Starting phenix.real_space_refine
on Wed Mar  4 05:39:03 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7oe7_12861/03_2026/7oe7_12861.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7oe7_12861/03_2026/7oe7_12861.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.73
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7oe7_12861/03_2026/7oe7_12861.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7oe7_12861/03_2026/7oe7_12861.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7oe7_12861/03_2026/7oe7_12861.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7oe7_12861/03_2026/7oe7_12861.cif"
  }
  resolution = 3.73
  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=   0.002 sd=   0.018
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     Mg      1      5.21       5
     S      63      5.16       5
     C    7088      2.51       5
     N    1881      2.21       5
     O    2082      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s

  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: 11116
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "L"
      Number of atoms: 11114
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1382, 11114
          Classifications: {'peptide': 1382}
          Link IDs: {'PTRANS': 42, 'TRANS': 1339}
          Chain breaks: 11
    Chain: "L"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MG': 1, ' ZN': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM    998  SG  CYS L 321      41.658 105.490  68.143  1.00100.99           S
  ATOM   1360  SG  CYS L 366      39.678 105.920  71.466  1.00108.15           S

  Time building chain proxies: 2.42, per 1000 atoms: 0.22
  Number of scatterers: 11116
  At special positions: 0
  Unit cell: (97.44, 133.11, 121.8, 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      63     16.00
     Mg      1     11.99
     O    2082      8.00
     N    1881      7.00
     C    7088      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS L1690 " - pdb=" SG  CYS L1790 " distance=2.03

  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: 0.66
  Conformation dependent library (CDL) restraints added in 519.0 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN L2301 "
        pdb="ZN    ZN L2301 " - pdb=" NE2 HIS L 364 "
        pdb="ZN    ZN L2301 " - pdb=" NE2 HIS L 316 "
        pdb="ZN    ZN L2301 " - pdb=" SG  CYS L 321 "
        pdb="ZN    ZN L2301 " - pdb=" SG  CYS L 366 "
      Number of angles added : 2


  2716 Ramachandran restraints generated.
    1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2646

  Finding SS restraints...
    Secondary structure from input PDB file:
      64 helices and 9 sheets defined
      54.8% alpha, 4.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.34
  Creating SS restraints...
    Processing helix  chain 'L' and resid 202 through 206
      removed outlier: 3.713A  pdb=" N   VAL L 205 " --> pdb=" O   SER L 202 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 212 through 222
      removed outlier: 4.263A  pdb=" N   GLU L 216 " --> pdb=" O   SER L 212 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   ILE L 217 " --> pdb=" O   HIS L 213 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   ILE L 218 " --> pdb=" O   TYR L 214 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 233 through 252
      removed outlier: 3.505A  pdb=" N   GLN L 237 " --> pdb=" O   GLU L 233 " (cutoff:3.500A)
      removed outlier: 3.675A  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: 3.577A  pdb=" N   LYS L 293 " --> pdb=" O   ILE L 289 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 296 through 302
    Processing helix  chain 'L' and resid 312 through 317
      removed outlier: 3.811A  pdb=" N   THR L 317 " --> pdb=" O   GLU L 313 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 323 through 336
      removed outlier: 3.542A  pdb=" N   LEU L 336 " --> pdb=" O   LYS L 332 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 343 through 361
      removed outlier: 3.850A  pdb=" N   LEU L 352 " --> pdb=" O   ILE L 348 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   ILE L 353 " --> pdb=" O   PHE L 349 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   LEU L 354 " --> pdb=" O   ASP L 350 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 385 through 404
    Processing helix  chain 'L' and resid 414 through 436
      removed outlier: 4.099A  pdb=" N   ILE L 418 " --> pdb=" O   ASN L 414 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   VAL L 435 " --> pdb=" O   ALA L 431 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   GLY L 436 " --> pdb=" O   LEU L 432 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 439 through 443
      removed outlier: 3.526A  pdb=" N   TYR L 442 " --> pdb=" O   VAL L 439 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   LYS L 443 " --> pdb=" O   GLU L 440 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 439 through 443'
    Processing helix  chain 'L' and resid 445 through 449
      removed outlier: 3.576A  pdb=" N   VAL L 448 " --> pdb=" O   ASN L 445 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   ILE L 449 " --> pdb=" O   MET L 446 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 445 through 449'
    Processing helix  chain 'L' and resid 453 through 458
      removed outlier: 3.627A  pdb=" N   LEU L 458 " --> pdb=" O   TYR L 454 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 491 through 507
      removed outlier: 3.864A  pdb=" N   GLU L 495 " --> pdb=" O   SER L 491 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   ARG L 496 " --> pdb=" O   THR L 492 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 588 through 599
    Processing helix  chain 'L' and resid 604 through 608
      removed outlier: 3.950A  pdb=" N   GLU L 608 " --> pdb=" O   SER L 605 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 611 through 628
      removed outlier: 3.596A  pdb=" N   ASN L 615 " --> pdb=" O   LEU L 611 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 633 through 639
      removed outlier: 3.628A  pdb=" N   LEU L 637 " --> pdb=" O   SER L 633 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   ASN L 639 " --> pdb=" O   LYS L 635 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 639 through 648
      removed outlier: 3.513A  pdb=" N   PHE L 643 " --> pdb=" O   ASN L 639 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   VAL L 648 " --> pdb=" O   ILE L 644 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 656 through 660
    Processing helix  chain 'L' and resid 668 through 684
    Processing helix  chain 'L' and resid 693 through 703
    Processing helix  chain 'L' and resid 704 through 709
      removed outlier: 3.542A  pdb=" N   HIS L 707 " --> pdb=" O   TYR L 704 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   ILE L 709 " --> pdb=" O   CYS L 706 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 717 through 729
      removed outlier: 4.087A  pdb=" N   LYS L 722 " --> pdb=" O   THR L 718 " (cutoff:3.500A)
      removed outlier: 4.214A  pdb=" N   CYS L 723 " --> pdb=" O   ASP L 719 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   PHE L 724 " --> pdb=" O   GLN L 720 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 729 through 734
      removed outlier: 3.939A  pdb=" N   GLU L 733 " --> pdb=" O   GLU L 729 " (cutoff:3.500A)
      removed outlier: 4.062A  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 760
    Processing helix  chain 'L' and resid 780 through 793
    Processing helix  chain 'L' and resid 800 through 804
      removed outlier: 3.656A  pdb=" N   LYS L 803 " --> pdb=" O   SER L 800 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 818 through 823
    Processing helix  chain 'L' and resid 843 through 862
      removed outlier: 4.485A  pdb=" N   ARG L 860 " --> pdb=" O   GLU L 856 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   LYS L 861 " --> pdb=" O   VAL L 857 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 870 through 881
      removed outlier: 3.663A  pdb=" N   ALA L 878 " --> pdb=" O   LYS L 874 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 907 through 925
      removed outlier: 3.965A  pdb=" N   LYS L 915 " --> pdb=" O   PHE L 911 " (cutoff:3.500A)
      removed outlier: 4.741A  pdb=" N   GLU L 916 " --> pdb=" O   ASP L 912 " (cutoff:3.500A)
      removed outlier: 4.326A  pdb=" N   THR L 917 " --> pdb=" O   GLN L 913 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   VAL L 918 " --> pdb=" O   LEU L 914 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1059 through 1068
    Processing helix  chain 'L' and resid 1075 through 1084
    Processing helix  chain 'L' and resid 1093 through 1098
      removed outlier: 3.714A  pdb=" N   CYS L1097 " --> pdb=" O   LEU L1093 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1137 through 1158
      removed outlier: 3.664A  pdb=" N   ARG L1145 " --> pdb=" O   LYS L1141 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   LEU L1146 " --> pdb=" O   MET L1142 " (cutoff:3.500A)
      removed outlier: 4.233A  pdb=" N   ILE L1147 " --> pdb=" O   PHE L1143 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   LEU L1158 " --> pdb=" O   LEU L1154 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1166 through 1182
      removed outlier: 3.646A  pdb=" N   GLU L1170 " --> pdb=" O   GLU L1166 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   LEU L1182 " --> pdb=" O   LEU L1178 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1199 through 1208
      removed outlier: 3.784A  pdb=" N   PHE L1203 " --> pdb=" O   CYS L1199 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1216 through 1236
      removed outlier: 3.779A  pdb=" N   ASP L1220 " --> pdb=" O   ASP L1216 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1242 through 1259
      removed outlier: 3.667A  pdb=" N   GLN L1257 " --> pdb=" O   PHE L1253 " (cutoff:3.500A)
      removed outlier: 4.457A  pdb=" N   LEU L1258 " --> pdb=" O   ILE L1254 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1270 through 1278
      removed outlier: 3.641A  pdb=" N   ASN L1276 " --> pdb=" O   PHE L1272 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1297 through 1320
      removed outlier: 3.522A  pdb=" N   SER L1301 " --> pdb=" O   LEU L1297 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1338 through 1348
      removed outlier: 3.719A  pdb=" N   GLN L1346 " --> pdb=" O   THR L1342 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   ARG L1347 " --> pdb=" O   GLU L1343 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1348 through 1365
      removed outlier: 3.851A  pdb=" N   THR L1354 " --> pdb=" O   GLU L1350 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1396 through 1406
      removed outlier: 3.860A  pdb=" N   HIS L1406 " --> pdb=" O   ALA L1402 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1414 through 1429
      removed outlier: 4.074A  pdb=" N   GLU L1418 " --> pdb=" O   HIS L1414 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   ALA L1429 " --> pdb=" O   ASP L1425 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1433 through 1451
      removed outlier: 4.030A  pdb=" N   CYS L1437 " --> pdb=" O   PRO L1433 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   ALA L1451 " --> pdb=" O   LEU L1447 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1466 through 1471
    Processing helix  chain 'L' and resid 1473 through 1486
      removed outlier: 3.576A  pdb=" N   ARG L1477 " --> pdb=" O   ASN L1473 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   ILE L1478 " --> pdb=" O   ARG L1474 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   ARG L1484 " --> pdb=" O   ARG L1480 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   LEU L1485 " --> pdb=" O   GLN L1481 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   ILE L1486 " --> pdb=" O   ILE L1482 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1492 through 1506
      removed outlier: 4.371A  pdb=" N   ARG L1498 " --> pdb=" O   ARG L1494 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   THR L1506 " --> pdb=" O   ASN L1502 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1521 through 1533
      removed outlier: 3.730A  pdb=" N   LEU L1533 " --> pdb=" O   LEU L1529 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1539 through 1543
      removed outlier: 3.878A  pdb=" N   LEU L1543 " --> pdb=" O   GLU L1540 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1579 through 1589
    Processing helix  chain 'L' and resid 1592 through 1605
    Processing helix  chain 'L' and resid 1613 through 1624
    Processing helix  chain 'L' and resid 1639 through 1649
    Processing helix  chain 'L' and resid 1668 through 1672
      removed outlier: 4.427A  pdb=" N   ASP L1672 " --> pdb=" O   ASN L1669 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1677 through 1679
      No H-bonds generated for 'chain 'L' and resid 1677 through 1679'
    Processing helix  chain 'L' and resid 1684 through 1699
    Processing helix  chain 'L' and resid 1701 through 1705
      removed outlier: 3.669A  pdb=" N   LEU L1704 " --> pdb=" O   ALA L1701 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1778 through 1790
      removed outlier: 4.136A  pdb=" N   VAL L1788 " --> pdb=" O   VAL L1784 " (cutoff:3.500A)
      removed outlier: 4.272A  pdb=" N   ASN L1789 " --> pdb=" O   ALA L1785 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   CYS L1790 " --> pdb=" O   LEU L1786 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1794 through 1800
      removed outlier: 3.585A  pdb=" N   HIS L1798 " --> pdb=" O   SER L1794 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1812 through 1817
      removed outlier: 3.690A  pdb=" N   ARG L1816 " --> pdb=" O   SER L1812 " (cutoff:3.500A)
      removed outlier: 4.665A  pdb=" N   LEU L1817 " --> pdb=" O   SER L1813 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 1812 through 1817'
    Processing sheet with id=AA1, first strand: chain 'L' and resid 207 through 208
      removed outlier: 6.631A  pdb=" N   LEU L 207 " --> pdb=" O   TYR L1107 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'L' and resid 259 through 260
    Processing sheet with id=AA3, first strand: chain 'L' and resid 535 through 541
      removed outlier: 3.950A  pdb=" N   CYS L 571 " --> pdb=" O   ILE L 562 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'L' and resid 826 through 828
      removed outlier: 3.534A  pdb=" N   VAL L 827 " --> pdb=" O   GLU L1073 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'L' and resid 1132 through 1136
      removed outlier: 4.450A  pdb=" N   LEU L1121 " --> pdb=" O   GLU L1240 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 1333 through 1336
      removed outlier: 3.949A  pdb=" N   GLN L1333 " --> pdb=" O   MET L1189 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'L' and resid 1381 through 1382
    Processing sheet with id=AA8, first strand: chain 'L' and resid 1653 through 1655
    Processing sheet with id=AA9, first strand: chain 'L' and resid 1723 through 1726
      removed outlier: 3.727A  pdb=" N   VAL L1810 " --> pdb=" O   PHE L1724 " (cutoff:3.500A)

    479 hydrogen bonds defined for protein.
    1371 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.89

  Time building geometry restraints manager: 0.95 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3590
        1.34 -     1.46: 2442
        1.46 -     1.58: 5196
        1.58 -     1.69: 0
        1.69 -     1.81: 94
  Bond restraints: 11322
  Sorted by residual:
  bond pdb=" C   PHE L 581 "
       pdb=" N   PRO L 582 "
    ideal  model  delta    sigma   weight residual
    1.335  1.359 -0.024 1.19e-02 7.06e+03 4.17e+00
  bond pdb=" CA  MET L 446 "
       pdb=" C   MET L 446 "
    ideal  model  delta    sigma   weight residual
    1.522  1.540 -0.018 1.38e-02 5.25e+03 1.62e+00
  bond pdb=" CA  ASP L1216 "
       pdb=" C   ASP L1216 "
    ideal  model  delta    sigma   weight residual
    1.523  1.533 -0.010 1.10e-02 8.26e+03 8.15e-01
  bond pdb=" CA  LYS L 635 "
       pdb=" C   LYS L 635 "
    ideal  model  delta    sigma   weight residual
    1.522  1.510  0.012 1.38e-02 5.25e+03 7.85e-01
  bond pdb=" CA  PRO L 410 "
       pdb=" C   PRO L 410 "
    ideal  model  delta    sigma   weight residual
    1.525  1.543 -0.018 2.10e-02 2.27e+03 7.43e-01
  ... (remaining 11317 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.46: 14907
        1.46 -     2.91: 294
        2.91 -     4.37: 56
        4.37 -     5.82: 11
        5.82 -     7.28: 1
  Bond angle restraints: 15269
  Sorted by residual:
  angle pdb=" N   ILE L1613 "
        pdb=" CA  ILE L1613 "
        pdb=" C   ILE L1613 "
      ideal   model   delta    sigma   weight residual
     111.90  108.46    3.44 8.10e-01 1.52e+00 1.80e+01
  angle pdb=" N   ILE L 318 "
        pdb=" CA  ILE L 318 "
        pdb=" C   ILE L 318 "
      ideal   model   delta    sigma   weight residual
     112.98  108.33    4.65 1.25e+00 6.40e-01 1.39e+01
  angle pdb=" N   ILE L1639 "
        pdb=" CA  ILE L1639 "
        pdb=" C   ILE L1639 "
      ideal   model   delta    sigma   weight residual
     111.81  108.66    3.15 8.60e-01 1.35e+00 1.34e+01
  angle pdb=" N   SER L 211 "
        pdb=" CA  SER L 211 "
        pdb=" C   SER L 211 "
      ideal   model   delta    sigma   weight residual
     110.97  114.81   -3.84 1.09e+00 8.42e-01 1.24e+01
  angle pdb=" C   ILE L1486 "
        pdb=" CA  ILE L1486 "
        pdb=" CB  ILE L1486 "
      ideal   model   delta    sigma   weight residual
     111.08  114.21   -3.13 9.50e-01 1.11e+00 1.09e+01
  ... (remaining 15264 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.94: 6055
       16.94 -    33.87: 684
       33.87 -    50.81: 126
       50.81 -    67.74: 20
       67.74 -    84.68: 10
  Dihedral angle restraints: 6895
    sinusoidal: 2827
      harmonic: 4068
  Sorted by residual:
  dihedral pdb=" CB  CYS L1690 "
           pdb=" SG  CYS L1690 "
           pdb=" SG  CYS L1790 "
           pdb=" CB  CYS L1790 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -131.89   45.89     1      1.00e+01 1.00e-02 2.92e+01
  dihedral pdb=" CA  THR L 710 "
           pdb=" C   THR L 710 "
           pdb=" N   LYS L 711 "
           pdb=" CA  LYS L 711 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.88   18.12     0      5.00e+00 4.00e-02 1.31e+01
  dihedral pdb=" CA  VAL L 275 "
           pdb=" C   VAL L 275 "
           pdb=" N   ASP L 276 "
           pdb=" CA  ASP L 276 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.93   17.07     0      5.00e+00 4.00e-02 1.17e+01
  ... (remaining 6892 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 1440
       0.049 -    0.097: 253
       0.097 -    0.146: 40
       0.146 -    0.195: 1
       0.195 -    0.244: 1
  Chirality restraints: 1735
  Sorted by residual:
  chirality pdb=" CB  THR L 710 "
            pdb=" CA  THR L 710 "
            pdb=" OG1 THR L 710 "
            pdb=" CG2 THR L 710 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.31    0.24 2.00e-01 2.50e+01 1.48e+00
  chirality pdb=" CB  VAL L 601 "
            pdb=" CA  VAL L 601 "
            pdb=" CG1 VAL L 601 "
            pdb=" CG2 VAL L 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.45   -0.18 2.00e-01 2.50e+01 7.71e-01
  chirality pdb=" CA  ILE L1241 "
            pdb=" N   ILE L1241 "
            pdb=" C   ILE L1241 "
            pdb=" CB  ILE L1241 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.62e-01
  ... (remaining 1732 not shown)

  Planarity restraints: 1928
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE L1486 "   -0.029 5.00e-02 4.00e+02   4.43e-02 3.14e+00
        pdb=" N   PRO L1487 "    0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO L1487 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO L1487 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU L1412 "    0.027 5.00e-02 4.00e+02   4.04e-02 2.61e+00
        pdb=" N   PRO L1413 "   -0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO L1413 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO L1413 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE L 709 "   -0.008 2.00e-02 2.50e+03   1.60e-02 2.57e+00
        pdb=" C   ILE L 709 "    0.028 2.00e-02 2.50e+03
        pdb=" O   ILE L 709 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   THR L 710 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 1925 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.65: 100
        2.65 -     3.21: 9785
        3.21 -     3.77: 14997
        3.77 -     4.34: 20108
        4.34 -     4.90: 33890
  Nonbonded interactions: 78880
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP L1332 "
            pdb="MG    MG L2302 "
     model   vdw
     2.084 2.170
  nonbonded pdb=" OD1 ASP L1657 "
            pdb=" N   SER L1658 "
     model   vdw
     2.125 3.120
  nonbonded pdb=" OG  SER L 498 "
            pdb=" O   ILE L 584 "
     model   vdw
     2.156 3.040
  nonbonded pdb=" OG  SER L 685 "
            pdb=" OD1 ASP L 687 "
     model   vdw
     2.158 3.040
  nonbonded pdb=" OG  SER L1161 "
            pdb=" OD2 ASP L1302 "
     model   vdw
     2.167 3.040
  ... (remaining 78875 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.730
  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:             0.000
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     11.450
  Find NCS groups from input model:        0.050
  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:             0.000
  Load rotamer database and sin/cos tables:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.810
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6419
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   0.024  11327  Z= 0.112
  Angle     :  0.528   7.276  15273  Z= 0.306
  Chirality :  0.038   0.244   1735
  Planarity :  0.003   0.044   1928
  Dihedral  : 14.332  84.676   4246
  Min Nonbonded Distance : 2.084

Molprobity Statistics.
  All-atom Clashscore : 3.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.77 %
    Favored  : 93.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.32 %
    Favored  : 99.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.48 (0.23), residues: 1358
  helix:  0.92 (0.21), residues: 697
  sheet: -1.94 (0.67), residues: 57
  loop : -3.38 (0.20), residues: 604

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG L1665 
 TYR   0.018   0.001   TYR L 574 
 PHE   0.015   0.001   PHE L1303 
 TRP   0.018   0.001   TRP L 395 
 HIS   0.002   0.001   HIS L 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00205 (11322)
  covalent geometry    : angle       0.52792 (15269)
  SS BOND              : bond        0.00078 (    1)
  SS BOND              : angle       0.38634 (    2)
  hydrogen bonds       : bond        0.16300 (  479)
  hydrogen bonds       : angle       4.66308 ( 1371)
  metal coordination   : bond        0.00258 (    4)
  metal coordination   : angle       0.80032 (    2)

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

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

  2716 Ramachandran restraints generated.
    1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2716 Ramachandran restraints generated.
    1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  259 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 259
  time to evaluate  : 0.428 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 259
  average time/residue: 0.1209
  time to fit residues: 42.5195
Evaluate side-chains
  106 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 98 optimal weight:    5.9990
   chunk 107 optimal weight:    0.6980
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:   10.0000
   chunk 130 optimal weight:   10.0000
   chunk 124 optimal weight:    6.9990
   chunk 103 optimal weight:    0.8980
   chunk 77 optimal weight:    0.6980
   chunk 122 optimal weight:    0.6980
   chunk 91 optimal weight:    4.9990
   chunk 55 optimal weight:    1.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
L 359 HIS
L 379 ASN
L 441 HIS
L1126 GLN
L1208 GLN
L1807 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.104840 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.084864 restraints weight = 40597.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.085662 restraints weight = 23945.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.086372 restraints weight = 17372.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.086856 restraints weight = 15583.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.087044 restraints weight = 13695.005|
|-----------------------------------------------------------------------------|
r_work (final): 0.3735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7381
moved from start:          0.2697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  11327  Z= 0.119
  Angle     :  0.618  12.138  15273  Z= 0.305
  Chirality :  0.040   0.209   1735
  Planarity :  0.004   0.044   1928
  Dihedral  :  3.951  18.968   1490
  Min Nonbonded Distance : 2.059

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.07 %
    Favored  : 92.93 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  :  9.67 %
    Favored  : 88.50 %
  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: -1.36 (0.23), residues: 1358
  helix:  0.92 (0.21), residues: 714
  sheet: -1.67 (0.67), residues: 55
  loop : -3.33 (0.20), residues: 589

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG L 920 
 TYR   0.017   0.001   TYR L 471 
 PHE   0.015   0.001   PHE L1303 
 TRP   0.015   0.001   TRP L1664 
 HIS   0.006   0.001   HIS L1798 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 (11322)
  covalent geometry    : angle       0.61737 (15269)
  SS BOND              : bond        0.00056 (    1)
  SS BOND              : angle       0.16464 (    2)
  hydrogen bonds       : bond        0.03711 (  479)
  hydrogen bonds       : angle       3.86329 ( 1371)
  metal coordination   : bond        0.01239 (    4)
  metal coordination   : angle       1.61426 (    2)

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

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

  2716 Ramachandran restraints generated.
    1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2716 Ramachandran restraints generated.
    1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 116
  time to evaluate  : 0.424 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L 1292 MET cc_start: 0.7965 (tmm) cc_final: 0.7627 (tmm)
  outliers start: 23
  outliers final: 13
  residues processed: 138
  average time/residue: 0.0945
  time to fit residues: 19.3395
Evaluate side-chains
  101 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 88
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue  390 ARG
Chi-restraints excluded: chain L residue  611 LEU
Chi-restraints excluded: chain L residue  671 LEU
Chi-restraints excluded: chain L residue  704 TYR
Chi-restraints excluded: chain L residue  846 LEU
Chi-restraints excluded: chain L residue  871 TYR
Chi-restraints excluded: chain L residue 1319 ILE
Chi-restraints excluded: chain L residue 1328 THR
Chi-restraints excluded: chain L residue 1408 ILE
Chi-restraints excluded: chain L residue 1434 VAL
Chi-restraints excluded: chain L residue 1524 SER
Chi-restraints excluded: chain L residue 1550 LEU
Chi-restraints excluded: chain L residue 1639 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 79 optimal weight:    7.9990
   chunk 3 optimal weight:    0.0970
   chunk 29 optimal weight:    7.9990
   chunk 92 optimal weight:    4.9990
   chunk 135 optimal weight:    9.9990
   chunk 56 optimal weight:    0.9990
   chunk 7 optimal weight:    6.9990
   chunk 99 optimal weight:    0.9980
   chunk 9 optimal weight:    5.9990
   chunk 35 optimal weight:    4.9990
   chunk 26 optimal weight:    4.9990
   overall best weight:    2.4184

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

Flipped N/Q/H residues before XYZ refinement:
L 591 GLN
L 830 ASN
L1055 ASN
** L1299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L1449 GLN
L1461 ASN
L1549 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.099627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.079767 restraints weight = 40880.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.080889 restraints weight = 24848.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.081566 restraints weight = 17829.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.081679 restraints weight = 15979.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.081838 restraints weight = 14901.231|
|-----------------------------------------------------------------------------|
r_work (final): 0.3631
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7514
moved from start:          0.4021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.091  11327  Z= 0.184
  Angle     :  0.662  11.204  15273  Z= 0.335
  Chirality :  0.042   0.264   1735
  Planarity :  0.004   0.057   1928
  Dihedral  :  4.371  18.254   1490
  Min Nonbonded Distance : 2.034

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.03 %
    Favored  : 91.97 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 13.01 %
    Favored  : 84.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.50 (0.23), residues: 1358
  helix:  0.78 (0.20), residues: 716
  sheet: -2.14 (0.59), residues: 67
  loop : -3.34 (0.21), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG L1347 
 TYR   0.018   0.002   TYR L1688 
 PHE   0.017   0.002   PHE L 585 
 TRP   0.016   0.002   TRP L1664 
 HIS   0.006   0.001   HIS L 707 

Details of bonding type rmsd
  covalent geometry    : bond        0.00426 (11322)
  covalent geometry    : angle       0.66174 (15269)
  SS BOND              : bond        0.00061 (    1)
  SS BOND              : angle       0.60184 (    2)
  hydrogen bonds       : bond        0.04801 (  479)
  hydrogen bonds       : angle       4.11639 ( 1371)
  metal coordination   : bond        0.01051 (    4)
  metal coordination   : angle       2.42760 (    2)

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

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

  2716 Ramachandran restraints generated.
    1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2716 Ramachandran restraints generated.
    1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 93
  time to evaluate  : 0.445 
Fit side-chains
   revert: symmetry clash
REVERT: L  302 LEU cc_start: 0.8106 (tp) cc_final: 0.7110 (mt)
REVERT: L  395 TRP cc_start: 0.8481 (t60) cc_final: 0.7953 (t60)
REVERT: L  607 LEU cc_start: 0.7270 (tt) cc_final: 0.7056 (tp)
REVERT: L 1292 MET cc_start: 0.8146 (tmm) cc_final: 0.7914 (tmm)
REVERT: L 1598 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.7720 (pptt)
REVERT: L 1709 LYS cc_start: 0.5839 (OUTLIER) cc_final: 0.5546 (ptpt)
  outliers start: 33
  outliers final: 20
  residues processed: 121
  average time/residue: 0.0861
  time to fit residues: 15.9349
Evaluate side-chains
  107 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 85
  time to evaluate  : 0.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue  379 ASN
Chi-restraints excluded: chain L residue  671 LEU
Chi-restraints excluded: chain L residue  710 THR
Chi-restraints excluded: chain L residue  830 ASN
Chi-restraints excluded: chain L residue  857 VAL
Chi-restraints excluded: chain L residue  871 TYR
Chi-restraints excluded: chain L residue  916 GLU
Chi-restraints excluded: chain L residue 1122 SER
Chi-restraints excluded: chain L residue 1234 HIS
Chi-restraints excluded: chain L residue 1319 ILE
Chi-restraints excluded: chain L residue 1328 THR
Chi-restraints excluded: chain L residue 1408 ILE
Chi-restraints excluded: chain L residue 1434 VAL
Chi-restraints excluded: chain L residue 1465 ASP
Chi-restraints excluded: chain L residue 1509 LEU
Chi-restraints excluded: chain L residue 1524 SER
Chi-restraints excluded: chain L residue 1526 LEU
Chi-restraints excluded: chain L residue 1598 LYS
Chi-restraints excluded: chain L residue 1624 LEU
Chi-restraints excluded: chain L residue 1639 ILE
Chi-restraints excluded: chain L residue 1659 HIS
Chi-restraints excluded: chain L residue 1709 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 111 optimal weight:    0.9980
   chunk 128 optimal weight:    0.0980
   chunk 16 optimal weight:    0.0060
   chunk 73 optimal weight:    5.9990
   chunk 69 optimal weight:    6.9990
   chunk 71 optimal weight:    0.0670
   chunk 49 optimal weight:    0.8980
   chunk 1 optimal weight:   10.0000
   chunk 131 optimal weight:    0.0030
   chunk 18 optimal weight:    5.9990
   chunk 100 optimal weight:    4.9990
   overall best weight:    0.2144

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

Flipped N/Q/H residues before XYZ refinement:
L 881 ASN
L1087 ASN
L1234 HIS
** L1299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L1449 GLN
L1461 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.102554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.082969 restraints weight = 39727.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.083991 restraints weight = 22685.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.084268 restraints weight = 17737.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.084984 restraints weight = 15328.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.085021 restraints weight = 13433.861|
|-----------------------------------------------------------------------------|
r_work (final): 0.3684
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7456
moved from start:          0.4024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  11327  Z= 0.100
  Angle     :  0.557  11.698  15273  Z= 0.274
  Chirality :  0.038   0.176   1735
  Planarity :  0.003   0.042   1928
  Dihedral  :  3.883  18.630   1490
  Min Nonbonded Distance : 2.045

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.60 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 14.67 %
    Favored  : 83.82 %
  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: -1.10 (0.23), residues: 1358
  helix:  1.05 (0.20), residues: 724
  sheet: -1.45 (0.65), residues: 57
  loop : -3.18 (0.21), residues: 577

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L1167 
 TYR   0.009   0.001   TYR L 274 
 PHE   0.012   0.001   PHE L1303 
 TRP   0.015   0.001   TRP L 395 
 HIS   0.004   0.001   HIS L 287 

Details of bonding type rmsd
  covalent geometry    : bond        0.00204 (11322)
  covalent geometry    : angle       0.55715 (15269)
  SS BOND              : bond        0.00107 (    1)
  SS BOND              : angle       0.52096 (    2)
  hydrogen bonds       : bond        0.03149 (  479)
  hydrogen bonds       : angle       3.67969 ( 1371)
  metal coordination   : bond        0.01110 (    4)
  metal coordination   : angle       0.88780 (    2)

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

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

  2716 Ramachandran restraints generated.
    1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2716 Ramachandran restraints generated.
    1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 93
  time to evaluate  : 0.477 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L  302 LEU cc_start: 0.8137 (tp) cc_final: 0.7190 (mt)
REVERT: L 1479 MET cc_start: 0.3899 (tpp) cc_final: 0.3497 (mmm)
REVERT: L 1624 LEU cc_start: 0.7665 (OUTLIER) cc_final: 0.7408 (tt)
  outliers start: 19
  outliers final: 9
  residues processed: 108
  average time/residue: 0.0730
  time to fit residues: 12.6070
Evaluate side-chains
  98 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 88
  time to evaluate  : 0.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue  313 GLU
Chi-restraints excluded: chain L residue  379 ASN
Chi-restraints excluded: chain L residue  704 TYR
Chi-restraints excluded: chain L residue  710 THR
Chi-restraints excluded: chain L residue  857 VAL
Chi-restraints excluded: chain L residue  871 TYR
Chi-restraints excluded: chain L residue  882 LEU
Chi-restraints excluded: chain L residue 1234 HIS
Chi-restraints excluded: chain L residue 1408 ILE
Chi-restraints excluded: chain L residue 1624 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 13 optimal weight:    8.9990
   chunk 118 optimal weight:    3.9990
   chunk 16 optimal weight:    7.9990
   chunk 67 optimal weight:    2.9990
   chunk 104 optimal weight:    4.9990
   chunk 28 optimal weight:    0.3980
   chunk 45 optimal weight:    0.8980
   chunk 115 optimal weight:    5.9990
   chunk 128 optimal weight:    3.9990
   chunk 83 optimal weight:    3.9990
   chunk 88 optimal weight:    4.9990
   overall best weight:    2.4586

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

Flipped N/Q/H residues before XYZ refinement:
L 415 GLN
** L1299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L1449 GLN
L1461 ASN
L1798 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.098963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.078825 restraints weight = 40638.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.080200 restraints weight = 25604.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.080655 restraints weight = 18342.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.081159 restraints weight = 15886.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.081350 restraints weight = 14524.859|
|-----------------------------------------------------------------------------|
r_work (final): 0.3619
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7555
moved from start:          0.4670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.076  11327  Z= 0.178
  Angle     :  0.635   9.878  15273  Z= 0.319
  Chirality :  0.041   0.211   1735
  Planarity :  0.004   0.039   1928
  Dihedral  :  4.228  18.879   1490
  Min Nonbonded Distance : 2.058

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.17 %
    Favored  : 91.83 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 16.65 %
    Favored  : 81.28 %
  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: -1.33 (0.23), residues: 1358
  helix:  0.85 (0.20), residues: 727
  sheet: -1.90 (0.60), residues: 67
  loop : -3.24 (0.22), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L 674 
 TYR   0.027   0.002   TYR L1688 
 PHE   0.015   0.002   PHE L 585 
 TRP   0.017   0.002   TRP L 395 
 HIS   0.035   0.002   HIS L1234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 (11322)
  covalent geometry    : angle       0.63474 (15269)
  SS BOND              : bond        0.00258 (    1)
  SS BOND              : angle       0.57362 (    2)
  hydrogen bonds       : bond        0.04490 (  479)
  hydrogen bonds       : angle       4.04994 ( 1371)
  metal coordination   : bond        0.00738 (    4)
  metal coordination   : angle       1.63174 (    2)

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

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

  2716 Ramachandran restraints generated.
    1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2716 Ramachandran restraints generated.
    1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 92
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L  302 LEU cc_start: 0.8131 (tp) cc_final: 0.7117 (mt)
REVERT: L  350 ASP cc_start: 0.6932 (p0) cc_final: 0.6133 (t0)
  outliers start: 26
  outliers final: 19
  residues processed: 112
  average time/residue: 0.0734
  time to fit residues: 13.4195
Evaluate side-chains
  103 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 84
  time to evaluate  : 0.444 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue  313 GLU
Chi-restraints excluded: chain L residue  379 ASN
Chi-restraints excluded: chain L residue  671 LEU
Chi-restraints excluded: chain L residue  710 THR
Chi-restraints excluded: chain L residue  857 VAL
Chi-restraints excluded: chain L residue  871 TYR
Chi-restraints excluded: chain L residue 1122 SER
Chi-restraints excluded: chain L residue 1319 ILE
Chi-restraints excluded: chain L residue 1328 THR
Chi-restraints excluded: chain L residue 1408 ILE
Chi-restraints excluded: chain L residue 1465 ASP
Chi-restraints excluded: chain L residue 1513 PHE
Chi-restraints excluded: chain L residue 1524 SER
Chi-restraints excluded: chain L residue 1580 ILE
Chi-restraints excluded: chain L residue 1624 LEU
Chi-restraints excluded: chain L residue 1628 CYS
Chi-restraints excluded: chain L residue 1639 ILE
Chi-restraints excluded: chain L residue 1659 HIS
Chi-restraints excluded: chain L residue 1661 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 133 optimal weight:    9.9990
   chunk 122 optimal weight:    0.6980
   chunk 30 optimal weight:    9.9990
   chunk 66 optimal weight:    4.9990
   chunk 46 optimal weight:    2.9990
   chunk 15 optimal weight:   20.0000
   chunk 86 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9980
   chunk 95 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
L 824 ASN
L1087 ASN
L1234 HIS
** L1299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.099899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.081445 restraints weight = 42555.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.080291 restraints weight = 29644.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.080891 restraints weight = 25943.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.081168 restraints weight = 21269.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.081344 restraints weight = 19630.592|
|-----------------------------------------------------------------------------|
r_work (final): 0.3595
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7604
moved from start:          0.5017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.075  11327  Z= 0.142
  Angle     :  0.587  11.873  15273  Z= 0.294
  Chirality :  0.040   0.294   1735
  Planarity :  0.003   0.041   1928
  Dihedral  :  4.138  17.664   1490
  Min Nonbonded Distance : 2.045

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.63 %
    Favored  : 93.37 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 18.16 %
    Favored  : 79.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.18 (0.23), residues: 1358
  helix:  1.02 (0.20), residues: 716
  sheet: -1.68 (0.55), residues: 82
  loop : -3.23 (0.22), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L1347 
 TYR   0.018   0.001   TYR L1688 
 PHE   0.021   0.001   PHE L 421 
 TRP   0.022   0.002   TRP L 395 
 HIS   0.005   0.001   HIS L1234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 (11322)
  covalent geometry    : angle       0.58689 (15269)
  SS BOND              : bond        0.00231 (    1)
  SS BOND              : angle       1.03508 (    2)
  hydrogen bonds       : bond        0.03743 (  479)
  hydrogen bonds       : angle       3.93673 ( 1371)
  metal coordination   : bond        0.00957 (    4)
  metal coordination   : angle       0.35246 (    2)

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

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

  2716 Ramachandran restraints generated.
    1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2716 Ramachandran restraints generated.
    1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 94
  time to evaluate  : 0.490 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L  302 LEU cc_start: 0.8094 (tp) cc_final: 0.7101 (mt)
REVERT: L  324 GLN cc_start: 0.7990 (mt0) cc_final: 0.7587 (pp30)
REVERT: L  350 ASP cc_start: 0.7117 (p0) cc_final: 0.6209 (t0)
REVERT: L 1532 LEU cc_start: 0.8919 (tp) cc_final: 0.8528 (pp)
REVERT: L 1558 MET cc_start: 0.6651 (mmm) cc_final: 0.5392 (mmm)
  outliers start: 30
  outliers final: 24
  residues processed: 114
  average time/residue: 0.0797
  time to fit residues: 14.3873
Evaluate side-chains
  106 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 82
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue  279 THR
Chi-restraints excluded: chain L residue  313 GLU
Chi-restraints excluded: chain L residue  379 ASN
Chi-restraints excluded: chain L residue  449 ILE
Chi-restraints excluded: chain L residue  508 MET
Chi-restraints excluded: chain L residue  625 ILE
Chi-restraints excluded: chain L residue  671 LEU
Chi-restraints excluded: chain L residue  710 THR
Chi-restraints excluded: chain L residue  817 THR
Chi-restraints excluded: chain L residue  857 VAL
Chi-restraints excluded: chain L residue  871 TYR
Chi-restraints excluded: chain L residue  882 LEU
Chi-restraints excluded: chain L residue 1234 HIS
Chi-restraints excluded: chain L residue 1319 ILE
Chi-restraints excluded: chain L residue 1328 THR
Chi-restraints excluded: chain L residue 1362 MET
Chi-restraints excluded: chain L residue 1408 ILE
Chi-restraints excluded: chain L residue 1465 ASP
Chi-restraints excluded: chain L residue 1513 PHE
Chi-restraints excluded: chain L residue 1524 SER
Chi-restraints excluded: chain L residue 1624 LEU
Chi-restraints excluded: chain L residue 1639 ILE
Chi-restraints excluded: chain L residue 1659 HIS
Chi-restraints excluded: chain L residue 1661 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 38 optimal weight:    4.9990
   chunk 4 optimal weight:    1.9990
   chunk 68 optimal weight:    2.9990
   chunk 128 optimal weight:    8.9990
   chunk 101 optimal weight:    2.9990
   chunk 127 optimal weight:    4.9990
   chunk 26 optimal weight:   20.0000
   chunk 39 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9990
   chunk 62 optimal weight:    0.7980
   chunk 61 optimal weight:    1.9990
   overall best weight:    1.5588

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

Flipped N/Q/H residues before XYZ refinement:
** L1299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L1586 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.099256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.079373 restraints weight = 40837.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.080526 restraints weight = 23582.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.080770 restraints weight = 17786.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.081136 restraints weight = 16342.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.081220 restraints weight = 14674.493|
|-----------------------------------------------------------------------------|
r_work (final): 0.3609
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7585
moved from start:          0.5140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065  11327  Z= 0.126
  Angle     :  0.587  11.556  15273  Z= 0.293
  Chirality :  0.039   0.272   1735
  Planarity :  0.003   0.041   1928
  Dihedral  :  4.082  17.289   1490
  Min Nonbonded Distance : 2.057

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.88 %
    Favored  : 92.12 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 18.64 %
    Favored  : 78.98 %
  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: -1.11 (0.23), residues: 1358
  helix:  1.09 (0.20), residues: 713
  sheet: -1.63 (0.56), residues: 82
  loop : -3.19 (0.22), residues: 563

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L 695 
 TYR   0.017   0.001   TYR L1688 
 PHE   0.024   0.001   PHE L 421 
 TRP   0.025   0.002   TRP L 395 
 HIS   0.004   0.001   HIS L1234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 (11322)
  covalent geometry    : angle       0.58741 (15269)
  SS BOND              : bond        0.00270 (    1)
  SS BOND              : angle       0.83817 (    2)
  hydrogen bonds       : bond        0.03716 (  479)
  hydrogen bonds       : angle       3.91574 ( 1371)
  metal coordination   : bond        0.00779 (    4)
  metal coordination   : angle       0.39703 (    2)

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

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

  2716 Ramachandran restraints generated.
    1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2716 Ramachandran restraints generated.
    1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 89
  time to evaluate  : 0.444 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L  324 GLN cc_start: 0.7901 (mt0) cc_final: 0.7461 (pp30)
REVERT: L  350 ASP cc_start: 0.7141 (p0) cc_final: 0.6198 (t0)
REVERT: L 1532 LEU cc_start: 0.8911 (tp) cc_final: 0.8525 (pp)
  outliers start: 30
  outliers final: 29
  residues processed: 110
  average time/residue: 0.0726
  time to fit residues: 13.2736
Evaluate side-chains
  109 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 80
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue  279 THR
Chi-restraints excluded: chain L residue  313 GLU
Chi-restraints excluded: chain L residue  379 ASN
Chi-restraints excluded: chain L residue  508 MET
Chi-restraints excluded: chain L residue  584 ILE
Chi-restraints excluded: chain L residue  625 ILE
Chi-restraints excluded: chain L residue  671 LEU
Chi-restraints excluded: chain L residue  710 THR
Chi-restraints excluded: chain L residue  817 THR
Chi-restraints excluded: chain L residue  830 ASN
Chi-restraints excluded: chain L residue  857 VAL
Chi-restraints excluded: chain L residue  871 TYR
Chi-restraints excluded: chain L residue  882 LEU
Chi-restraints excluded: chain L residue 1319 ILE
Chi-restraints excluded: chain L residue 1328 THR
Chi-restraints excluded: chain L residue 1362 MET
Chi-restraints excluded: chain L residue 1375 VAL
Chi-restraints excluded: chain L residue 1408 ILE
Chi-restraints excluded: chain L residue 1434 VAL
Chi-restraints excluded: chain L residue 1465 ASP
Chi-restraints excluded: chain L residue 1478 ILE
Chi-restraints excluded: chain L residue 1513 PHE
Chi-restraints excluded: chain L residue 1524 SER
Chi-restraints excluded: chain L residue 1559 VAL
Chi-restraints excluded: chain L residue 1580 ILE
Chi-restraints excluded: chain L residue 1624 LEU
Chi-restraints excluded: chain L residue 1639 ILE
Chi-restraints excluded: chain L residue 1659 HIS
Chi-restraints excluded: chain L residue 1661 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 45 optimal weight:    0.8980
   chunk 137 optimal weight:    5.9990
   chunk 121 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 27 optimal weight:    0.0980
   chunk 118 optimal weight:   10.0000
   chunk 70 optimal weight:    0.8980
   chunk 49 optimal weight:    4.9990
   chunk 103 optimal weight:    7.9990
   chunk 46 optimal weight:    0.6980
   chunk 114 optimal weight:    6.9990
   overall best weight:    1.5182

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

Flipped N/Q/H residues before XYZ refinement:
L1087 ASN
** L1299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L1549 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.098723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.078945 restraints weight = 42587.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.080096 restraints weight = 25388.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.080449 restraints weight = 18632.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.080696 restraints weight = 16990.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.080827 restraints weight = 15284.185|
|-----------------------------------------------------------------------------|
r_work (final): 0.3604
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7579
moved from start:          0.5319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067  11327  Z= 0.123
  Angle     :  0.582  12.260  15273  Z= 0.289
  Chirality :  0.039   0.261   1735
  Planarity :  0.003   0.039   1928
  Dihedral  :  4.056  17.018   1490
  Min Nonbonded Distance : 2.057

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.81 %
    Favored  : 92.19 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 18.72 %
    Favored  : 78.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.01 (0.23), residues: 1358
  helix:  1.16 (0.20), residues: 710
  sheet: -1.54 (0.56), residues: 82
  loop : -3.10 (0.23), residues: 566

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L1484 
 TYR   0.017   0.001   TYR L1688 
 PHE   0.025   0.001   PHE L 421 
 TRP   0.030   0.002   TRP L 395 
 HIS   0.004   0.001   HIS L 287 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 (11322)
  covalent geometry    : angle       0.58149 (15269)
  SS BOND              : bond        0.00242 (    1)
  SS BOND              : angle       0.83398 (    2)
  hydrogen bonds       : bond        0.03641 (  479)
  hydrogen bonds       : angle       3.90384 ( 1371)
  metal coordination   : bond        0.00855 (    4)
  metal coordination   : angle       0.44983 (    2)

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

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

  2716 Ramachandran restraints generated.
    1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2716 Ramachandran restraints generated.
    1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 84
  time to evaluate  : 0.424 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L  313 GLU cc_start: 0.6765 (OUTLIER) cc_final: 0.6294 (mp0)
REVERT: L  350 ASP cc_start: 0.7180 (p0) cc_final: 0.6197 (t0)
REVERT: L 1479 MET cc_start: 0.4042 (tpp) cc_final: 0.3636 (mmt)
REVERT: L 1532 LEU cc_start: 0.8892 (tp) cc_final: 0.8525 (pp)
REVERT: L 1558 MET cc_start: 0.6539 (mmm) cc_final: 0.5462 (mmm)
  outliers start: 35
  outliers final: 28
  residues processed: 110
  average time/residue: 0.0748
  time to fit residues: 13.3944
Evaluate side-chains
  108 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 79
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue  279 THR
Chi-restraints excluded: chain L residue  313 GLU
Chi-restraints excluded: chain L residue  379 ASN
Chi-restraints excluded: chain L residue  508 MET
Chi-restraints excluded: chain L residue  584 ILE
Chi-restraints excluded: chain L residue  625 ILE
Chi-restraints excluded: chain L residue  671 LEU
Chi-restraints excluded: chain L residue  688 VAL
Chi-restraints excluded: chain L residue  710 THR
Chi-restraints excluded: chain L residue  817 THR
Chi-restraints excluded: chain L residue  830 ASN
Chi-restraints excluded: chain L residue  857 VAL
Chi-restraints excluded: chain L residue  871 TYR
Chi-restraints excluded: chain L residue  882 LEU
Chi-restraints excluded: chain L residue 1319 ILE
Chi-restraints excluded: chain L residue 1328 THR
Chi-restraints excluded: chain L residue 1362 MET
Chi-restraints excluded: chain L residue 1408 ILE
Chi-restraints excluded: chain L residue 1434 VAL
Chi-restraints excluded: chain L residue 1465 ASP
Chi-restraints excluded: chain L residue 1478 ILE
Chi-restraints excluded: chain L residue 1513 PHE
Chi-restraints excluded: chain L residue 1524 SER
Chi-restraints excluded: chain L residue 1559 VAL
Chi-restraints excluded: chain L residue 1580 ILE
Chi-restraints excluded: chain L residue 1624 LEU
Chi-restraints excluded: chain L residue 1628 CYS
Chi-restraints excluded: chain L residue 1639 ILE
Chi-restraints excluded: chain L residue 1661 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 30 optimal weight:    6.9990
   chunk 76 optimal weight:    0.7980
   chunk 42 optimal weight:    4.9990
   chunk 94 optimal weight:    0.0980
   chunk 89 optimal weight:    4.9990
   chunk 11 optimal weight:   20.0000
   chunk 99 optimal weight:    0.6980
   chunk 73 optimal weight:   10.0000
   chunk 105 optimal weight:    6.9990
   chunk 44 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
L1234 HIS
L1299 ASN
L1449 GLN
L1461 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.100056 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.080471 restraints weight = 41631.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.081428 restraints weight = 25137.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.082200 restraints weight = 18589.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.082340 restraints weight = 14810.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.082599 restraints weight = 14728.980|
|-----------------------------------------------------------------------------|
r_work (final): 0.3645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7508
moved from start:          0.5334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  11327  Z= 0.094
  Angle     :  0.571  14.297  15273  Z= 0.277
  Chirality :  0.038   0.256   1735
  Planarity :  0.003   0.041   1928
  Dihedral  :  3.841  17.946   1490
  Min Nonbonded Distance : 2.066

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.55 %
    Favored  : 93.45 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 19.51 %
    Favored  : 78.51 %
  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 (0.23), residues: 1358
  helix:  1.29 (0.20), residues: 713
  sheet: -1.28 (0.58), residues: 76
  loop : -3.00 (0.22), residues: 569

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG L 920 
 TYR   0.010   0.001   TYR L 574 
 PHE   0.026   0.001   PHE L 421 
 TRP   0.030   0.001   TRP L 395 
 HIS   0.004   0.001   HIS L 287 

Details of bonding type rmsd
  covalent geometry    : bond        0.00210 (11322)
  covalent geometry    : angle       0.57134 (15269)
  SS BOND              : bond        0.00180 (    1)
  SS BOND              : angle       0.73201 (    2)
  hydrogen bonds       : bond        0.03093 (  479)
  hydrogen bonds       : angle       3.74414 ( 1371)
  metal coordination   : bond        0.00912 (    4)
  metal coordination   : angle       0.50604 (    2)

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

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

  2716 Ramachandran restraints generated.
    1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2716 Ramachandran restraints generated.
    1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 85
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
REVERT: L  302 LEU cc_start: 0.8043 (tp) cc_final: 0.7023 (mt)
REVERT: L  313 GLU cc_start: 0.6789 (OUTLIER) cc_final: 0.6396 (mp0)
REVERT: L  324 GLN cc_start: 0.7757 (mt0) cc_final: 0.7485 (pp30)
REVERT: L  350 ASP cc_start: 0.7159 (p0) cc_final: 0.6068 (t0)
REVERT: L 1092 MET cc_start: 0.7668 (mmm) cc_final: 0.7104 (mmm)
REVERT: L 1479 MET cc_start: 0.4279 (tpp) cc_final: 0.3830 (mmt)
REVERT: L 1532 LEU cc_start: 0.8874 (tp) cc_final: 0.8539 (pp)
REVERT: L 1558 MET cc_start: 0.6363 (mmm) cc_final: 0.5350 (mmm)
  outliers start: 25
  outliers final: 22
  residues processed: 106
  average time/residue: 0.0709
  time to fit residues: 12.4554
Evaluate side-chains
  101 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 78
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue  279 THR
Chi-restraints excluded: chain L residue  313 GLU
Chi-restraints excluded: chain L residue  379 ASN
Chi-restraints excluded: chain L residue  625 ILE
Chi-restraints excluded: chain L residue  671 LEU
Chi-restraints excluded: chain L residue  688 VAL
Chi-restraints excluded: chain L residue  710 THR
Chi-restraints excluded: chain L residue  857 VAL
Chi-restraints excluded: chain L residue  871 TYR
Chi-restraints excluded: chain L residue  882 LEU
Chi-restraints excluded: chain L residue 1234 HIS
Chi-restraints excluded: chain L residue 1319 ILE
Chi-restraints excluded: chain L residue 1328 THR
Chi-restraints excluded: chain L residue 1375 VAL
Chi-restraints excluded: chain L residue 1408 ILE
Chi-restraints excluded: chain L residue 1434 VAL
Chi-restraints excluded: chain L residue 1478 ILE
Chi-restraints excluded: chain L residue 1513 PHE
Chi-restraints excluded: chain L residue 1524 SER
Chi-restraints excluded: chain L residue 1559 VAL
Chi-restraints excluded: chain L residue 1624 LEU
Chi-restraints excluded: chain L residue 1639 ILE
Chi-restraints excluded: chain L residue 1661 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 119 optimal weight:    1.9990
   chunk 77 optimal weight:    0.7980
   chunk 75 optimal weight:    4.9990
   chunk 45 optimal weight:    0.8980
   chunk 29 optimal weight:    0.8980
   chunk 52 optimal weight:    0.9990
   chunk 137 optimal weight:    7.9990
   chunk 96 optimal weight:    0.2980
   chunk 41 optimal weight:    1.9990
   chunk 116 optimal weight:    0.3980
   chunk 57 optimal weight:    0.7980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
L1087 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.100931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.082383 restraints weight = 41063.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.082136 restraints weight = 22871.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.082528 restraints weight = 21894.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.083054 restraints weight = 17739.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.083399 restraints weight = 15769.806|
|-----------------------------------------------------------------------------|
r_work (final): 0.3654
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7509
moved from start:          0.5402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  11327  Z= 0.096
  Angle     :  0.603  16.419  15273  Z= 0.287
  Chirality :  0.039   0.319   1735
  Planarity :  0.003   0.042   1928
  Dihedral  :  3.778  17.092   1490
  Min Nonbonded Distance : 2.074

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.41 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 19.83 %
    Favored  : 78.35 %
  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: -0.73 (0.23), residues: 1358
  helix:  1.38 (0.21), residues: 709
  sheet: -1.27 (0.56), residues: 82
  loop : -2.97 (0.22), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG L 920 
 TYR   0.011   0.001   TYR L 574 
 PHE   0.032   0.001   PHE L 421 
 TRP   0.031   0.001   TRP L 395 
 HIS   0.005   0.001   HIS L1234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00216 (11322)
  covalent geometry    : angle       0.60342 (15269)
  SS BOND              : bond        0.00178 (    1)
  SS BOND              : angle       0.71304 (    2)
  hydrogen bonds       : bond        0.03055 (  479)
  hydrogen bonds       : angle       3.68902 ( 1371)
  metal coordination   : bond        0.00839 (    4)
  metal coordination   : angle       0.38416 (    2)

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

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

  2716 Ramachandran restraints generated.
    1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2716 Ramachandran restraints generated.
    1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 86
  time to evaluate  : 0.368 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L  302 LEU cc_start: 0.8020 (tp) cc_final: 0.7018 (mt)
REVERT: L  313 GLU cc_start: 0.6817 (OUTLIER) cc_final: 0.6447 (mp0)
REVERT: L  324 GLN cc_start: 0.7815 (mt0) cc_final: 0.7513 (pp30)
REVERT: L  336 LEU cc_start: 0.7354 (tp) cc_final: 0.7026 (mp)
REVERT: L  350 ASP cc_start: 0.7156 (p0) cc_final: 0.6147 (t0)
REVERT: L 1092 MET cc_start: 0.7755 (mmm) cc_final: 0.7227 (mmm)
REVERT: L 1479 MET cc_start: 0.4238 (tpp) cc_final: 0.3797 (mmt)
REVERT: L 1532 LEU cc_start: 0.8845 (tp) cc_final: 0.8565 (pp)
REVERT: L 1558 MET cc_start: 0.6393 (mmm) cc_final: 0.5346 (mmm)
  outliers start: 23
  outliers final: 22
  residues processed: 106
  average time/residue: 0.0758
  time to fit residues: 12.9115
Evaluate side-chains
  107 residues out of total 1261 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 84
  time to evaluate  : 0.472 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue  279 THR
Chi-restraints excluded: chain L residue  313 GLU
Chi-restraints excluded: chain L residue  379 ASN
Chi-restraints excluded: chain L residue  508 MET
Chi-restraints excluded: chain L residue  625 ILE
Chi-restraints excluded: chain L residue  671 LEU
Chi-restraints excluded: chain L residue  688 VAL
Chi-restraints excluded: chain L residue  704 TYR
Chi-restraints excluded: chain L residue  710 THR
Chi-restraints excluded: chain L residue  830 ASN
Chi-restraints excluded: chain L residue  857 VAL
Chi-restraints excluded: chain L residue  871 TYR
Chi-restraints excluded: chain L residue  882 LEU
Chi-restraints excluded: chain L residue 1319 ILE
Chi-restraints excluded: chain L residue 1328 THR
Chi-restraints excluded: chain L residue 1375 VAL
Chi-restraints excluded: chain L residue 1408 ILE
Chi-restraints excluded: chain L residue 1478 ILE
Chi-restraints excluded: chain L residue 1513 PHE
Chi-restraints excluded: chain L residue 1524 SER
Chi-restraints excluded: chain L residue 1624 LEU
Chi-restraints excluded: chain L residue 1639 ILE
Chi-restraints excluded: chain L residue 1661 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    0.1980
   chunk 8 optimal weight:    0.0040
   chunk 15 optimal weight:    5.9990
   chunk 68 optimal weight:    5.9990
   chunk 46 optimal weight:    3.9990
   chunk 135 optimal weight:   10.0000
   chunk 51 optimal weight:    8.9990
   chunk 27 optimal weight:    9.9990
   chunk 130 optimal weight:    0.5980
   chunk 83 optimal weight:    6.9990
   overall best weight:    2.1596

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

Flipped N/Q/H residues before XYZ refinement:
L1449 GLN
L1461 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.099396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.080402 restraints weight = 42620.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.080813 restraints weight = 26269.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.081576 restraints weight = 19750.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.081883 restraints weight = 17390.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.082005 restraints weight = 15587.160|
|-----------------------------------------------------------------------------|
r_work (final): 0.3652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7569
moved from start:          0.5722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.082  11327  Z= 0.161
  Angle     :  0.651  13.575  15273  Z= 0.318
  Chirality :  0.040   0.282   1735
  Planarity :  0.003   0.041   1928
  Dihedral  :  4.133  17.903   1490
  Min Nonbonded Distance : 2.060

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.98 %
    Favored  : 91.02 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 19.11 %
    Favored  : 78.59 %
  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: -0.93 (0.23), residues: 1358
  helix:  1.18 (0.21), residues: 711
  sheet: -1.50 (0.56), residues: 82
  loop : -3.00 (0.23), residues: 565

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG L 920 
 TYR   0.024   0.001   TYR L1688 
 PHE   0.034   0.002   PHE L 421 
 TRP   0.031   0.002   TRP L 395 
 HIS   0.005   0.001   HIS L 707 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 (11322)
  covalent geometry    : angle       0.65087 (15269)
  SS BOND              : bond        0.00325 (    1)
  SS BOND              : angle       0.65253 (    2)
  hydrogen bonds       : bond        0.04174 (  479)
  hydrogen bonds       : angle       4.01088 ( 1371)
  metal coordination   : bond        0.00560 (    4)
  metal coordination   : angle       0.36626 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1677.86 seconds
wall clock time: 29 minutes 51.41 seconds (1791.41 seconds total)