Starting phenix.real_space_refine
on Fri Jul  3 11:37:29 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9qkv_53222/07_2026/9qkv_53222.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9qkv_53222/07_2026/9qkv_53222.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.74
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9qkv_53222/07_2026/9qkv_53222.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9qkv_53222/07_2026/9qkv_53222.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9qkv_53222/07_2026/9qkv_53222.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9qkv_53222/07_2026/9qkv_53222.map"
  }
  resolution = 2.74
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.004
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
     Ca     10      9.91       5
     P       2      5.49       5
     S      58      5.16       5
     C    8782      2.51       5
     N    2352      2.21       5
     O    2560      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 63 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 13764
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "D"
      Number of atoms: 13694
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1688, 13694
          Classifications: {'peptide': 1688}
          Link IDs: {'PCIS': 3, 'PTRANS': 103, 'TRANS': 1581}
          Chain breaks: 6
    Chain: "D"
      Number of atoms: 70
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 60
          Ad-hoc single atom residues: {' CA': 10}
          Unusual residues: {'PSF': 2}
          Classifications: {'undetermined': 2}
          Chain breaks: 10
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" N   PSF D2001 " occ=0.91
      ... (28 atoms not shown)
      pdb=" P   PSF D2001 " occ=0.91
    residue:
      pdb=" N   PSF D2010 " occ=0.81
      ... (28 atoms not shown)
      pdb=" P   PSF D2010 " occ=0.81
  Time building chain proxies: 2.30, per 1000 atoms: 0.17
  Number of scatterers: 13764
  At special positions: 0
  Unit cell: (101.52, 123.12, 155.52, 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)
     Ca     10     19.99
     S      58     16.00
     P       2     15.00
     O    2560      8.00
     N    2352      7.00
     C    8782      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.01
  Conformation dependent library (CDL) restraints added in 489.5 milliseconds
  

  3348 Ramachandran restraints generated.
    1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3180

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 18 sheets defined
      17.1% alpha, 28.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.46
  Creating SS restraints...
    Processing helix  chain 'D' and resid 172 through 189
    Processing helix  chain 'D' and resid 252 through 257
    Processing helix  chain 'D' and resid 284 through 290
    Processing helix  chain 'D' and resid 307 through 310
    Processing helix  chain 'D' and resid 343 through 347
      removed outlier: 3.975A  pdb=" N   LEU D 347 " --> pdb=" O   GLU D 344 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 377 through 382
    Processing helix  chain 'D' and resid 390 through 394
      removed outlier: 3.677A  pdb=" N   ASN D 393 " --> pdb=" O   ASP D 390 " (cutoff:3.500A)
      removed outlier: 4.329A  pdb=" N   LEU D 394 " --> pdb=" O   LYS D 391 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 390 through 394'
    Processing helix  chain 'D' and resid 520 through 525
      removed outlier: 3.901A  pdb=" N   ASN D 524 " --> pdb=" O   TYR D 520 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   THR D 525 " --> pdb=" O   ASP D 521 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 520 through 525'
    Processing helix  chain 'D' and resid 560 through 565
    Processing helix  chain 'D' and resid 566 through 569
    Processing helix  chain 'D' and resid 650 through 680
      removed outlier: 4.458A  pdb=" N   ALA D 656 " --> pdb=" O   HIS D 652 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 683 through 702
    Processing helix  chain 'D' and resid 716 through 744
      removed outlier: 4.004A  pdb=" N   SER D 742 " --> pdb=" O   VAL D 738 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 746 through 765
      removed outlier: 3.903A  pdb=" N   THR D 750 " --> pdb=" O   ASP D 746 " (cutoff:3.500A)
      removed outlier: 4.911A  pdb=" N   ALA D 752 " --> pdb=" O   LYS D 748 " (cutoff:3.500A)
      removed outlier: 4.575A  pdb=" N   GLU D 753 " --> pdb=" O   SER D 749 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 792 through 796
      removed outlier: 3.511A  pdb=" N   VAL D 796 " --> pdb=" O   ALA D 793 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 844 through 852
      removed outlier: 5.296A  pdb=" N   LYS D 847 " --> pdb=" O   ALA D 844 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   SER D 851 " --> pdb=" O   LYS D 848 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1086 through 1094
      removed outlier: 3.606A  pdb=" N   ALA D1089 " --> pdb=" O   HIS D1086 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ALA D1090 " --> pdb=" O   GLY D1087 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   ILE D1091 " --> pdb=" O   ALA D1088 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   LEU D1094 " --> pdb=" O   ILE D1091 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1200 through 1207
    Processing helix  chain 'D' and resid 1275 through 1279
      removed outlier: 4.387A  pdb=" N   ASN D1278 " --> pdb=" O   ASP D1275 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1381 through 1385
      removed outlier: 3.766A  pdb=" N   GLY D1384 " --> pdb=" O   ARG D1381 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1452 through 1462
      removed outlier: 3.702A  pdb=" N   LYS D1456 " --> pdb=" O   ASP D1452 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1470 through 1474
    Processing helix  chain 'D' and resid 1488 through 1495
      removed outlier: 3.517A  pdb=" N   PHE D1491 " --> pdb=" O   VAL D1488 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   GLU D1492 " --> pdb=" O   ALA D1489 " (cutoff:3.500A)
      removed outlier: 6.229A  pdb=" N   GLY D1493 " --> pdb=" O   GLU D1490 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   THR D1495 " --> pdb=" O   GLU D1492 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1590 through 1593
      removed outlier: 3.915A  pdb=" N   TYR D1593 " --> pdb=" O   ARG D1590 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 1590 through 1593'
    Processing helix  chain 'D' and resid 1641 through 1647
    Processing helix  chain 'D' and resid 1662 through 1666
      removed outlier: 4.198A  pdb=" N   ASN D1665 " --> pdb=" O   SER D1662 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   THR D1666 " --> pdb=" O   GLY D1663 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 1662 through 1666'
    Processing helix  chain 'D' and resid 1672 through 1685
    Processing helix  chain 'D' and resid 1708 through 1710
      No H-bonds generated for 'chain 'D' and resid 1708 through 1710'
    Processing helix  chain 'D' and resid 1722 through 1734
      removed outlier: 3.903A  pdb=" N   THR D1734 " --> pdb=" O   HIS D1730 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1770 through 1772
      No H-bonds generated for 'chain 'D' and resid 1770 through 1772'
    Processing helix  chain 'D' and resid 1975 through 1981
      removed outlier: 3.534A  pdb=" N   ASP D1979 " --> pdb=" O   GLU D1975 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'D' and resid 240 through 250
      removed outlier: 6.766A  pdb=" N   PHE D 241 " --> pdb=" O   GLU D 207 " (cutoff:3.500A)
      removed outlier: 7.062A  pdb=" N   GLU D 207 " --> pdb=" O   PHE D 241 " (cutoff:3.500A)
      removed outlier: 6.963A  pdb=" N   LYS D 317 " --> pdb=" O   ILE D 206 " (cutoff:3.500A)
      removed outlier: 4.582A  pdb=" N   GLY D 208 " --> pdb=" O   TYR D 315 " (cutoff:3.500A)
      removed outlier: 6.740A  pdb=" N   TYR D 315 " --> pdb=" O   GLY D 208 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   GLY D 314 " --> pdb=" O   LEU D 302 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   MET D 316 " --> pdb=" O   LEU D 300 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 227 through 230
      removed outlier: 6.864A  pdb=" N   ILE D 261 " --> pdb=" O   LYS D 281 " (cutoff:3.500A)
      removed outlier: 4.619A  pdb=" N   LYS D 281 " --> pdb=" O   ILE D 261 " (cutoff:3.500A)
      removed outlier: 7.169A  pdb=" N   ILE D 263 " --> pdb=" O   GLU D 279 " (cutoff:3.500A)
      removed outlier: 4.718A  pdb=" N   GLU D 279 " --> pdb=" O   ILE D 263 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   VAL D 265 " --> pdb=" O   MET D 277 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 499 through 508
      removed outlier: 5.281A  pdb=" N   GLY D 500 " --> pdb=" O   LEU D 541 " (cutoff:3.500A)
      removed outlier: 5.606A  pdb=" N   LEU D 541 " --> pdb=" O   GLY D 500 " (cutoff:3.500A)
      removed outlier: 4.227A  pdb=" N   GLY D 535 " --> pdb=" O   LEU D 506 " (cutoff:3.500A)
      removed outlier: 6.317A  pdb=" N   GLY D 508 " --> pdb=" O   TYR D 533 " (cutoff:3.500A)
      removed outlier: 5.822A  pdb=" N   TYR D 533 " --> pdb=" O   GLY D 508 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   ARG D 536 " --> pdb=" O   ALA D 367 " (cutoff:3.500A)
      removed outlier: 4.569A  pdb=" N   ALA D 367 " --> pdb=" O   ARG D 536 " (cutoff:3.500A)
      removed outlier: 6.820A  pdb=" N   LEU D 538 " --> pdb=" O   TYR D 365 " (cutoff:3.500A)
      removed outlier: 7.054A  pdb=" N   ARG D 366 " --> pdb=" O   TRP D 421 " (cutoff:3.500A)
      removed outlier: 6.257A  pdb=" N   TRP D 421 " --> pdb=" O   ARG D 366 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 406 through 409
      removed outlier: 6.746A  pdb=" N   ILE D 438 " --> pdb=" O   TYR D 458 " (cutoff:3.500A)
      removed outlier: 4.501A  pdb=" N   TYR D 458 " --> pdb=" O   ILE D 438 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   LEU D 440 " --> pdb=" O   THR D 456 " (cutoff:3.500A)
      removed outlier: 4.456A  pdb=" N   THR D 456 " --> pdb=" O   LEU D 440 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   ILE D 442 " --> pdb=" O   VAL D 454 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 571 through 584
      removed outlier: 8.647A  pdb=" N   SER D 582 " --> pdb=" O   THR D 637 " (cutoff:3.500A)
      removed outlier: 12.298A  pdb=" N   THR D 637 " --> pdb=" O   SER D 582 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'D' and resid 637 through 648
    current: chain 'D' and resid 833 through 842
  WARNING: can't find start of bonding for strands!
    previous: chain 'D' and resid 833 through 842
    current: chain 'D' and resid 873 through 875
  WARNING: can't find start of bonding for strands!
    previous: chain 'D' and resid 873 through 875
    current: chain 'D' and resid 1071 through 1082
    Processing sheet with id=AA6, first strand: chain 'D' and resid 593 through 599
      removed outlier: 3.529A  pdb=" N   ALA D 787 " --> pdb=" O   MET D 779 " (cutoff:3.500A)
      removed outlier: 6.092A  pdb=" N   ARG D 781 " --> pdb=" O   ARG D 785 " (cutoff:3.500A)
      removed outlier: 5.381A  pdb=" N   ARG D 785 " --> pdb=" O   ARG D 781 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 623 through 624
    Processing sheet with id=AA8, first strand: chain 'D' and resid 930 through 939
      removed outlier: 12.777A  pdb=" N   GLU D 933 " --> pdb=" O   TYR D 953 " (cutoff:3.500A)
      removed outlier: 11.006A  pdb=" N   TYR D 953 " --> pdb=" O   GLU D 933 " (cutoff:3.500A)
      removed outlier: 8.977A  pdb=" N   TYR D 935 " --> pdb=" O   ASP D 951 " (cutoff:3.500A)
      removed outlier: 9.503A  pdb=" N   ASP D 951 " --> pdb=" O   TYR D 935 " (cutoff:3.500A)
      removed outlier: 7.596A  pdb=" N   ASN D 937 " --> pdb=" O   ALA D 949 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'D' and resid 947 through 954
    current: chain 'D' and resid 1018 through 1028
    Processing sheet with id=AA9, first strand: chain 'D' and resid 1137 through 1149
      removed outlier: 6.938A  pdb=" N   TYR D1137 " --> pdb=" O   GLU D1196 " (cutoff:3.500A)
      removed outlier: 4.865A  pdb=" N   GLU D1196 " --> pdb=" O   TYR D1137 " (cutoff:3.500A)
      removed outlier: 5.895A  pdb=" N   TYR D1139 " --> pdb=" O   GLU D1194 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'D' and resid 1188 through 1197
    current: chain 'D' and resid 1258 through 1271
  WARNING: can't find start of bonding for strands!
    previous: chain 'D' and resid 1258 through 1271
    current: chain 'D' and resid 1290 through 1292
    Processing sheet with id=AB1, first strand: chain 'D' and resid 1171 through 1174
      removed outlier: 3.605A  pdb=" N   GLY D1228 " --> pdb=" O   LEU D1215 " (cutoff:3.500A)
      removed outlier: 6.074A  pdb=" N   ASP D1217 " --> pdb=" O   PHE D1226 " (cutoff:3.500A)
      removed outlier: 5.940A  pdb=" N   PHE D1226 " --> pdb=" O   ASP D1217 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 1356 through 1364
      removed outlier: 5.323A  pdb=" N   ILE D1306 " --> pdb=" O   TYR D1527 " (cutoff:3.500A)
      removed outlier: 7.659A  pdb=" N   TYR D1527 " --> pdb=" O   ILE D1306 " (cutoff:3.500A)
      removed outlier: 5.839A  pdb=" N   ILE D1308 " --> pdb=" O   ARG D1525 " (cutoff:3.500A)
      removed outlier: 7.499A  pdb=" N   ARG D1525 " --> pdb=" O   ILE D1308 " (cutoff:3.500A)
      removed outlier: 5.442A  pdb=" N   ALA D1310 " --> pdb=" O   SER D1523 " (cutoff:3.500A)
      removed outlier: 7.963A  pdb=" N   SER D1523 " --> pdb=" O   ALA D1310 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   GLY D1312 " --> pdb=" O   LYS D1521 " (cutoff:3.500A)
      removed outlier: 6.010A  pdb=" N   VAL D1516 " --> pdb=" O   ARG D1505 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   ARG D1505 " --> pdb=" O   VAL D1516 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   GLY D1518 " --> pdb=" O   LEU D1503 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 1336 through 1339
      removed outlier: 3.854A  pdb=" N   GLY D1390 " --> pdb=" O   VAL D1377 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 1479 through 1480
      removed outlier: 6.846A  pdb=" N   LYS D1479 " --> pdb=" O   VAL D1742 " (cutoff:3.500A)
      removed outlier: 7.479A  pdb=" N   THR D1744 " --> pdb=" O   LYS D1479 " (cutoff:3.500A)
      removed outlier: 8.291A  pdb=" N   HIS D1741 " --> pdb=" O   VAL D1764 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   VAL D1764 " --> pdb=" O   HIS D1741 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   LYS D1759 " --> pdb=" O   GLY D1562 " (cutoff:3.500A)
      removed outlier: 4.726A  pdb=" N   GLY D1562 " --> pdb=" O   LYS D1759 " (cutoff:3.500A)
      removed outlier: 6.994A  pdb=" N   GLN D1761 " --> pdb=" O   VAL D1560 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 1585 through 1588
      removed outlier: 6.538A  pdb=" N   LEU D1618 " --> pdb=" O   ILE D1638 " (cutoff:3.500A)
      removed outlier: 4.275A  pdb=" N   ILE D1638 " --> pdb=" O   LEU D1618 " (cutoff:3.500A)
      removed outlier: 6.756A  pdb=" N   ILE D1620 " --> pdb=" O   GLU D1636 " (cutoff:3.500A)
      removed outlier: 4.338A  pdb=" N   GLU D1636 " --> pdb=" O   ILE D1620 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   VAL D1622 " --> pdb=" O   VAL D1634 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   GLU D1632 " --> pdb=" O   ASP D1624 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 1690 through 1691
      removed outlier: 3.710A  pdb=" N   TYR D1705 " --> pdb=" O   ILE D1698 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   TYR D1700 " --> pdb=" O   ARG D1703 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 1875 through 1879
      removed outlier: 3.882A  pdb=" N   ASP D1853 " --> pdb=" O   ILE D1862 " (cutoff:3.500A)
      removed outlier: 9.099A  pdb=" N   ALA D1864 " --> pdb=" O   PRO D1851 " (cutoff:3.500A)
      removed outlier: 7.365A  pdb=" N   GLY D1842 " --> pdb=" O   LYS D1798 " (cutoff:3.500A)
      removed outlier: 5.877A  pdb=" N   LYS D1798 " --> pdb=" O   GLY D1842 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   PHE D1844 " --> pdb=" O   ASN D1796 " (cutoff:3.500A)
      removed outlier: 7.823A  pdb=" N   ASN D1796 " --> pdb=" O   PHE D1844 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   TRP D1846 " --> pdb=" O   ILE D1794 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   ILE D1793 " --> pdb=" O   THR D1969 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   THR D1969 " --> pdb=" O   ILE D1793 " (cutoff:3.500A)
      removed outlier: 6.638A  pdb=" N   GLU D1967 " --> pdb=" O   TRP D1795 " (cutoff:3.500A)
      removed outlier: 4.657A  pdb=" N   THR D1797 " --> pdb=" O   LYS D1965 " (cutoff:3.500A)
      removed outlier: 6.830A  pdb=" N   LYS D1965 " --> pdb=" O   THR D1797 " (cutoff:3.500A)
      removed outlier: 5.172A  pdb=" N   ARG D1960 " --> pdb=" O   LYS D1956 " (cutoff:3.500A)
      removed outlier: 6.243A  pdb=" N   LYS D1956 " --> pdb=" O   ARG D1960 " (cutoff:3.500A)
      removed outlier: 5.205A  pdb=" N   MET D1962 " --> pdb=" O   ALA D1954 " (cutoff:3.500A)
      removed outlier: 5.745A  pdb=" N   ALA D1954 " --> pdb=" O   MET D1962 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'D' and resid 1813 through 1820
  WARNING: can't find start of bonding for strands!
    previous: chain 'D' and resid 1829 through 1830
    current: chain 'D' and resid 1897 through 1905
    Processing sheet with id=AB9, first strand: chain 'D' and resid 1909 through 1910

    365 hydrogen bonds defined for protein.
    978 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: 2.13

  Time building geometry restraints manager: 1.39 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 2781
        1.33 -     1.45: 3474
        1.45 -     1.58: 7744
        1.58 -     1.70: 8
        1.70 -     1.83: 92
  Bond restraints: 14099
  Sorted by residual:
  bond pdb=" C   PHE D 431 "
       pdb=" N   PRO D 432 "
    ideal  model  delta    sigma   weight residual
    1.335  1.375 -0.040 1.28e-02 6.10e+03 9.95e+00
  bond pdb=" C   LYS D 947 "
       pdb=" N   PRO D 948 "
    ideal  model  delta    sigma   weight residual
    1.332  1.363 -0.031 1.30e-02 5.92e+03 5.75e+00
  bond pdb=" C   ALA D1287 "
       pdb=" N   PRO D1288 "
    ideal  model  delta    sigma   weight residual
    1.331  1.358 -0.027 1.20e-02 6.94e+03 5.16e+00
  bond pdb=" CB  GLU D1826 "
       pdb=" CG  GLU D1826 "
    ideal  model  delta    sigma   weight residual
    1.520  1.585 -0.065 3.00e-02 1.11e+03 4.66e+00
  bond pdb=" O2  PSF D2001 "
       pdb=" P   PSF D2001 "
    ideal  model  delta    sigma   weight residual
    1.637  1.594  0.043 2.00e-02 2.50e+03 4.52e+00
  ... (remaining 14094 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.66: 18941
        3.66 -     7.32: 122
        7.32 -    10.98: 30
       10.98 -    14.64: 6
       14.64 -    18.29: 5
  Bond angle restraints: 19104
  Sorted by residual:
  angle pdb=" CB  MET D 316 "
        pdb=" CG  MET D 316 "
        pdb=" SD  MET D 316 "
      ideal   model   delta    sigma   weight residual
     112.70  130.99  -18.29 3.00e+00 1.11e-01 3.72e+01
  angle pdb=" CA  GLU D 344 "
        pdb=" CB  GLU D 344 "
        pdb=" CG  GLU D 344 "
      ideal   model   delta    sigma   weight residual
     114.10  126.28  -12.18 2.00e+00 2.50e-01 3.71e+01
  angle pdb=" CB  MET D 191 "
        pdb=" CG  MET D 191 "
        pdb=" SD  MET D 191 "
      ideal   model   delta    sigma   weight residual
     112.70  128.95  -16.25 3.00e+00 1.11e-01 2.93e+01
  angle pdb=" CB  GLU D1826 "
        pdb=" CG  GLU D1826 "
        pdb=" CD  GLU D1826 "
      ideal   model   delta    sigma   weight residual
     112.60  121.33   -8.73 1.70e+00 3.46e-01 2.64e+01
  angle pdb=" C   PRO D1595 "
        pdb=" N   ASN D1596 "
        pdb=" CA  ASN D1596 "
      ideal   model   delta    sigma   weight residual
     121.54  131.24   -9.70 1.91e+00 2.74e-01 2.58e+01
  ... (remaining 19099 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.74: 8083
       26.74 -    53.48: 394
       53.48 -    80.22: 55
       80.22 -   106.96: 10
      106.96 -   133.70: 1
  Dihedral angle restraints: 8543
    sinusoidal: 3616
      harmonic: 4927
  Sorted by residual:
  dihedral pdb=" CA  GLU D1811 "
           pdb=" C   GLU D1811 "
           pdb=" N   MET D1812 "
           pdb=" CA  MET D1812 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -155.42  -24.58     0      5.00e+00 4.00e-02 2.42e+01
  dihedral pdb=" CA  LYS D 547 "
           pdb=" C   LYS D 547 "
           pdb=" N   THR D 548 "
           pdb=" CA  THR D 548 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.33   22.67     0      5.00e+00 4.00e-02 2.06e+01
  dihedral pdb=" CA  LYS D 195 "
           pdb=" C   LYS D 195 "
           pdb=" N   PRO D 196 "
           pdb=" CA  PRO D 196 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.62   22.38     0      5.00e+00 4.00e-02 2.00e+01
  ... (remaining 8540 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 1471
       0.051 -    0.102: 411
       0.102 -    0.153: 141
       0.153 -    0.204: 12
       0.204 -    0.255: 5
  Chirality restraints: 2040
  Sorted by residual:
  chirality pdb=" CA  ASN D1596 "
            pdb=" N   ASN D1596 "
            pdb=" C   ASN D1596 "
            pdb=" CB  ASN D1596 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.26 2.00e-01 2.50e+01 1.63e+00
  chirality pdb=" CB  VAL D 343 "
            pdb=" CA  VAL D 343 "
            pdb=" CG1 VAL D 343 "
            pdb=" CG2 VAL D 343 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.38   -0.24 2.00e-01 2.50e+01 1.49e+00
  chirality pdb=" CB  THR D 548 "
            pdb=" CA  THR D 548 "
            pdb=" OG1 THR D 548 "
            pdb=" CG2 THR D 548 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.31    0.24 2.00e-01 2.50e+01 1.46e+00
  ... (remaining 2037 not shown)

  Planarity restraints: 2472
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE D1645 "    0.018 2.00e-02 2.50e+03   2.77e-02 1.35e+01
        pdb=" CG  PHE D1645 "   -0.063 2.00e-02 2.50e+03
        pdb=" CD1 PHE D1645 "    0.025 2.00e-02 2.50e+03
        pdb=" CD2 PHE D1645 "    0.022 2.00e-02 2.50e+03
        pdb=" CE1 PHE D1645 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE D1645 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE D1645 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE D 286 "   -0.021 2.00e-02 2.50e+03   2.74e-02 1.31e+01
        pdb=" CG  PHE D 286 "    0.063 2.00e-02 2.50e+03
        pdb=" CD1 PHE D 286 "   -0.024 2.00e-02 2.50e+03
        pdb=" CD2 PHE D 286 "   -0.017 2.00e-02 2.50e+03
        pdb=" CE1 PHE D 286 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 PHE D 286 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE D 286 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE D1751 "    0.020 2.00e-02 2.50e+03   2.73e-02 1.30e+01
        pdb=" CG  PHE D1751 "   -0.063 2.00e-02 2.50e+03
        pdb=" CD1 PHE D1751 "    0.022 2.00e-02 2.50e+03
        pdb=" CD2 PHE D1751 "    0.020 2.00e-02 2.50e+03
        pdb=" CE1 PHE D1751 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE D1751 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ  PHE D1751 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 2469 not shown)

  Histogram of nonbonded interaction distances:
        2.35 -     2.86: 4260
        2.86 -     3.37: 12054
        3.37 -     3.88: 23568
        3.88 -     4.39: 26282
        4.39 -     4.90: 45535
  Nonbonded interactions: 111699
  Sorted by model distance:
  nonbonded pdb="CA    CA D2007 "
            pdb=" O3  PSF D2010 "
     model   vdw
     2.345 3.250
  nonbonded pdb=" OD1 ASP D1569 "
            pdb="CA    CA D2006 "
     model   vdw
     2.350 3.250
  nonbonded pdb=" OD2 ASP D1624 "
            pdb="CA    CA D2007 "
     model   vdw
     2.351 3.250
  nonbonded pdb=" OD1 ASP D1569 "
            pdb="CA    CA D2007 "
     model   vdw
     2.354 3.250
  nonbonded pdb=" O4  PSF D2001 "
            pdb="CA    CA D2003 "
     model   vdw
     2.367 3.250
  ... (remaining 111694 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.81 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.870
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     11.390
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:5.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.630
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8499
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      :  0.005   0.065  14099  Z= 0.232
  Angle     :  0.974  18.294  19104  Z= 0.515
  Chirality :  0.053   0.255   2040
  Planarity :  0.007   0.086   2472
  Dihedral  : 15.624 133.701   5363
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 2.01
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  3.88 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  0.73 %
    Allowed  : 14.95 %
    Favored  : 84.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.83 %
    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 (0.19), residues: 1674
  helix: -1.69 (0.29), residues: 215
  sheet: -0.39 (0.23), residues: 493
  loop : -0.90 (0.18), residues: 966

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.023   0.001   ARG D 781 
 TYR   0.019   0.002   TYR D 533 
 PHE   0.063   0.003   PHE D 286 
 TRP   0.054   0.002   TRP D1076 
 HIS   0.004   0.001   HIS D1018 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00487 /  0.23 (14099)
  covalent geometry    : angle       0.97352 /  0.51 (19104)
  hydrogen bonds       : bond        0.18801 / 12.68 (  365)
  hydrogen bonds       : angle       8.69747 /  6.14 (  978)

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

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

  3348 Ramachandran restraints generated.
    1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3348 Ramachandran restraints generated.
    1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 118
  time to evaluate  : 0.437 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  210 GLN cc_start: 0.8163 (tt0) cc_final: 0.7886 (tt0)
REVERT: D  227 GLN cc_start: 0.8216 (tp-100) cc_final: 0.7941 (tt0)
REVERT: D  255 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8454 (tm-30)
REVERT: D  277 MET cc_start: 0.7872 (mmt) cc_final: 0.7433 (mmm)
REVERT: D  280 PHE cc_start: 0.8718 (t80) cc_final: 0.8432 (t80)
REVERT: D  348 LEU cc_start: 0.8440 (tp) cc_final: 0.8143 (pt)
REVERT: D  450 LYS cc_start: 0.8976 (ttmm) cc_final: 0.8690 (pmtt)
REVERT: D  518 ASP cc_start: 0.7561 (t70) cc_final: 0.7242 (t70)
REVERT: D  756 ASP cc_start: 0.6740 (t70) cc_final: 0.6458 (t70)
REVERT: D  762 MET cc_start: 0.8512 (mmm) cc_final: 0.8238 (ptt)
REVERT: D  784 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8669 (mtpp)
REVERT: D  870 MET cc_start: 0.1160 (mpt) cc_final: -0.0166 (ptp)
REVERT: D 1014 MET cc_start: 0.5051 (mtp) cc_final: 0.4533 (mtm)
REVERT: D 1321 MET cc_start: 0.8535 (mmm) cc_final: 0.8158 (mpt)
REVERT: D 1519 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8202 (mt-10)
REVERT: D 1564 GLU cc_start: 0.8394 (mt-10) cc_final: 0.8189 (pt0)
REVERT: D 1640 ASP cc_start: 0.8281 (t0) cc_final: 0.7975 (t0)
REVERT: D 1812 MET cc_start: 0.5316 (tpt) cc_final: 0.5021 (tmt)
REVERT: D 1870 TRP cc_start: 0.8368 (p-90) cc_final: 0.7977 (p90)
REVERT: D 1962 MET cc_start: 0.8082 (tpp) cc_final: 0.7756 (tpp)
  outliers start: 11
  outliers final: 5
  residues processed: 128
  average time/residue: 0.4452
  time to fit residues: 63.2614
Evaluate side-chains
  117 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 110
  time to evaluate  : 0.531 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  255 GLU
Chi-restraints excluded: chain D residue  496 VAL
Chi-restraints excluded: chain D residue  589 VAL
Chi-restraints excluded: chain D residue  738 VAL
Chi-restraints excluded: chain D residue  784 LYS
Chi-restraints excluded: chain D residue 1290 LEU
Chi-restraints excluded: chain D residue 1792 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 107 optimal weight:    5.9990
   chunk 10 optimal weight:    8.9990
   chunk 66 optimal weight:    7.9990
   chunk 130 optimal weight:    3.9990
   chunk 124 optimal weight:    3.9990
   chunk 103 optimal weight:    0.0980
   chunk 77 optimal weight:    0.9990
   chunk 122 optimal weight:    2.9990
   chunk 91 optimal weight:    0.9990
   chunk 149 optimal weight:    2.9990
   overall best weight:    1.4188

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D 177 GLN
D 215 ASN
D 269 HIS
D 618 GLN
D1206 GLN
D1568 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.147635 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.097436 restraints weight = 26136.325|
|-----------------------------------------------------------------------------|
r_work (start): 0.3372 rms_B_bonded: 3.59
r_work: 0.3230 rms_B_bonded: 4.07 restraints_weight: 0.5000
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3259
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3259 r_free = 0.3259    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3259 r_free = 0.3259    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3259
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8034
moved from start:          0.1065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  14099  Z= 0.165
  Angle     :  0.559   8.907  19104  Z= 0.287
  Chirality :  0.044   0.165   2040
  Planarity :  0.004   0.041   2472
  Dihedral  :  8.356 128.101   1923
  Min Nonbonded Distance : 2.341

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  2.51 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 14.02 %
    Favored  : 83.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.83 %
    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: -0.60 (0.20), residues: 1674
  helix: -0.26 (0.34), residues: 221
  sheet: -0.17 (0.22), residues: 519
  loop : -0.48 (0.20), residues: 934

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D 781 
 TYR   0.013   0.001   TYR D 443 
 PHE   0.020   0.001   PHE D1751 
 TRP   0.020   0.001   TRP D1888 
 HIS   0.003   0.001   HIS D 734 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00377 /  0.17 (14099)
  covalent geometry    : angle       0.55877 /  0.29 (19104)
  hydrogen bonds       : bond        0.03357 /  2.27 (  365)
  hydrogen bonds       : angle       6.16881 /  4.33 (  978)

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

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

  3348 Ramachandran restraints generated.
    1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3348 Ramachandran restraints generated.
    1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 111
  time to evaluate  : 0.577 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  210 GLN cc_start: 0.7672 (tt0) cc_final: 0.7336 (tt0)
REVERT: D  227 GLN cc_start: 0.7651 (tp-100) cc_final: 0.7259 (tt0)
REVERT: D  277 MET cc_start: 0.7643 (mmt) cc_final: 0.7217 (mmm)
REVERT: D  450 LYS cc_start: 0.8643 (ttmm) cc_final: 0.8236 (mtmm)
REVERT: D  522 GLU cc_start: 0.8048 (tm-30) cc_final: 0.7664 (tm-30)
REVERT: D  527 LYS cc_start: 0.8672 (mppt) cc_final: 0.8309 (mttt)
REVERT: D  655 ASP cc_start: 0.8202 (m-30) cc_final: 0.7987 (m-30)
REVERT: D  756 ASP cc_start: 0.7523 (t70) cc_final: 0.7100 (t0)
REVERT: D  762 MET cc_start: 0.8601 (mmm) cc_final: 0.7773 (ptm)
REVERT: D  870 MET cc_start: 0.1324 (mpt) cc_final: 0.0092 (ptp)
REVERT: D 1014 MET cc_start: 0.4632 (mtp) cc_final: 0.4369 (mtt)
REVERT: D 1321 MET cc_start: 0.9024 (mmm) cc_final: 0.8303 (mpt)
REVERT: D 1519 GLU cc_start: 0.8875 (mt-10) cc_final: 0.8445 (mt-10)
REVERT: D 1564 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8017 (pt0)
REVERT: D 1640 ASP cc_start: 0.8551 (t0) cc_final: 0.7884 (t0)
REVERT: D 1812 MET cc_start: 0.5156 (tpt) cc_final: 0.4829 (tmt)
REVERT: D 1870 TRP cc_start: 0.8421 (p-90) cc_final: 0.7974 (p90)
REVERT: D 1876 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7455 (pp20)
REVERT: D 1943 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7817 (tm-30)
  outliers start: 30
  outliers final: 8
  residues processed: 136
  average time/residue: 0.5774
  time to fit residues: 86.6940
Evaluate side-chains
  110 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 100
  time to evaluate  : 0.563 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  260 ILE
Chi-restraints excluded: chain D residue  320 MET
Chi-restraints excluded: chain D residue  509 SER
Chi-restraints excluded: chain D residue  589 VAL
Chi-restraints excluded: chain D residue  747 VAL
Chi-restraints excluded: chain D residue 1203 THR
Chi-restraints excluded: chain D residue 1290 LEU
Chi-restraints excluded: chain D residue 1792 VAL
Chi-restraints excluded: chain D residue 1876 GLU
Chi-restraints excluded: chain D residue 1943 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 73 optimal weight:   20.0000
   chunk 83 optimal weight:    3.9990
   chunk 152 optimal weight:    6.9990
   chunk 120 optimal weight:    0.9980
   chunk 47 optimal weight:    0.4980
   chunk 158 optimal weight:    0.9980
   chunk 63 optimal weight:    0.8980
   chunk 129 optimal weight:    0.0020
   chunk 5 optimal weight:    0.7980
   chunk 20 optimal weight:    1.9990
   chunk 161 optimal weight:    7.9990
   overall best weight:    0.6388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D 618 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.148901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.099263 restraints weight = 26287.147|
|-----------------------------------------------------------------------------|
r_work (start): 0.3415 rms_B_bonded: 3.54
r_work: 0.3273 rms_B_bonded: 4.04 restraints_weight: 0.5000
r_work (final): 0.3273
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3291
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3291 r_free = 0.3291    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3291 r_free = 0.3291    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.86   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3291
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
moved from start:          0.1195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  14099  Z= 0.103
  Angle     :  0.507   8.359  19104  Z= 0.259
  Chirality :  0.043   0.159   2040
  Planarity :  0.004   0.037   2472
  Dihedral  :  7.430 128.454   1914
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  2.81 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 14.29 %
    Favored  : 83.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.83 %
    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: -0.27 (0.20), residues: 1674
  helix:  0.32 (0.35), residues: 221
  sheet: -0.06 (0.22), residues: 519
  loop : -0.28 (0.20), residues: 934

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 781 
 TYR   0.012   0.001   TYR D 315 
 PHE   0.023   0.001   PHE D1751 
 TRP   0.016   0.001   TRP D1888 
 HIS   0.002   0.000   HIS D 223 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00226 /  0.10 (14099)
  covalent geometry    : angle       0.50705 /  0.26 (19104)
  hydrogen bonds       : bond        0.02940 /  1.97 (  365)
  hydrogen bonds       : angle       5.60754 /  3.95 (  978)

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

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

  3348 Ramachandran restraints generated.
    1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3348 Ramachandran restraints generated.
    1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 116
  time to evaluate  : 0.415 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  210 GLN cc_start: 0.7736 (tt0) cc_final: 0.7406 (tt0)
REVERT: D  227 GLN cc_start: 0.7574 (tp-100) cc_final: 0.7203 (tt0)
REVERT: D  230 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7879 (tmm160)
REVERT: D  242 ASP cc_start: 0.8249 (t0) cc_final: 0.7886 (t0)
REVERT: D  277 MET cc_start: 0.7643 (mmt) cc_final: 0.7193 (mmm)
REVERT: D  450 LYS cc_start: 0.8667 (ttmm) cc_final: 0.8093 (pmtt)
REVERT: D  522 GLU cc_start: 0.8016 (tm-30) cc_final: 0.7646 (tm-30)
REVERT: D  527 LYS cc_start: 0.8632 (mppt) cc_final: 0.8344 (mppt)
REVERT: D  762 MET cc_start: 0.8570 (mmm) cc_final: 0.7772 (ptm)
REVERT: D  803 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7470 (tm-30)
REVERT: D  870 MET cc_start: 0.1246 (mpt) cc_final: 0.0121 (ptp)
REVERT: D 1014 MET cc_start: 0.4809 (mtp) cc_final: 0.4338 (mtm)
REVERT: D 1321 MET cc_start: 0.9026 (mmm) cc_final: 0.8357 (mpt)
REVERT: D 1519 GLU cc_start: 0.8891 (mt-10) cc_final: 0.8462 (mt-10)
REVERT: D 1640 ASP cc_start: 0.8498 (t0) cc_final: 0.7812 (t0)
REVERT: D 1697 ARG cc_start: 0.8873 (ptm160) cc_final: 0.8536 (ptm160)
REVERT: D 1812 MET cc_start: 0.5215 (tpt) cc_final: 0.4782 (tmt)
REVERT: D 1870 TRP cc_start: 0.8434 (p-90) cc_final: 0.7994 (p90)
  outliers start: 34
  outliers final: 11
  residues processed: 146
  average time/residue: 0.5069
  time to fit residues: 82.2204
Evaluate side-chains
  119 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 106
  time to evaluate  : 0.562 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  230 ARG
Chi-restraints excluded: chain D residue  260 ILE
Chi-restraints excluded: chain D residue  509 SER
Chi-restraints excluded: chain D residue  589 VAL
Chi-restraints excluded: chain D residue  738 VAL
Chi-restraints excluded: chain D residue  747 VAL
Chi-restraints excluded: chain D residue  803 GLU
Chi-restraints excluded: chain D residue  913 VAL
Chi-restraints excluded: chain D residue 1290 LEU
Chi-restraints excluded: chain D residue 1512 GLU
Chi-restraints excluded: chain D residue 1792 VAL
Chi-restraints excluded: chain D residue 1887 ILE
Chi-restraints excluded: chain D residue 1923 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 54 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   chunk 98 optimal weight:    1.9990
   chunk 103 optimal weight:    2.9990
   chunk 157 optimal weight:    2.9990
   chunk 97 optimal weight:    0.0970
   chunk 44 optimal weight:    0.9980
   chunk 87 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9990
   chunk 81 optimal weight:    7.9990
   chunk 79 optimal weight:    0.0010
   overall best weight:    0.8188

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D 293 HIS
D 618 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.148241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.098317 restraints weight = 26188.934|
|-----------------------------------------------------------------------------|
r_work (start): 0.3394 rms_B_bonded: 3.58
r_work: 0.3254 rms_B_bonded: 4.09 restraints_weight: 0.5000
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3280
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3280 r_free = 0.3280    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.86   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3280 r_free = 0.3280    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.86   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3280
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8003
moved from start:          0.1471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  14099  Z= 0.113
  Angle     :  0.504   7.667  19104  Z= 0.256
  Chirality :  0.043   0.157   2040
  Planarity :  0.004   0.034   2472
  Dihedral  :  7.257 128.155   1914
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  2.69 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 14.75 %
    Favored  : 82.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.83 %
    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: -0.10 (0.20), residues: 1674
  helix:  0.60 (0.35), residues: 222
  sheet: -0.02 (0.22), residues: 519
  loop : -0.15 (0.21), residues: 933

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D1907 
 TYR   0.015   0.001   TYR D 288 
 PHE   0.025   0.001   PHE D1751 
 TRP   0.017   0.001   TRP D1888 
 HIS   0.002   0.000   HIS D 293 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00257 /  0.11 (14099)
  covalent geometry    : angle       0.50370 /  0.26 (19104)
  hydrogen bonds       : bond        0.02762 /  1.84 (  365)
  hydrogen bonds       : angle       5.34327 /  3.76 (  978)

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

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

  3348 Ramachandran restraints generated.
    1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3348 Ramachandran restraints generated.
    1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 112
  time to evaluate  : 0.568 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  210 GLN cc_start: 0.7839 (tt0) cc_final: 0.7471 (tt0)
REVERT: D  227 GLN cc_start: 0.7558 (tp-100) cc_final: 0.7178 (tt0)
REVERT: D  230 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7890 (tmm160)
REVERT: D  242 ASP cc_start: 0.8256 (t0) cc_final: 0.7888 (t0)
REVERT: D  277 MET cc_start: 0.7618 (mmt) cc_final: 0.7204 (mmm)
REVERT: D  450 LYS cc_start: 0.8702 (ttmm) cc_final: 0.8132 (pmtt)
REVERT: D  522 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7745 (tm-30)
REVERT: D  527 LYS cc_start: 0.8625 (mppt) cc_final: 0.8241 (mppt)
REVERT: D  588 ASP cc_start: 0.8611 (OUTLIER) cc_final: 0.8247 (p0)
REVERT: D  762 MET cc_start: 0.8545 (mmm) cc_final: 0.7723 (ptm)
REVERT: D  870 MET cc_start: 0.1309 (mpt) cc_final: 0.0268 (ptp)
REVERT: D 1014 MET cc_start: 0.4550 (mtp) cc_final: 0.4190 (mtm)
REVERT: D 1321 MET cc_start: 0.9021 (mmm) cc_final: 0.8369 (mpt)
REVERT: D 1519 GLU cc_start: 0.8904 (mt-10) cc_final: 0.8471 (mt-10)
REVERT: D 1564 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8049 (pt0)
REVERT: D 1636 GLU cc_start: 0.8170 (tm-30) cc_final: 0.7727 (tm-30)
REVERT: D 1640 ASP cc_start: 0.8484 (t0) cc_final: 0.7815 (t0)
  outliers start: 41
  outliers final: 16
  residues processed: 144
  average time/residue: 0.5680
  time to fit residues: 90.6359
Evaluate side-chains
  120 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 102
  time to evaluate  : 0.576 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  230 ARG
Chi-restraints excluded: chain D residue  260 ILE
Chi-restraints excluded: chain D residue  295 VAL
Chi-restraints excluded: chain D residue  509 SER
Chi-restraints excluded: chain D residue  588 ASP
Chi-restraints excluded: chain D residue  589 VAL
Chi-restraints excluded: chain D residue  708 LEU
Chi-restraints excluded: chain D residue  738 VAL
Chi-restraints excluded: chain D residue  747 VAL
Chi-restraints excluded: chain D residue  913 VAL
Chi-restraints excluded: chain D residue 1290 LEU
Chi-restraints excluded: chain D residue 1512 GLU
Chi-restraints excluded: chain D residue 1581 THR
Chi-restraints excluded: chain D residue 1792 VAL
Chi-restraints excluded: chain D residue 1861 CYS
Chi-restraints excluded: chain D residue 1863 VAL
Chi-restraints excluded: chain D residue 1887 ILE
Chi-restraints excluded: chain D residue 1946 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 108 optimal weight:    0.9980
   chunk 110 optimal weight:    1.9990
   chunk 105 optimal weight:    0.9990
   chunk 63 optimal weight:    3.9990
   chunk 15 optimal weight:    4.9990
   chunk 117 optimal weight:    0.7980
   chunk 84 optimal weight:   10.0000
   chunk 102 optimal weight:    1.9990
   chunk 31 optimal weight:    0.6980
   chunk 33 optimal weight:    4.9990
   chunk 82 optimal weight:    5.9990
   overall best weight:    1.0984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D 618 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.147443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.097352 restraints weight = 26129.110|
|-----------------------------------------------------------------------------|
r_work (start): 0.3383 rms_B_bonded: 3.58
r_work: 0.3243 rms_B_bonded: 4.07 restraints_weight: 0.5000
r_work (final): 0.3243
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3263
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3263 r_free = 0.3263    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.86   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3263 r_free = 0.3263    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.86   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3263
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8010
moved from start:          0.1603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  14099  Z= 0.134
  Angle     :  0.523  11.697  19104  Z= 0.263
  Chirality :  0.043   0.155   2040
  Planarity :  0.004   0.032   2472
  Dihedral  :  7.192 128.956   1914
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  2.81 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 15.61 %
    Favored  : 81.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.83 %
    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: -0.01 (0.21), residues: 1674
  helix:  0.78 (0.35), residues: 222
  sheet: -0.07 (0.22), residues: 536
  loop : -0.05 (0.21), residues: 916

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 781 
 TYR   0.012   0.001   TYR D1558 
 PHE   0.026   0.001   PHE D1751 
 TRP   0.019   0.001   TRP D1888 
 HIS   0.002   0.001   HIS D 581 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00308 /  0.13 (14099)
  covalent geometry    : angle       0.52303 /  0.26 (19104)
  hydrogen bonds       : bond        0.02761 /  1.84 (  365)
  hydrogen bonds       : angle       5.26412 /  3.71 (  978)

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

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

  3348 Ramachandran restraints generated.
    1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3348 Ramachandran restraints generated.
    1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 113
  time to evaluate  : 0.613 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  175 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7897 (pt0)
REVERT: D  210 GLN cc_start: 0.7899 (tt0) cc_final: 0.7548 (tt0)
REVERT: D  227 GLN cc_start: 0.7554 (tp-100) cc_final: 0.7175 (tt0)
REVERT: D  277 MET cc_start: 0.7620 (mmt) cc_final: 0.7145 (mmm)
REVERT: D  450 LYS cc_start: 0.8724 (ttmm) cc_final: 0.8184 (pmtt)
REVERT: D  522 GLU cc_start: 0.8092 (tm-30) cc_final: 0.7799 (tm-30)
REVERT: D  571 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.8046 (mtt90)
REVERT: D  588 ASP cc_start: 0.8619 (OUTLIER) cc_final: 0.8259 (p0)
REVERT: D  762 MET cc_start: 0.8540 (mmm) cc_final: 0.7729 (ptm)
REVERT: D  870 MET cc_start: 0.1352 (mpt) cc_final: 0.0158 (pmm)
REVERT: D 1014 MET cc_start: 0.4577 (mtp) cc_final: 0.4168 (mtm)
REVERT: D 1455 SER cc_start: 0.8957 (OUTLIER) cc_final: 0.8637 (p)
REVERT: D 1519 GLU cc_start: 0.8901 (mt-10) cc_final: 0.8524 (mt-10)
REVERT: D 1564 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8078 (pt0)
REVERT: D 1636 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7968 (tm-30)
REVERT: D 1640 ASP cc_start: 0.8504 (t0) cc_final: 0.7825 (t0)
REVERT: D 1870 TRP cc_start: 0.8340 (p-90) cc_final: 0.7851 (p90)
REVERT: D 1930 MET cc_start: 0.4698 (ppp) cc_final: 0.3172 (tpt)
  outliers start: 38
  outliers final: 16
  residues processed: 147
  average time/residue: 0.5354
  time to fit residues: 87.6650
Evaluate side-chains
  123 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 103
  time to evaluate  : 0.524 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  175 GLU
Chi-restraints excluded: chain D residue  260 ILE
Chi-restraints excluded: chain D residue  295 VAL
Chi-restraints excluded: chain D residue  509 SER
Chi-restraints excluded: chain D residue  571 ARG
Chi-restraints excluded: chain D residue  588 ASP
Chi-restraints excluded: chain D residue  589 VAL
Chi-restraints excluded: chain D residue  708 LEU
Chi-restraints excluded: chain D residue  738 VAL
Chi-restraints excluded: chain D residue  747 VAL
Chi-restraints excluded: chain D residue  913 VAL
Chi-restraints excluded: chain D residue 1238 LEU
Chi-restraints excluded: chain D residue 1290 LEU
Chi-restraints excluded: chain D residue 1455 SER
Chi-restraints excluded: chain D residue 1512 GLU
Chi-restraints excluded: chain D residue 1581 THR
Chi-restraints excluded: chain D residue 1792 VAL
Chi-restraints excluded: chain D residue 1863 VAL
Chi-restraints excluded: chain D residue 1902 LEU
Chi-restraints excluded: chain D residue 1946 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 35 optimal weight:    6.9990
   chunk 138 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9980
   chunk 32 optimal weight:    0.6980
   chunk 112 optimal weight:    2.9990
   chunk 26 optimal weight:    0.0670
   chunk 91 optimal weight:    1.9990
   chunk 11 optimal weight:    0.2980
   chunk 31 optimal weight:    0.9980
   chunk 65 optimal weight:    3.9990
   chunk 51 optimal weight:    3.9990
   overall best weight:    0.6118

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D 293 HIS
D 618 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.148676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.098833 restraints weight = 26062.817|
|-----------------------------------------------------------------------------|
r_work (start): 0.3403 rms_B_bonded: 3.59
r_work: 0.3262 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3287
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3287 r_free = 0.3287    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.86   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3287 r_free = 0.3287    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.86   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (18 function evaluations)
r_final: 0.3287
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
moved from start:          0.1723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  14099  Z= 0.101
  Angle     :  0.522  14.481  19104  Z= 0.258
  Chirality :  0.043   0.174   2040
  Planarity :  0.003   0.033   2472
  Dihedral  :  7.079 129.109   1914
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  2.51 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 15.35 %
    Favored  : 81.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.83 %
    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:  0.08 (0.21), residues: 1674
  helix:  0.88 (0.35), residues: 222
  sheet: -0.02 (0.22), residues: 538
  loop :  0.02 (0.21), residues: 914

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 232 
 TYR   0.013   0.001   TYR D1558 
 PHE   0.028   0.001   PHE D1751 
 TRP   0.021   0.001   TRP D1888 
 HIS   0.005   0.000   HIS D 293 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00230 /  0.10 (14099)
  covalent geometry    : angle       0.52191 /  0.26 (19104)
  hydrogen bonds       : bond        0.02628 /  1.75 (  365)
  hydrogen bonds       : angle       5.11100 /  3.60 (  978)

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

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

  3348 Ramachandran restraints generated.
    1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3348 Ramachandran restraints generated.
    1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 115
  time to evaluate  : 0.368 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  175 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7921 (pt0)
REVERT: D  204 ARG cc_start: 0.7706 (ttm110) cc_final: 0.6879 (ttm-80)
REVERT: D  210 GLN cc_start: 0.7825 (tt0) cc_final: 0.7452 (tt0)
REVERT: D  227 GLN cc_start: 0.7542 (tp-100) cc_final: 0.7165 (tt0)
REVERT: D  230 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7722 (tmm160)
REVERT: D  277 MET cc_start: 0.7576 (mmt) cc_final: 0.7084 (mmm)
REVERT: D  450 LYS cc_start: 0.8687 (ttmm) cc_final: 0.8155 (pmtt)
REVERT: D  522 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7702 (tm-30)
REVERT: D  588 ASP cc_start: 0.8597 (OUTLIER) cc_final: 0.8236 (p0)
REVERT: D  762 MET cc_start: 0.8501 (mmm) cc_final: 0.7692 (ptm)
REVERT: D  824 LYS cc_start: 0.7497 (pmtt) cc_final: 0.6637 (ttpp)
REVERT: D  870 MET cc_start: 0.1386 (mpt) cc_final: 0.0183 (pmm)
REVERT: D 1014 MET cc_start: 0.4480 (mtp) cc_final: 0.4111 (mtm)
REVERT: D 1257 ASP cc_start: 0.8605 (p0) cc_final: 0.8302 (p0)
REVERT: D 1321 MET cc_start: 0.8931 (mmm) cc_final: 0.8208 (mpt)
REVERT: D 1455 SER cc_start: 0.8944 (OUTLIER) cc_final: 0.8618 (p)
REVERT: D 1519 GLU cc_start: 0.8883 (mt-10) cc_final: 0.8499 (mt-10)
REVERT: D 1564 GLU cc_start: 0.8515 (mt-10) cc_final: 0.7979 (pt0)
REVERT: D 1636 GLU cc_start: 0.8159 (tm-30) cc_final: 0.7952 (tm-30)
REVERT: D 1640 ASP cc_start: 0.8474 (t0) cc_final: 0.7804 (t0)
REVERT: D 1688 GLN cc_start: 0.7841 (mm-40) cc_final: 0.7551 (tp-100)
REVERT: D 1820 TRP cc_start: 0.8418 (p-90) cc_final: 0.7997 (p-90)
REVERT: D 1870 TRP cc_start: 0.8361 (p-90) cc_final: 0.7867 (p90)
REVERT: D 1930 MET cc_start: 0.4636 (ppp) cc_final: 0.3314 (tpt)
REVERT: D 1962 MET cc_start: 0.7287 (tpp) cc_final: 0.7062 (tpp)
  outliers start: 42
  outliers final: 17
  residues processed: 150
  average time/residue: 0.5134
  time to fit residues: 85.7720
Evaluate side-chains
  128 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 107
  time to evaluate  : 0.542 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  175 GLU
Chi-restraints excluded: chain D residue  230 ARG
Chi-restraints excluded: chain D residue  260 ILE
Chi-restraints excluded: chain D residue  295 VAL
Chi-restraints excluded: chain D residue  509 SER
Chi-restraints excluded: chain D residue  588 ASP
Chi-restraints excluded: chain D residue  589 VAL
Chi-restraints excluded: chain D residue  708 LEU
Chi-restraints excluded: chain D residue  738 VAL
Chi-restraints excluded: chain D residue  747 VAL
Chi-restraints excluded: chain D residue  913 VAL
Chi-restraints excluded: chain D residue 1238 LEU
Chi-restraints excluded: chain D residue 1290 LEU
Chi-restraints excluded: chain D residue 1455 SER
Chi-restraints excluded: chain D residue 1512 GLU
Chi-restraints excluded: chain D residue 1581 THR
Chi-restraints excluded: chain D residue 1792 VAL
Chi-restraints excluded: chain D residue 1861 CYS
Chi-restraints excluded: chain D residue 1863 VAL
Chi-restraints excluded: chain D residue 1887 ILE
Chi-restraints excluded: chain D residue 1946 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 146 optimal weight:    3.9990
   chunk 128 optimal weight:    5.9990
   chunk 114 optimal weight:    0.9990
   chunk 92 optimal weight:    3.9990
   chunk 99 optimal weight:    0.0020
   chunk 12 optimal weight:    5.9990
   chunk 131 optimal weight:    0.9980
   chunk 87 optimal weight:    0.9990
   chunk 106 optimal weight:    5.9990
   chunk 21 optimal weight:    1.9990
   chunk 125 optimal weight:    0.9990
   overall best weight:    0.7994

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D 618 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.148417 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.098358 restraints weight = 26095.019|
|-----------------------------------------------------------------------------|
r_work (start): 0.3401 rms_B_bonded: 3.56
r_work: 0.3260 rms_B_bonded: 4.09 restraints_weight: 0.5000
r_work (final): 0.3260
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3282
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3282 r_free = 0.3282    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.86   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3282 r_free = 0.3282    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.86   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3282
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8000
moved from start:          0.1774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  14099  Z= 0.113
  Angle     :  0.528  11.079  19104  Z= 0.261
  Chirality :  0.043   0.169   2040
  Planarity :  0.004   0.033   2472
  Dihedral  :  7.033 129.325   1914
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  2.93 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 16.15 %
    Favored  : 81.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.83 %
    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:  0.14 (0.21), residues: 1674
  helix:  1.02 (0.35), residues: 222
  sheet: -0.01 (0.22), residues: 538
  loop :  0.04 (0.22), residues: 914

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 781 
 TYR   0.013   0.001   TYR D1558 
 PHE   0.028   0.001   PHE D1751 
 TRP   0.024   0.001   TRP D1076 
 HIS   0.001   0.000   HIS D 652 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00259 /  0.11 (14099)
  covalent geometry    : angle       0.52769 /  0.26 (19104)
  hydrogen bonds       : bond        0.02628 /  1.75 (  365)
  hydrogen bonds       : angle       5.02288 /  3.53 (  978)

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

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

  3348 Ramachandran restraints generated.
    1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3348 Ramachandran restraints generated.
    1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 111
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  175 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7984 (pt0)
REVERT: D  204 ARG cc_start: 0.7750 (ttm110) cc_final: 0.6901 (ttm-80)
REVERT: D  210 GLN cc_start: 0.7870 (tt0) cc_final: 0.7490 (tt0)
REVERT: D  227 GLN cc_start: 0.7580 (tp-100) cc_final: 0.7204 (tt0)
REVERT: D  230 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7823 (tmm160)
REVERT: D  277 MET cc_start: 0.7607 (mmt) cc_final: 0.7177 (mmm)
REVERT: D  450 LYS cc_start: 0.8708 (ttmm) cc_final: 0.8179 (pmtt)
REVERT: D  522 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7654 (tm-30)
REVERT: D  527 LYS cc_start: 0.8624 (mppt) cc_final: 0.8279 (mttt)
REVERT: D  571 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.7992 (mtt90)
REVERT: D  588 ASP cc_start: 0.8601 (OUTLIER) cc_final: 0.8246 (p0)
REVERT: D  762 MET cc_start: 0.8505 (mmm) cc_final: 0.7693 (ptm)
REVERT: D  824 LYS cc_start: 0.7473 (pmtt) cc_final: 0.6598 (ttpp)
REVERT: D  870 MET cc_start: 0.1413 (mpt) cc_final: 0.0211 (pmm)
REVERT: D 1014 MET cc_start: 0.4455 (mtp) cc_final: 0.4011 (mtm)
REVERT: D 1257 ASP cc_start: 0.8624 (p0) cc_final: 0.8347 (p0)
REVERT: D 1321 MET cc_start: 0.8979 (mmm) cc_final: 0.8285 (mpt)
REVERT: D 1455 SER cc_start: 0.8951 (OUTLIER) cc_final: 0.8632 (p)
REVERT: D 1519 GLU cc_start: 0.8889 (mt-10) cc_final: 0.8520 (mt-10)
REVERT: D 1564 GLU cc_start: 0.8526 (mt-10) cc_final: 0.7987 (pt0)
REVERT: D 1640 ASP cc_start: 0.8465 (t0) cc_final: 0.7778 (t0)
REVERT: D 1688 GLN cc_start: 0.7862 (mm-40) cc_final: 0.7564 (tp-100)
REVERT: D 1870 TRP cc_start: 0.8394 (p-90) cc_final: 0.7893 (p90)
REVERT: D 1882 ARG cc_start: 0.8435 (ptp-170) cc_final: 0.8091 (ptp-170)
REVERT: D 1930 MET cc_start: 0.4578 (ppp) cc_final: 0.3301 (tpt)
  outliers start: 34
  outliers final: 17
  residues processed: 139
  average time/residue: 0.4790
  time to fit residues: 73.6257
Evaluate side-chains
  127 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 105
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  175 GLU
Chi-restraints excluded: chain D residue  230 ARG
Chi-restraints excluded: chain D residue  260 ILE
Chi-restraints excluded: chain D residue  509 SER
Chi-restraints excluded: chain D residue  571 ARG
Chi-restraints excluded: chain D residue  588 ASP
Chi-restraints excluded: chain D residue  589 VAL
Chi-restraints excluded: chain D residue  738 VAL
Chi-restraints excluded: chain D residue  747 VAL
Chi-restraints excluded: chain D residue  913 VAL
Chi-restraints excluded: chain D residue 1238 LEU
Chi-restraints excluded: chain D residue 1290 LEU
Chi-restraints excluded: chain D residue 1455 SER
Chi-restraints excluded: chain D residue 1512 GLU
Chi-restraints excluded: chain D residue 1581 THR
Chi-restraints excluded: chain D residue 1792 VAL
Chi-restraints excluded: chain D residue 1855 LEU
Chi-restraints excluded: chain D residue 1861 CYS
Chi-restraints excluded: chain D residue 1862 ILE
Chi-restraints excluded: chain D residue 1863 VAL
Chi-restraints excluded: chain D residue 1887 ILE
Chi-restraints excluded: chain D residue 1946 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 23 optimal weight:    3.9990
   chunk 89 optimal weight:    2.9990
   chunk 3 optimal weight:    3.9990
   chunk 131 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 8 optimal weight:    0.8980
   chunk 83 optimal weight:   30.0000
   chunk 19 optimal weight:    3.9990
   chunk 50 optimal weight:    4.9990
   chunk 120 optimal weight:    4.9990
   chunk 21 optimal weight:    0.8980
   overall best weight:    2.1586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D 618 GLN
D1652 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.145535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.094564 restraints weight = 25908.376|
|-----------------------------------------------------------------------------|
r_work (start): 0.3330 rms_B_bonded: 3.56
r_work: 0.3187 rms_B_bonded: 4.05 restraints_weight: 0.5000
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3194
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3194 r_free = 0.3194    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.86   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3194 r_free = 0.3194    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.85   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3194
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.2032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  14099  Z= 0.226
  Angle     :  0.592  11.277  19104  Z= 0.295
  Chirality :  0.045   0.180   2040
  Planarity :  0.004   0.037   2472
  Dihedral  :  7.243 129.383   1914
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  3.58 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 16.41 %
    Favored  : 81.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.83 %
    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:  0.04 (0.21), residues: 1674
  helix:  0.81 (0.35), residues: 222
  sheet: -0.06 (0.22), residues: 523
  loop : -0.00 (0.22), residues: 929

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG D 232 
 TYR   0.022   0.001   TYR D1558 
 PHE   0.030   0.002   PHE D1751 
 TRP   0.030   0.001   TRP D1888 
 HIS   0.003   0.001   HIS D 734 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00522 /  0.23 (14099)
  covalent geometry    : angle       0.59227 /  0.29 (19104)
  hydrogen bonds       : bond        0.03132 /  2.09 (  365)
  hydrogen bonds       : angle       5.38756 /  3.79 (  978)

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

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

  3348 Ramachandran restraints generated.
    1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3348 Ramachandran restraints generated.
    1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 108
  time to evaluate  : 0.559 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  175 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8069 (pt0)
REVERT: D  210 GLN cc_start: 0.7947 (tt0) cc_final: 0.7721 (tt0)
REVERT: D  227 GLN cc_start: 0.7663 (tp-100) cc_final: 0.7296 (tt0)
REVERT: D  242 ASP cc_start: 0.8292 (t0) cc_final: 0.7922 (t0)
REVERT: D  277 MET cc_start: 0.7638 (mmt) cc_final: 0.7218 (mmm)
REVERT: D  450 LYS cc_start: 0.8745 (ttmm) cc_final: 0.8184 (pmtt)
REVERT: D  498 THR cc_start: 0.7881 (OUTLIER) cc_final: 0.7493 (t)
REVERT: D  571 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.6782 (mmt90)
REVERT: D  588 ASP cc_start: 0.8653 (OUTLIER) cc_final: 0.8288 (p0)
REVERT: D  762 MET cc_start: 0.8564 (mmm) cc_final: 0.7736 (ptm)
REVERT: D  824 LYS cc_start: 0.7334 (pmtt) cc_final: 0.6340 (ttpp)
REVERT: D  870 MET cc_start: 0.1298 (mpt) cc_final: 0.0071 (pmm)
REVERT: D 1014 MET cc_start: 0.4524 (mtp) cc_final: 0.4052 (mtm)
REVERT: D 1257 ASP cc_start: 0.8756 (p0) cc_final: 0.8516 (p0)
REVERT: D 1321 MET cc_start: 0.9002 (mmm) cc_final: 0.8313 (mpt)
REVERT: D 1519 GLU cc_start: 0.8889 (mt-10) cc_final: 0.8626 (mt-10)
REVERT: D 1564 GLU cc_start: 0.8528 (mt-10) cc_final: 0.7977 (pt0)
REVERT: D 1640 ASP cc_start: 0.8567 (t0) cc_final: 0.7916 (t0)
REVERT: D 1704 ASP cc_start: 0.8932 (OUTLIER) cc_final: 0.8155 (p0)
REVERT: D 1870 TRP cc_start: 0.8382 (p-90) cc_final: 0.7879 (p90)
REVERT: D 1882 ARG cc_start: 0.8487 (ptp-170) cc_final: 0.8137 (ptp-170)
REVERT: D 1930 MET cc_start: 0.4708 (ppp) cc_final: 0.3462 (tpt)
  outliers start: 32
  outliers final: 15
  residues processed: 133
  average time/residue: 0.5116
  time to fit residues: 75.7109
Evaluate side-chains
  125 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 105
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  175 GLU
Chi-restraints excluded: chain D residue  260 ILE
Chi-restraints excluded: chain D residue  295 VAL
Chi-restraints excluded: chain D residue  498 THR
Chi-restraints excluded: chain D residue  509 SER
Chi-restraints excluded: chain D residue  571 ARG
Chi-restraints excluded: chain D residue  588 ASP
Chi-restraints excluded: chain D residue  589 VAL
Chi-restraints excluded: chain D residue  738 VAL
Chi-restraints excluded: chain D residue  747 VAL
Chi-restraints excluded: chain D residue  913 VAL
Chi-restraints excluded: chain D residue 1290 LEU
Chi-restraints excluded: chain D residue 1512 GLU
Chi-restraints excluded: chain D residue 1581 THR
Chi-restraints excluded: chain D residue 1704 ASP
Chi-restraints excluded: chain D residue 1792 VAL
Chi-restraints excluded: chain D residue 1861 CYS
Chi-restraints excluded: chain D residue 1863 VAL
Chi-restraints excluded: chain D residue 1887 ILE
Chi-restraints excluded: chain D residue 1946 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 65 optimal weight:    3.9990
   chunk 115 optimal weight:    0.0370
   chunk 23 optimal weight:    0.9980
   chunk 107 optimal weight:    0.9980
   chunk 159 optimal weight:    0.5980
   chunk 37 optimal weight:    0.9980
   chunk 135 optimal weight:    3.9990
   chunk 3 optimal weight:    4.9990
   chunk 54 optimal weight:    3.9990
   chunk 30 optimal weight:    0.8980
   chunk 48 optimal weight:    6.9990
   overall best weight:    0.7058

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D 618 GLN
D1827 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.147991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.097587 restraints weight = 26164.377|
|-----------------------------------------------------------------------------|
r_work (start): 0.3394 rms_B_bonded: 3.60
r_work: 0.3249 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.3249
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3272
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3272 r_free = 0.3272    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.85   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3272 r_free = 0.3272    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.87   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3272
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7968
moved from start:          0.1983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  14099  Z= 0.110
  Angle     :  0.544  10.508  19104  Z= 0.270
  Chirality :  0.043   0.163   2040
  Planarity :  0.004   0.051   2472
  Dihedral  :  7.049 128.935   1914
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  2.87 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 17.01 %
    Favored  : 81.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.83 %
    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:  0.07 (0.21), residues: 1674
  helix:  0.85 (0.35), residues: 229
  sheet: -0.03 (0.22), residues: 528
  loop :  0.01 (0.22), residues: 917

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D1697 
 TYR   0.010   0.001   TYR D 443 
 PHE   0.029   0.001   PHE D1751 
 TRP   0.031   0.001   TRP D1888 
 HIS   0.003   0.000   HIS D1380 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00251 /  0.11 (14099)
  covalent geometry    : angle       0.54394 /  0.27 (19104)
  hydrogen bonds       : bond        0.02665 /  1.77 (  365)
  hydrogen bonds       : angle       5.10945 /  3.59 (  978)

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

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

  3348 Ramachandran restraints generated.
    1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3348 Ramachandran restraints generated.
    1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 114
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
REVERT: D  175 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8076 (pt0)
REVERT: D  210 GLN cc_start: 0.7849 (tt0) cc_final: 0.7460 (tt0)
REVERT: D  227 GLN cc_start: 0.7551 (tp-100) cc_final: 0.7179 (tt0)
REVERT: D  230 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.8111 (tmm160)
REVERT: D  242 ASP cc_start: 0.8208 (t0) cc_final: 0.7868 (t0)
REVERT: D  277 MET cc_start: 0.7565 (mmt) cc_final: 0.7146 (mmm)
REVERT: D  450 LYS cc_start: 0.8649 (ttmm) cc_final: 0.8120 (pmtt)
REVERT: D  498 THR cc_start: 0.7658 (OUTLIER) cc_final: 0.7332 (t)
REVERT: D  522 GLU cc_start: 0.7995 (tm-30) cc_final: 0.7565 (tm-30)
REVERT: D  588 ASP cc_start: 0.8609 (OUTLIER) cc_final: 0.8249 (p0)
REVERT: D  762 MET cc_start: 0.8487 (mmm) cc_final: 0.7677 (ptm)
REVERT: D  824 LYS cc_start: 0.7603 (pmtt) cc_final: 0.6786 (ttpp)
REVERT: D  863 MET cc_start: 0.0613 (mmm) cc_final: 0.0386 (tmm)
REVERT: D  870 MET cc_start: 0.1311 (mpt) cc_final: 0.0083 (pmm)
REVERT: D 1014 MET cc_start: 0.4370 (mtp) cc_final: 0.3913 (mtm)
REVERT: D 1076 TRP cc_start: 0.8015 (t-100) cc_final: 0.7806 (t-100)
REVERT: D 1257 ASP cc_start: 0.8672 (p0) cc_final: 0.8426 (p0)
REVERT: D 1321 MET cc_start: 0.9008 (mmm) cc_final: 0.8341 (mpt)
REVERT: D 1455 SER cc_start: 0.8927 (OUTLIER) cc_final: 0.8588 (p)
REVERT: D 1512 GLU cc_start: 0.6879 (OUTLIER) cc_final: 0.5973 (pm20)
REVERT: D 1519 GLU cc_start: 0.8888 (mt-10) cc_final: 0.8507 (mt-10)
REVERT: D 1564 GLU cc_start: 0.8500 (mt-10) cc_final: 0.7999 (pt0)
REVERT: D 1640 ASP cc_start: 0.8491 (t0) cc_final: 0.7822 (t0)
REVERT: D 1688 GLN cc_start: 0.7912 (mm-40) cc_final: 0.7629 (tp-100)
REVERT: D 1704 ASP cc_start: 0.8969 (t0) cc_final: 0.8279 (p0)
REVERT: D 1870 TRP cc_start: 0.8391 (p-90) cc_final: 0.7920 (p90)
REVERT: D 1882 ARG cc_start: 0.8422 (ptp-170) cc_final: 0.8111 (ptp-170)
REVERT: D 1907 ARG cc_start: 0.8033 (mtm-85) cc_final: 0.7730 (mtm-85)
REVERT: D 1930 MET cc_start: 0.4583 (ppp) cc_final: 0.3770 (tmt)
  outliers start: 26
  outliers final: 14
  residues processed: 134
  average time/residue: 0.4849
  time to fit residues: 72.1815
Evaluate side-chains
  123 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 103
  time to evaluate  : 0.437 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  175 GLU
Chi-restraints excluded: chain D residue  230 ARG
Chi-restraints excluded: chain D residue  260 ILE
Chi-restraints excluded: chain D residue  295 VAL
Chi-restraints excluded: chain D residue  498 THR
Chi-restraints excluded: chain D residue  509 SER
Chi-restraints excluded: chain D residue  588 ASP
Chi-restraints excluded: chain D residue  589 VAL
Chi-restraints excluded: chain D residue  738 VAL
Chi-restraints excluded: chain D residue  747 VAL
Chi-restraints excluded: chain D residue  913 VAL
Chi-restraints excluded: chain D residue 1290 LEU
Chi-restraints excluded: chain D residue 1455 SER
Chi-restraints excluded: chain D residue 1512 GLU
Chi-restraints excluded: chain D residue 1581 THR
Chi-restraints excluded: chain D residue 1792 VAL
Chi-restraints excluded: chain D residue 1855 LEU
Chi-restraints excluded: chain D residue 1861 CYS
Chi-restraints excluded: chain D residue 1863 VAL
Chi-restraints excluded: chain D residue 1946 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 113 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9980
   chunk 1 optimal weight:    2.9990
   chunk 86 optimal weight:    9.9990
   chunk 83 optimal weight:   20.0000
   chunk 10 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9990
   chunk 55 optimal weight:    0.8980
   chunk 131 optimal weight:    0.9990
   chunk 22 optimal weight:    0.0980
   chunk 163 optimal weight:   20.0000
   overall best weight:    0.7782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D 618 GLN
D1754 ASN
D1827 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.148056 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.097937 restraints weight = 25981.927|
|-----------------------------------------------------------------------------|
r_work (start): 0.3401 rms_B_bonded: 3.53
r_work: 0.3255 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3276
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3276 r_free = 0.3276    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.87   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3276 r_free = 0.3276    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.87   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3276
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7966
moved from start:          0.2057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  14099  Z= 0.118
  Angle     :  0.556  12.792  19104  Z= 0.273
  Chirality :  0.043   0.165   2040
  Planarity :  0.004   0.046   2472
  Dihedral  :  6.972 128.510   1914
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  3.17 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 17.54 %
    Favored  : 81.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.83 %
    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:  0.11 (0.21), residues: 1674
  helix:  0.88 (0.35), residues: 229
  sheet:  0.01 (0.22), residues: 528
  loop :  0.03 (0.22), residues: 917

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D1697 
 TYR   0.012   0.001   TYR D1558 
 PHE   0.031   0.001   PHE D1751 
 TRP   0.043   0.001   TRP D1888 
 HIS   0.001   0.000   HIS D1018 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00270 /  0.12 (14099)
  covalent geometry    : angle       0.55573 /  0.27 (19104)
  hydrogen bonds       : bond        0.02677 /  1.79 (  365)
  hydrogen bonds       : angle       5.06621 /  3.56 (  978)

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

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

  3348 Ramachandran restraints generated.
    1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3348 Ramachandran restraints generated.
    1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 109
  time to evaluate  : 0.552 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  175 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8105 (pt0)
REVERT: D  210 GLN cc_start: 0.7850 (tt0) cc_final: 0.7452 (tt0)
REVERT: D  227 GLN cc_start: 0.7585 (tp-100) cc_final: 0.7212 (tt0)
REVERT: D  230 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.8095 (tmm160)
REVERT: D  242 ASP cc_start: 0.8205 (t0) cc_final: 0.7857 (t0)
REVERT: D  277 MET cc_start: 0.7539 (mmt) cc_final: 0.7123 (mmm)
REVERT: D  450 LYS cc_start: 0.8674 (ttmm) cc_final: 0.8138 (pmtt)
REVERT: D  522 GLU cc_start: 0.7989 (tm-30) cc_final: 0.7537 (tm-30)
REVERT: D  588 ASP cc_start: 0.8620 (OUTLIER) cc_final: 0.8269 (p0)
REVERT: D  591 GLU cc_start: 0.8905 (mp0) cc_final: 0.8516 (pm20)
REVERT: D  762 MET cc_start: 0.8465 (mmm) cc_final: 0.7660 (ptm)
REVERT: D  824 LYS cc_start: 0.7607 (pmtt) cc_final: 0.6787 (ttpp)
REVERT: D  863 MET cc_start: 0.0629 (mmm) cc_final: 0.0391 (tmm)
REVERT: D  870 MET cc_start: 0.1270 (mpt) cc_final: 0.0054 (pmm)
REVERT: D 1014 MET cc_start: 0.4347 (mtp) cc_final: 0.3883 (mtm)
REVERT: D 1076 TRP cc_start: 0.8043 (t-100) cc_final: 0.7827 (t-100)
REVERT: D 1257 ASP cc_start: 0.8702 (p0) cc_final: 0.8462 (p0)
REVERT: D 1321 MET cc_start: 0.9007 (mmm) cc_final: 0.8345 (mpt)
REVERT: D 1519 GLU cc_start: 0.8864 (mt-10) cc_final: 0.8472 (mt-10)
REVERT: D 1564 GLU cc_start: 0.8462 (mt-10) cc_final: 0.7975 (pt0)
REVERT: D 1640 ASP cc_start: 0.8463 (t0) cc_final: 0.7787 (t0)
REVERT: D 1688 GLN cc_start: 0.7890 (mm-40) cc_final: 0.7588 (tp-100)
REVERT: D 1704 ASP cc_start: 0.8953 (t0) cc_final: 0.8268 (p0)
REVERT: D 1870 TRP cc_start: 0.8383 (p-90) cc_final: 0.7911 (p90)
REVERT: D 1882 ARG cc_start: 0.8444 (ptp-170) cc_final: 0.8112 (ptp-170)
REVERT: D 1907 ARG cc_start: 0.8032 (mtm-85) cc_final: 0.7739 (mtm-85)
REVERT: D 1930 MET cc_start: 0.4568 (ppp) cc_final: 0.3824 (tmt)
  outliers start: 20
  outliers final: 15
  residues processed: 124
  average time/residue: 0.5151
  time to fit residues: 71.0288
Evaluate side-chains
  123 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 105
  time to evaluate  : 0.600 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  175 GLU
Chi-restraints excluded: chain D residue  230 ARG
Chi-restraints excluded: chain D residue  260 ILE
Chi-restraints excluded: chain D residue  295 VAL
Chi-restraints excluded: chain D residue  509 SER
Chi-restraints excluded: chain D residue  588 ASP
Chi-restraints excluded: chain D residue  589 VAL
Chi-restraints excluded: chain D residue  738 VAL
Chi-restraints excluded: chain D residue  747 VAL
Chi-restraints excluded: chain D residue  913 VAL
Chi-restraints excluded: chain D residue 1290 LEU
Chi-restraints excluded: chain D residue 1512 GLU
Chi-restraints excluded: chain D residue 1581 THR
Chi-restraints excluded: chain D residue 1792 VAL
Chi-restraints excluded: chain D residue 1855 LEU
Chi-restraints excluded: chain D residue 1861 CYS
Chi-restraints excluded: chain D residue 1863 VAL
Chi-restraints excluded: chain D residue 1946 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 137 optimal weight:    4.9990
   chunk 136 optimal weight:    0.6980
   chunk 162 optimal weight:    0.8980
   chunk 51 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 167 optimal weight:    8.9990
   chunk 19 optimal weight:    4.9990
   chunk 74 optimal weight:   10.0000
   chunk 48 optimal weight:    5.9990
   chunk 150 optimal weight:    9.9990
   chunk 14 optimal weight:    8.9990
   overall best weight:    2.9186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D 618 GLN
D1062 HIS
D1827 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.144243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.093037 restraints weight = 26025.241|
|-----------------------------------------------------------------------------|
r_work (start): 0.3307 rms_B_bonded: 3.55
r_work: 0.3164 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3173
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3173 r_free = 0.3173    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.87   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3173 r_free = 0.3173    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.85   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3173
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8069
moved from start:          0.2266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.054  14099  Z= 0.298
  Angle     :  0.648  13.726  19104  Z= 0.321
  Chirality :  0.046   0.180   2040
  Planarity :  0.004   0.048   2472
  Dihedral  :  7.250 127.897   1914
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  3.76 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 17.48 %
    Favored  : 80.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.83 %
    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: -0.08 (0.21), residues: 1674
  helix:  0.55 (0.34), residues: 228
  sheet: -0.11 (0.22), residues: 526
  loop : -0.05 (0.22), residues: 920

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 785 
 TYR   0.022   0.001   TYR D1558 
 PHE   0.032   0.002   PHE D1751 
 TRP   0.048   0.002   TRP D1888 
 HIS   0.004   0.001   HIS D1251 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00696 /  0.30 (14099)
  covalent geometry    : angle       0.64809 /  0.32 (19104)
  hydrogen bonds       : bond        0.03362 /  2.25 (  365)
  hydrogen bonds       : angle       5.50332 /  3.87 (  978)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5083.51 seconds
wall clock time: 87 minutes 19.04 seconds (5239.04 seconds total)