 (mmp)
  outliers start: 28
  outliers final: 15
  residues processed: 131
  average time/residue: 0.1168
  time to fit residues: 23.4623
Evaluate side-chains
  112 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 94
  time to evaluate  : 0.490 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   38 LEU
Chi-restraints excluded: chain L residue   45 LEU
Chi-restraints excluded: chain L residue  160 LEU
Chi-restraints excluded: chain L residue  205 VAL
Chi-restraints excluded: chain L residue  259 LEU
Chi-restraints excluded: chain L residue  465 VAL
Chi-restraints excluded: chain L residue  502 LEU
Chi-restraints excluded: chain L residue  513 THR
Chi-restraints excluded: chain L residue  540 LEU
Chi-restraints excluded: chain L residue  829 VAL
Chi-restraints excluded: chain L residue  882 LEU
Chi-restraints excluded: chain L residue 1030 PHE
Chi-restraints excluded: chain L residue 1328 THR
Chi-restraints excluded: chain L residue 1458 PHE
Chi-restraints excluded: chain L residue 1481 GLN
Chi-restraints excluded: chain L residue 1770 LYS
Chi-restraints excluded: chain L residue 1780 LEU
Chi-restraints excluded: chain L residue 2118 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 116 optimal weight:    1.9990
   chunk 136 optimal weight:    0.7980
   chunk 37 optimal weight:    3.9990
   chunk 157 optimal weight:    5.9990
   chunk 78 optimal weight:    1.9990
   chunk 180 optimal weight:    0.9990
   chunk 182 optimal weight:    0.7980
   chunk 152 optimal weight:    0.8980
   chunk 35 optimal weight:    4.9990
   chunk 93 optimal weight:    3.9990
   chunk 24 optimal weight:    0.0980
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
** L 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.081209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.056489 restraints weight = 63769.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.058116 restraints weight = 33765.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.059149 restraints weight = 22692.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.059807 restraints weight = 17748.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.060214 restraints weight = 15261.533|
|-----------------------------------------------------------------------------|
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8157
moved from start:          0.3420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  15661  Z= 0.113
  Angle     :  0.570  11.690  21226  Z= 0.286
  Chirality :  0.037   0.157   2403
  Planarity :  0.003   0.047   2618
  Dihedral  : 10.280 112.438   2320
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  9.08 %
    Favored  : 90.86 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 15.24 %
    Favored  : 83.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.12 (0.20), residues: 1817
  helix:  0.94 (0.17), residues: 944
  sheet: -1.90 (0.48), residues: 109
  loop : -2.86 (0.21), residues: 764

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG L2084 
 TYR   0.010   0.001   TYR L1187 
 PHE   0.040   0.001   PHE L 421 
 TRP   0.015   0.001   TRP L2088 
 HIS   0.003   0.001   HIS L 652 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 (15658)
  covalent geometry    : angle       0.57019 (21226)
  hydrogen bonds       : bond        0.03352 (  665)
  hydrogen bonds       : angle       3.93118 ( 1891)
  metal coordination   : bond        0.00226 (    3)

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

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

  3634 Ramachandran restraints generated.
    1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3634 Ramachandran restraints generated.
    1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 101
  time to evaluate  : 0.606 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   38 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8329 (mm)
REVERT: L  154 ASP cc_start: 0.8784 (m-30) cc_final: 0.8169 (m-30)
REVERT: L  393 GLU cc_start: 0.8723 (tt0) cc_final: 0.8460 (tp30)
REVERT: L  394 LYS cc_start: 0.9267 (tppt) cc_final: 0.9032 (tppt)
REVERT: L  483 MET cc_start: 0.8755 (mmt) cc_final: 0.8488 (mmm)
REVERT: L 1060 MET cc_start: 0.8188 (mmm) cc_final: 0.7772 (tpp)
REVERT: L 1077 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7821 (mt-10)
REVERT: L 1092 MET cc_start: 0.8105 (tpt) cc_final: 0.7367 (mtm)
REVERT: L 1770 LYS cc_start: 0.7273 (OUTLIER) cc_final: 0.7067 (tmtt)
REVERT: L 1885 PHE cc_start: 0.8447 (t80) cc_final: 0.8238 (t80)
REVERT: L 1901 MET cc_start: 0.6350 (mmm) cc_final: 0.5679 (mmp)
REVERT: L 2137 MET cc_start: 0.0707 (ptp) cc_final: 0.0416 (ptp)
  outliers start: 29
  outliers final: 21
  residues processed: 126
  average time/residue: 0.1213
  time to fit residues: 23.4617
Evaluate side-chains
  115 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 92
  time to evaluate  : 0.607 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   38 LEU
Chi-restraints excluded: chain L residue   45 LEU
Chi-restraints excluded: chain L residue  160 LEU
Chi-restraints excluded: chain L residue  205 VAL
Chi-restraints excluded: chain L residue  254 ILE
Chi-restraints excluded: chain L residue  259 LEU
Chi-restraints excluded: chain L residue  435 VAL
Chi-restraints excluded: chain L residue  465 VAL
Chi-restraints excluded: chain L residue  502 LEU
Chi-restraints excluded: chain L residue  513 THR
Chi-restraints excluded: chain L residue  540 LEU
Chi-restraints excluded: chain L residue  829 VAL
Chi-restraints excluded: chain L residue  882 LEU
Chi-restraints excluded: chain L residue 1084 SER
Chi-restraints excluded: chain L residue 1300 THR
Chi-restraints excluded: chain L residue 1328 THR
Chi-restraints excluded: chain L residue 1458 PHE
Chi-restraints excluded: chain L residue 1481 GLN
Chi-restraints excluded: chain L residue 1770 LYS
Chi-restraints excluded: chain L residue 1780 LEU
Chi-restraints excluded: chain L residue 2118 LEU
Chi-restraints excluded: chain L residue 2144 ILE
Chi-restraints excluded: chain L residue 2157 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 17 optimal weight:   10.0000
   chunk 163 optimal weight:    9.9990
   chunk 77 optimal weight:    0.9990
   chunk 124 optimal weight:    2.9990
   chunk 104 optimal weight:    0.7980
   chunk 183 optimal weight:    1.9990
   chunk 158 optimal weight:    0.7980
   chunk 181 optimal weight:    0.6980
   chunk 122 optimal weight:    0.0470
   chunk 65 optimal weight:    0.4980
   chunk 34 optimal weight:    0.6980
   overall best weight:    0.5478

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

Flipped N/Q/H residues before XYZ refinement:
** L 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.081736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.056916 restraints weight = 64149.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.058616 restraints weight = 33085.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.059714 restraints weight = 21895.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.060397 restraints weight = 16940.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.060800 restraints weight = 14489.395|
|-----------------------------------------------------------------------------|
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8152
moved from start:          0.3549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  15661  Z= 0.103
  Angle     :  0.564  12.298  21226  Z= 0.283
  Chirality :  0.037   0.155   2403
  Planarity :  0.003   0.046   2618
  Dihedral  : 10.228 112.699   2320
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  8.04 %
    Favored  : 91.91 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 15.42 %
    Favored  : 82.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.98 (0.20), residues: 1817
  helix:  1.00 (0.17), residues: 951
  sheet: -1.71 (0.49), residues: 109
  loop : -2.77 (0.22), residues: 757

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L1019 
 TYR   0.013   0.001   TYR L 442 
 PHE   0.036   0.001   PHE L 421 
 TRP   0.009   0.001   TRP L2088 
 HIS   0.003   0.000   HIS L 652 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 (15658)
  covalent geometry    : angle       0.56410 (21226)
  hydrogen bonds       : bond        0.03199 (  665)
  hydrogen bonds       : angle       3.84335 ( 1891)
  metal coordination   : bond        0.00212 (    3)

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

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

  3634 Ramachandran restraints generated.
    1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3634 Ramachandran restraints generated.
    1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 104
  time to evaluate  : 0.546 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   38 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8136 (mm)
REVERT: L  144 ARG cc_start: 0.9209 (mmp-170) cc_final: 0.8982 (mmp80)
REVERT: L  154 ASP cc_start: 0.8780 (m-30) cc_final: 0.8145 (m-30)
REVERT: L  393 GLU cc_start: 0.8861 (tt0) cc_final: 0.8538 (tp30)
REVERT: L  394 LYS cc_start: 0.9306 (tppt) cc_final: 0.9062 (tppt)
REVERT: L  483 MET cc_start: 0.8751 (mmt) cc_final: 0.8481 (mmm)
REVERT: L  856 GLU cc_start: 0.8689 (tt0) cc_final: 0.8483 (tt0)
REVERT: L 1060 MET cc_start: 0.8259 (mmm) cc_final: 0.7835 (tpp)
REVERT: L 1077 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7841 (mt-10)
REVERT: L 1092 MET cc_start: 0.8152 (tpt) cc_final: 0.7385 (mtt)
REVERT: L 1901 MET cc_start: 0.6237 (mmm) cc_final: 0.5618 (mmp)
  outliers start: 29
  outliers final: 20
  residues processed: 128
  average time/residue: 0.1173
  time to fit residues: 22.6380
Evaluate side-chains
  116 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 95
  time to evaluate  : 0.597 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   38 LEU
Chi-restraints excluded: chain L residue  160 LEU
Chi-restraints excluded: chain L residue  205 VAL
Chi-restraints excluded: chain L residue  254 ILE
Chi-restraints excluded: chain L residue  259 LEU
Chi-restraints excluded: chain L residue  342 ARG
Chi-restraints excluded: chain L residue  435 VAL
Chi-restraints excluded: chain L residue  465 VAL
Chi-restraints excluded: chain L residue  502 LEU
Chi-restraints excluded: chain L residue  513 THR
Chi-restraints excluded: chain L residue  540 LEU
Chi-restraints excluded: chain L residue  829 VAL
Chi-restraints excluded: chain L residue  882 LEU
Chi-restraints excluded: chain L residue 1084 SER
Chi-restraints excluded: chain L residue 1300 THR
Chi-restraints excluded: chain L residue 1328 THR
Chi-restraints excluded: chain L residue 1458 PHE
Chi-restraints excluded: chain L residue 1481 GLN
Chi-restraints excluded: chain L residue 1780 LEU
Chi-restraints excluded: chain L residue 2118 LEU
Chi-restraints excluded: chain L residue 2157 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 102 optimal weight:    2.9990
   chunk 172 optimal weight:    5.9990
   chunk 30 optimal weight:    0.7980
   chunk 130 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   chunk 118 optimal weight:    0.7980
   chunk 45 optimal weight:    1.9990
   chunk 142 optimal weight:    0.0570
   chunk 51 optimal weight:    2.9990
   chunk 152 optimal weight:    0.8980
   overall best weight:    0.9100

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

Flipped N/Q/H residues before XYZ refinement:
** L 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.080883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.056125 restraints weight = 63512.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.057756 restraints weight = 33785.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.058783 restraints weight = 22740.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.059467 restraints weight = 17766.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.059880 restraints weight = 15200.723|
|-----------------------------------------------------------------------------|
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.3683

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  15661  Z= 0.128
  Angle     :  0.595  12.084  21226  Z= 0.299
  Chirality :  0.038   0.223   2403
  Planarity :  0.003   0.045   2618
  Dihedral  : 10.277 113.151   2320
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  8.97 %
    Favored  : 90.97 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 16.49 %
    Favored  : 82.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.94 (0.20), residues: 1817
  helix:  0.98 (0.17), residues: 952
  sheet: -1.62 (0.49), residues: 109
  loop : -2.70 (0.22), residues: 756

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L1480 
 TYR   0.021   0.001   TYR L 442 
 PHE   0.043   0.002   PHE L 421 
 TRP   0.008   0.001   TRP L2139 
 HIS   0.003   0.001   HIS L 652 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 (15658)
  covalent geometry    : angle       0.59482 (21226)
  hydrogen bonds       : bond        0.03492 (  665)
  hydrogen bonds       : angle       4.00769 ( 1891)
  metal coordination   : bond        0.00227 (    3)

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

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

  3634 Ramachandran restraints generated.
    1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3634 Ramachandran restraints generated.
    1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 97
  time to evaluate  : 0.577 
Fit side-chains
   revert: symmetry clash
REVERT: L   38 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8215 (mm)
REVERT: L  154 ASP cc_start: 0.8745 (m-30) cc_final: 0.8155 (m-30)
REVERT: L  393 GLU cc_start: 0.8729 (tt0) cc_final: 0.8468 (tp30)
REVERT: L  394 LYS cc_start: 0.9267 (tppt) cc_final: 0.9040 (tppt)
REVERT: L  483 MET cc_start: 0.8784 (mmt) cc_final: 0.8212 (mmm)
REVERT: L 1060 MET cc_start: 0.8227 (mmm) cc_final: 0.7795 (tpp)
REVERT: L 1077 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7875 (mt-10)
REVERT: L 1092 MET cc_start: 0.8123 (tpt) cc_final: 0.7525 (mtt)
REVERT: L 1901 MET cc_start: 0.6237 (mmm) cc_final: 0.5675 (mmp)
  outliers start: 23
  outliers final: 20
  residues processed: 115
  average time/residue: 0.1103
  time to fit residues: 20.0368
Evaluate side-chains
  116 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 95
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   38 LEU
Chi-restraints excluded: chain L residue  160 LEU
Chi-restraints excluded: chain L residue  205 VAL
Chi-restraints excluded: chain L residue  254 ILE
Chi-restraints excluded: chain L residue  259 LEU
Chi-restraints excluded: chain L residue  435 VAL
Chi-restraints excluded: chain L residue  465 VAL
Chi-restraints excluded: chain L residue  502 LEU
Chi-restraints excluded: chain L residue  513 THR
Chi-restraints excluded: chain L residue  540 LEU
Chi-restraints excluded: chain L residue  829 VAL
Chi-restraints excluded: chain L residue  882 LEU
Chi-restraints excluded: chain L residue 1084 SER
Chi-restraints excluded: chain L residue 1300 THR
Chi-restraints excluded: chain L residue 1328 THR
Chi-restraints excluded: chain L residue 1458 PHE
Chi-restraints excluded: chain L residue 1481 GLN
Chi-restraints excluded: chain L residue 1780 LEU
Chi-restraints excluded: chain L residue 1864 PHE
Chi-restraints excluded: chain L residue 2118 LEU
Chi-restraints excluded: chain L residue 2157 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 145 optimal weight:    0.3980
   chunk 76 optimal weight:    0.6980
   chunk 34 optimal weight:    0.6980
   chunk 122 optimal weight:    2.9990
   chunk 148 optimal weight:    0.5980
   chunk 175 optimal weight:    6.9990
   chunk 152 optimal weight:    1.9990
   chunk 125 optimal weight:    0.0030
   chunk 64 optimal weight:    0.9990
   chunk 149 optimal weight:    0.5980
   chunk 60 optimal weight:    0.7980
   overall best weight:    0.4590

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

Flipped N/Q/H residues before XYZ refinement:
** L 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.081883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.057189 restraints weight = 63644.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.058872 restraints weight = 33519.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.059950 restraints weight = 22377.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.060619 restraints weight = 17383.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.060993 restraints weight = 14912.372|
|-----------------------------------------------------------------------------|
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8130
moved from start:          0.3788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  15661  Z= 0.103
  Angle     :  0.585  12.959  21226  Z= 0.292
  Chirality :  0.038   0.251   2403
  Planarity :  0.003   0.047   2618
  Dihedral  : 10.241 112.919   2320
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.82 %
    Favored  : 92.18 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 16.61 %
    Favored  : 82.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.87 (0.20), residues: 1817
  helix:  1.05 (0.17), residues: 953
  sheet: -1.53 (0.49), residues: 109
  loop : -2.70 (0.22), residues: 755

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L 343 
 TYR   0.012   0.001   TYR L 442 
 PHE   0.042   0.001   PHE L 954 
 TRP   0.008   0.001   TRP L2139 
 HIS   0.002   0.000   HIS L 652 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 (15658)
  covalent geometry    : angle       0.58452 (21226)
  hydrogen bonds       : bond        0.03174 (  665)
  hydrogen bonds       : angle       3.86272 ( 1891)
  metal coordination   : bond        0.00167 (    3)

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

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

  3634 Ramachandran restraints generated.
    1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3634 Ramachandran restraints generated.
    1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 102
  time to evaluate  : 0.449 
Fit side-chains
REVERT: L   38 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8150 (mm)
REVERT: L  154 ASP cc_start: 0.8746 (m-30) cc_final: 0.8098 (m-30)
REVERT: L  393 GLU cc_start: 0.8731 (tt0) cc_final: 0.8451 (tp30)
REVERT: L  394 LYS cc_start: 0.9275 (tppt) cc_final: 0.9041 (tppt)
REVERT: L  483 MET cc_start: 0.8755 (mmt) cc_final: 0.8398 (mmm)
REVERT: L 1060 MET cc_start: 0.8238 (mmm) cc_final: 0.7752 (tpp)
REVERT: L 1077 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7871 (mt-10)
REVERT: L 1092 MET cc_start: 0.8076 (tpt) cc_final: 0.7555 (mtt)
REVERT: L 1901 MET cc_start: 0.6135 (mmm) cc_final: 0.5575 (mmp)
  outliers start: 21
  outliers final: 19
  residues processed: 118
  average time/residue: 0.1167
  time to fit residues: 21.7545
Evaluate side-chains
  115 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 95
  time to evaluate  : 0.580 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   38 LEU
Chi-restraints excluded: chain L residue  160 LEU
Chi-restraints excluded: chain L residue  205 VAL
Chi-restraints excluded: chain L residue  254 ILE
Chi-restraints excluded: chain L residue  259 LEU
Chi-restraints excluded: chain L residue  435 VAL
Chi-restraints excluded: chain L residue  465 VAL
Chi-restraints excluded: chain L residue  502 LEU
Chi-restraints excluded: chain L residue  513 THR
Chi-restraints excluded: chain L residue  540 LEU
Chi-restraints excluded: chain L residue  829 VAL
Chi-restraints excluded: chain L residue  882 LEU
Chi-restraints excluded: chain L residue 1084 SER
Chi-restraints excluded: chain L residue 1300 THR
Chi-restraints excluded: chain L residue 1328 THR
Chi-restraints excluded: chain L residue 1458 PHE
Chi-restraints excluded: chain L residue 1481 GLN
Chi-restraints excluded: chain L residue 1780 LEU
Chi-restraints excluded: chain L residue 2118 LEU
Chi-restraints excluded: chain L residue 2157 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 117 optimal weight:    0.9980
   chunk 84 optimal weight:    0.0980
   chunk 71 optimal weight:    0.0040
   chunk 120 optimal weight:    0.9990
   chunk 159 optimal weight:    0.9990
   chunk 26 optimal weight:    0.6980
   chunk 176 optimal weight:    5.9990
   chunk 75 optimal weight:    3.9990
   chunk 99 optimal weight:    0.9980
   chunk 19 optimal weight:    7.9990
   chunk 51 optimal weight:    1.9990
   overall best weight:    0.5592

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

Flipped N/Q/H residues before XYZ refinement:
** L 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.081946 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.057316 restraints weight = 63059.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.058997 restraints weight = 33372.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.060084 restraints weight = 22287.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.060744 restraints weight = 17296.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.061115 restraints weight = 14841.974|
|-----------------------------------------------------------------------------|
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8128
moved from start:          0.3878

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  15661  Z= 0.106
  Angle     :  0.593  12.900  21226  Z= 0.295
  Chirality :  0.038   0.217   2403
  Planarity :  0.004   0.075   2618
  Dihedral  : 10.228 112.813   2320
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 8.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.26 %
    Favored  : 91.74 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 16.67 %
    Favored  : 81.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.81 (0.20), residues: 1817
  helix:  1.09 (0.17), residues: 953
  sheet: -1.37 (0.49), residues: 109
  loop : -2.68 (0.22), residues: 755

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG L 337 
 TYR   0.013   0.001   TYR L 442 
 PHE   0.044   0.001   PHE L 954 
 TRP   0.008   0.001   TRP L1194 
 HIS   0.003   0.000   HIS L 652 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 (15658)
  covalent geometry    : angle       0.59277 (21226)
  hydrogen bonds       : bond        0.03194 (  665)
  hydrogen bonds       : angle       3.87312 ( 1891)
  metal coordination   : bond        0.00165 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2717.47 seconds
wall clock time: 47 minutes 42.75 seconds (2862.75 seconds total)