Starting phenix.real_space_refine
on Fri Jul  3 11:43:27 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9qlf_53226/07_2026/9qlf_53226.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9qlf_53226/07_2026/9qlf_53226.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.65
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9qlf_53226/07_2026/9qlf_53226.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9qlf_53226/07_2026/9qlf_53226.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9qlf_53226/07_2026/9qlf_53226.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9qlf_53226/07_2026/9qlf_53226.map"
  }
  resolution = 2.65
  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      59      5.16       5
     C    8780      2.51       5
     N    2352      2.21       5
     O    2559      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 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: 13762
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "D"
      Number of atoms: 13692
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1687, 13692
          Classifications: {'peptide': 1687}
          Link IDs: {'PCIS': 3, 'PTRANS': 103, 'TRANS': 1580}
          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=0.78
      ... (28 atoms not shown)
      pdb=" P   PSF D2001 " occ=0.78
    residue:
      pdb=" N   PSF D2010 " occ=0.89
      ... (28 atoms not shown)
      pdb=" P   PSF D2010 " occ=0.89
  Time building chain proxies: 3.07, per 1000 atoms: 0.22
  Number of scatterers: 13762
  At special positions: 0
  Unit cell: (102.24, 123.12, 153.36, 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      59     16.00
     P       2     15.00
     O    2559      8.00
     N    2352      7.00
     C    8780      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: 1.08
  Conformation dependent library (CDL) restraints added in 745.2 milliseconds
  

  3346 Ramachandran restraints generated.
    1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3176

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 19 sheets defined
      16.7% alpha, 28.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.54
  Creating SS restraints...
    Processing helix  chain 'D' and resid 172 through 189
    Processing helix  chain 'D' and resid 255 through 258
    Processing helix  chain 'D' and resid 284 through 290
    Processing helix  chain 'D' and resid 307 through 311
    Processing helix  chain 'D' and resid 335 through 340
    Processing helix  chain 'D' and resid 342 through 346
      removed outlier: 3.687A  pdb=" N   SER D 345 " --> pdb=" O   ASP D 342 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 376 through 382
    Processing helix  chain 'D' and resid 520 through 524
    Processing helix  chain 'D' and resid 558 through 565
    Processing helix  chain 'D' and resid 566 through 569
    Processing helix  chain 'D' and resid 650 through 680
      removed outlier: 4.015A  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
    Processing helix  chain 'D' and resid 750 through 765
    Processing helix  chain 'D' and resid 792 through 796
    Processing helix  chain 'D' and resid 844 through 847
      removed outlier: 4.881A  pdb=" N   LYS D 847 " --> pdb=" O   ALA D 844 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 844 through 847'
    Processing helix  chain 'D' and resid 848 through 853
      removed outlier: 4.112A  pdb=" N   PHE D 852 " --> pdb=" O   LYS D 848 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 895 through 899
      removed outlier: 3.695A  pdb=" N   PHE D 898 " --> pdb=" O   LYS D 895 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   PHE D 899 " --> pdb=" O   ARG D 896 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 895 through 899'
    Processing helix  chain 'D' and resid 1086 through 1093
      removed outlier: 3.705A  pdb=" N   ALA D1089 " --> pdb=" O   HIS D1086 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   ALA D1090 " --> pdb=" O   GLY D1087 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   ILE D1091 " --> pdb=" O   ALA D1088 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1200 through 1207
    Processing helix  chain 'D' and resid 1381 through 1385
      removed outlier: 3.821A  pdb=" N   GLY D1384 " --> pdb=" O   ARG D1381 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1452 through 1462
      removed outlier: 3.748A  pdb=" N   LYS D1456 " --> pdb=" O   ASP D1452 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1468 through 1473
      removed outlier: 3.954A  pdb=" N   GLN D1472 " --> pdb=" O   GLY D1468 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1484 through 1495
      removed outlier: 3.602A  pdb=" N   VAL D1488 " --> pdb=" O   LEU D1485 " (cutoff:3.500A)
      removed outlier: 5.926A  pdb=" N   ALA D1489 " --> pdb=" O   GLU D1486 " (cutoff:3.500A)
      removed outlier: 6.193A  pdb=" N   GLU D1490 " --> pdb=" O   ASN D1487 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   GLU D1492 " --> pdb=" O   ALA D1489 " (cutoff:3.500A)
      removed outlier: 6.372A  pdb=" N   GLY D1493 " --> pdb=" O   GLU D1490 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   THR D1495 " --> pdb=" O   GLU D1492 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1590 through 1593
      removed outlier: 3.694A  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 1672 through 1684
    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 1731
    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
    Processing sheet with id=AA1, first strand: chain 'D' and resid 240 through 249
      removed outlier: 6.876A  pdb=" N   PHE D 241 " --> pdb=" O   GLU D 207 " (cutoff:3.500A)
      removed outlier: 7.303A  pdb=" N   GLU D 207 " --> pdb=" O   PHE D 241 " (cutoff:3.500A)
      removed outlier: 5.724A  pdb=" N   ILE D 201 " --> pdb=" O   LEU D 323 " (cutoff:3.500A)
      removed outlier: 7.778A  pdb=" N   LEU D 323 " --> pdb=" O   ILE D 201 " (cutoff:3.500A)
      removed outlier: 5.710A  pdb=" N   VAL D 203 " --> pdb=" O   PHE D 321 " (cutoff:3.500A)
      removed outlier: 7.473A  pdb=" N   PHE D 321 " --> pdb=" O   VAL D 203 " (cutoff:3.500A)
      removed outlier: 5.400A  pdb=" N   VAL D 205 " --> pdb=" O   SER D 319 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   SER D 319 " --> pdb=" O   VAL D 205 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   GLU D 207 " --> pdb=" O   LYS D 317 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   GLY D 314 " --> pdb=" O   LEU D 302 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   MET D 316 " --> pdb=" O   LEU D 300 " (cutoff:3.500A)
      removed outlier: 7.396A  pdb=" N   MET D 320 " --> pdb=" O   MET D 296 " (cutoff:3.500A)
      removed outlier: 5.422A  pdb=" N   MET D 296 " --> pdb=" O   MET D 320 " (cutoff:3.500A)
      removed outlier: 7.047A  pdb=" N   VAL D 322 " --> pdb=" O   ALA D 294 " (cutoff:3.500A)
      removed outlier: 5.159A  pdb=" N   ALA D 294 " --> pdb=" O   VAL D 322 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 227 through 230
      removed outlier: 5.882A  pdb=" N   ASN D 267 " --> pdb=" O   LEU D 276 " (cutoff:3.500A)
      removed outlier: 5.592A  pdb=" N   LEU D 276 " --> pdb=" O   ASN D 267 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 499 through 508
      removed outlier: 5.330A  pdb=" N   GLY D 500 " --> pdb=" O   LEU D 541 " (cutoff:3.500A)
      removed outlier: 5.630A  pdb=" N   LEU D 541 " --> pdb=" O   GLY D 500 " (cutoff:3.500A)
      removed outlier: 4.343A  pdb=" N   GLY D 535 " --> pdb=" O   LEU D 506 " (cutoff:3.500A)
      removed outlier: 6.309A  pdb=" N   GLY D 508 " --> pdb=" O   TYR D 533 " (cutoff:3.500A)
      removed outlier: 5.767A  pdb=" N   TYR D 533 " --> pdb=" O   GLY D 508 " (cutoff:3.500A)
      removed outlier: 6.776A  pdb=" N   ARG D 536 " --> pdb=" O   ALA D 367 " (cutoff:3.500A)
      removed outlier: 4.564A  pdb=" N   ALA D 367 " --> pdb=" O   ARG D 536 " (cutoff:3.500A)
      removed outlier: 6.861A  pdb=" N   LEU D 538 " --> pdb=" O   TYR D 365 " (cutoff:3.500A)
      removed outlier: 7.096A  pdb=" N   ARG D 366 " --> pdb=" O   TRP D 421 " (cutoff:3.500A)
      removed outlier: 6.374A  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: 6.604A  pdb=" N   ILE D 438 " --> pdb=" O   TYR D 458 " (cutoff:3.500A)
      removed outlier: 4.377A  pdb=" N   TYR D 458 " --> pdb=" O   ILE D 438 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   LEU D 440 " --> pdb=" O   THR D 456 " (cutoff:3.500A)
      removed outlier: 4.413A  pdb=" N   THR D 456 " --> pdb=" O   LEU D 440 " (cutoff:3.500A)
      removed outlier: 6.765A  pdb=" N   ILE D 442 " --> pdb=" O   VAL D 454 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 572 through 584
      removed outlier: 8.741A  pdb=" N   SER D 582 " --> pdb=" O   THR D 637 " (cutoff:3.500A)
      removed outlier: 12.209A  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 647
    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: 3.557A  pdb=" N   ALA D 787 " --> pdb=" O   MET D 779 " (cutoff:3.500A)
      removed outlier: 6.324A  pdb=" N   ARG D 781 " --> pdb=" O   ARG D 785 " (cutoff:3.500A)
      removed outlier: 5.533A  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 929 through 939
      removed outlier: 11.684A  pdb=" N   GLU D 933 " --> pdb=" O   TYR D 953 " (cutoff:3.500A)
      removed outlier: 10.283A  pdb=" N   TYR D 953 " --> pdb=" O   GLU D 933 " (cutoff:3.500A)
      removed outlier: 8.296A  pdb=" N   TYR D 935 " --> pdb=" O   ASP D 951 " (cutoff:3.500A)
      removed outlier: 8.782A  pdb=" N   ASP D 951 " --> pdb=" O   TYR D 935 " (cutoff:3.500A)
      removed outlier: 7.389A  pdb=" N   ASN D 937 " --> pdb=" O   ALA D 949 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   ALA D 949 " --> pdb=" O   ASN D 937 " (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: 6.622A  pdb=" N   TYR D1137 " --> pdb=" O   GLU D1196 " (cutoff:3.500A)
      removed outlier: 4.587A  pdb=" N   GLU D1196 " --> pdb=" O   TYR D1137 " (cutoff:3.500A)
      removed outlier: 6.018A  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: 3.694A  pdb=" N   GLY D1228 " --> pdb=" O   LEU D1215 " (cutoff:3.500A)
      removed outlier: 5.944A  pdb=" N   ASP D1217 " --> pdb=" O   PHE D1226 " (cutoff:3.500A)
      removed outlier: 5.749A  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
    Processing sheet with id=AB3, first strand: chain 'D' and resid 1312 through 1314
      removed outlier: 6.328A  pdb=" N   VAL D1516 " --> pdb=" O   ARG D1505 " (cutoff:3.500A)
      removed outlier: 6.797A  pdb=" N   ARG D1505 " --> pdb=" O   VAL D1516 " (cutoff:3.500A)
      removed outlier: 4.029A  pdb=" N   GLY D1518 " --> pdb=" O   LEU D1503 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 1336 through 1339
      removed outlier: 3.804A  pdb=" N   GLY D1390 " --> pdb=" O   VAL D1377 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 1479 through 1480
      removed outlier: 6.977A  pdb=" N   LYS D1479 " --> pdb=" O   VAL D1742 " (cutoff:3.500A)
      removed outlier: 7.690A  pdb=" N   THR D1744 " --> pdb=" O   LYS D1479 " (cutoff:3.500A)
      removed outlier: 8.175A  pdb=" N   HIS D1741 " --> pdb=" O   VAL D1764 " (cutoff:3.500A)
      removed outlier: 6.420A  pdb=" N   VAL D1764 " --> pdb=" O   HIS D1741 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   LYS D1759 " --> pdb=" O   GLY D1562 " (cutoff:3.500A)
      removed outlier: 4.738A  pdb=" N   GLY D1562 " --> pdb=" O   LYS D1759 " (cutoff:3.500A)
      removed outlier: 6.997A  pdb=" N   GLN D1761 " --> pdb=" O   VAL D1560 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 1585 through 1588
      removed outlier: 3.641A  pdb=" N   GLY D1635 " --> pdb=" O   VAL D1622 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   ASP D1624 " --> pdb=" O   LYS D1633 " (cutoff:3.500A)
      removed outlier: 6.317A  pdb=" N   LYS D1633 " --> pdb=" O   ASP D1624 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 1697 through 1700
    Processing sheet with id=AB8, first strand: chain 'D' and resid 1876 through 1879
      removed outlier: 3.973A  pdb=" N   ASP D1853 " --> pdb=" O   ILE D1862 " (cutoff:3.500A)
      removed outlier: 9.327A  pdb=" N   ALA D1864 " --> pdb=" O   PRO D1851 " (cutoff:3.500A)
      removed outlier: 7.504A  pdb=" N   GLY D1842 " --> pdb=" O   LYS D1798 " (cutoff:3.500A)
      removed outlier: 6.030A  pdb=" N   LYS D1798 " --> pdb=" O   GLY D1842 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   PHE D1844 " --> pdb=" O   ASN D1796 " (cutoff:3.500A)
      removed outlier: 7.890A  pdb=" N   ASN D1796 " --> pdb=" O   PHE D1844 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   TRP D1846 " --> pdb=" O   ILE D1794 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   ILE D1794 " --> pdb=" O   TRP D1846 " (cutoff:3.500A)
      removed outlier: 6.586A  pdb=" N   GLU D1967 " --> pdb=" O   TRP D1795 " (cutoff:3.500A)
      removed outlier: 4.597A  pdb=" N   THR D1797 " --> pdb=" O   LYS D1965 " (cutoff:3.500A)
      removed outlier: 6.787A  pdb=" N   LYS D1965 " --> pdb=" O   THR D1797 " (cutoff:3.500A)
      removed outlier: 5.247A  pdb=" N   ARG D1960 " --> pdb=" O   LYS D1956 " (cutoff:3.500A)
      removed outlier: 6.149A  pdb=" N   LYS D1956 " --> pdb=" O   ARG D1960 " (cutoff:3.500A)
      removed outlier: 5.379A  pdb=" N   MET D1962 " --> pdb=" O   ALA D1954 " (cutoff:3.500A)
      removed outlier: 6.453A  pdb=" N   ALA D1954 " --> pdb=" O   MET D1962 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   GLY D1964 " --> pdb=" O   CYS D1952 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'D' and resid 1824 through 1830
      removed outlier: 4.385A  pdb=" N   VAL D1821 " --> pdb=" O   ASN D1824 " (cutoff:3.500A)
      removed outlier: 8.707A  pdb=" N   GLU D1826 " --> pdb=" O   GLY D1819 " (cutoff:3.500A)
      removed outlier: 10.741A  pdb=" N   GLY D1819 " --> pdb=" O   GLU D1826 " (cutoff:3.500A)
      removed outlier: 10.250A  pdb=" N   LYS D1828 " --> pdb=" O   VAL D1817 " (cutoff:3.500A)
      removed outlier: 11.345A  pdb=" N   VAL D1817 " --> pdb=" O   LYS D1828 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   GLY D1900 " --> pdb=" O   ILE D1887 " (cutoff:3.500A)
      removed outlier: 6.820A  pdb=" N   ASP D1889 " --> pdb=" O   TYR D1898 " (cutoff:3.500A)
      removed outlier: 6.066A  pdb=" N   TYR D1898 " --> pdb=" O   ASP D1889 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'D' and resid 1909 through 1910

    382 hydrogen bonds defined for protein.
    1029 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: 3.10

  Time building geometry restraints manager: 1.54 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: 2827
        1.33 -     1.45: 3380
        1.45 -     1.58: 7793
        1.58 -     1.70: 5
        1.70 -     1.83: 93
  Bond restraints: 14098
  Sorted by residual:
  bond pdb=" C   THR D 252 "
       pdb=" N   PRO D 253 "
    ideal  model  delta    sigma   weight residual
    1.334  1.355 -0.022 8.40e-03 1.42e+04 6.73e+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 4.68e+00
  bond pdb=" O2  PSF D2010 "
       pdb=" P   PSF D2010 "
    ideal  model  delta    sigma   weight residual
    1.637  1.594  0.043 2.00e-02 2.50e+03 4.57e+00
  bond pdb=" CB  GLU D 546 "
       pdb=" CG  GLU D 546 "
    ideal  model  delta    sigma   weight residual
    1.520  1.583 -0.063 3.00e-02 1.11e+03 4.47e+00
  bond pdb=" O1  PSF D2001 "
       pdb=" P   PSF D2001 "
    ideal  model  delta    sigma   weight residual
    1.636  1.594  0.042 2.00e-02 2.50e+03 4.36e+00
  ... (remaining 14093 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.37: 18988
        4.37 -     8.75: 88
        8.75 -    13.12: 17
       13.12 -    17.50: 5
       17.50 -    21.87: 1
  Bond angle restraints: 19099
  Sorted by residual:
  angle pdb=" CB  MET D1242 "
        pdb=" CG  MET D1242 "
        pdb=" SD  MET D1242 "
      ideal   model   delta    sigma   weight residual
     112.70  134.57  -21.87 3.00e+00 1.11e-01 5.32e+01
  angle pdb=" C   ASP D1509 "
        pdb=" N   GLU D1510 "
        pdb=" CA  GLU D1510 "
      ideal   model   delta    sigma   weight residual
     121.54  133.02  -11.48 1.91e+00 2.74e-01 3.61e+01
  angle pdb=" CB  MET D1812 "
        pdb=" CG  MET D1812 "
        pdb=" SD  MET D1812 "
      ideal   model   delta    sigma   weight residual
     112.70  128.30  -15.60 3.00e+00 1.11e-01 2.70e+01
  angle pdb=" CB  MET D 863 "
        pdb=" CG  MET D 863 "
        pdb=" SD  MET D 863 "
      ideal   model   delta    sigma   weight residual
     112.70  128.13  -15.43 3.00e+00 1.11e-01 2.65e+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  128.10  -15.40 3.00e+00 1.11e-01 2.63e+01
  ... (remaining 19094 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 7611
       17.96 -    35.91: 694
       35.91 -    53.87: 168
       53.87 -    71.83: 47
       71.83 -    89.79: 22
  Dihedral angle restraints: 8542
    sinusoidal: 3620
      harmonic: 4922
  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 -158.68  -21.32     0      5.00e+00 4.00e-02 1.82e+01
  dihedral pdb=" CA  GLU D1867 "
           pdb=" C   GLU D1867 "
           pdb=" N   HIS D1868 "
           pdb=" CA  HIS D1868 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.81   21.19     0      5.00e+00 4.00e-02 1.80e+01
  dihedral pdb=" CA  ASP D1922 "
           pdb=" C   ASP D1922 "
           pdb=" N   MET D1923 "
           pdb=" CA  MET D1923 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.58   20.42     0      5.00e+00 4.00e-02 1.67e+01
  ... (remaining 8539 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.102: 1883
       0.102 -    0.203: 147
       0.203 -    0.305: 2
       0.305 -    0.407: 2
       0.407 -    0.508: 1
  Chirality restraints: 2035
  Sorted by residual:
  chirality pdb=" CB  ILE D1793 "
            pdb=" CA  ILE D1793 "
            pdb=" CG1 ILE D1793 "
            pdb=" CG2 ILE D1793 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.14    0.51 2.00e-01 2.50e+01 6.46e+00
  chirality pdb=" CG  LEU D 563 "
            pdb=" CB  LEU D 563 "
            pdb=" CD1 LEU D 563 "
            pdb=" CD2 LEU D 563 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.21   -0.38 2.00e-01 2.50e+01 3.66e+00
  chirality pdb=" CB  ILE D1862 "
            pdb=" CA  ILE D1862 "
            pdb=" CG1 ILE D1862 "
            pdb=" CG2 ILE D1862 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.31    0.34 2.00e-01 2.50e+01 2.82e+00
  ... (remaining 2032 not shown)

  Planarity restraints: 2472
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP D1076 "    0.023 2.00e-02 2.50e+03   2.02e-02 1.02e+01
        pdb=" CG  TRP D1076 "   -0.055 2.00e-02 2.50e+03
        pdb=" CD1 TRP D1076 "    0.022 2.00e-02 2.50e+03
        pdb=" CD2 TRP D1076 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP D1076 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP D1076 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP D1076 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ2 TRP D1076 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ3 TRP D1076 "    0.006 2.00e-02 2.50e+03
        pdb=" CH2 TRP D1076 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE D 431 "   -0.044 5.00e-02 4.00e+02   6.62e-02 7.00e+00
        pdb=" N   PRO D 432 "    0.114 5.00e-02 4.00e+02
        pdb=" CA  PRO D 432 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO D 432 "   -0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP D 759 "    0.013 2.00e-02 2.50e+03   2.63e-02 6.93e+00
        pdb=" CG  ASP D 759 "   -0.046 2.00e-02 2.50e+03
        pdb=" OD1 ASP D 759 "    0.017 2.00e-02 2.50e+03
        pdb=" OD2 ASP D 759 "    0.016 2.00e-02 2.50e+03
  ... (remaining 2469 not shown)

  Histogram of nonbonded interaction distances:
        2.35 -     2.86: 4329
        2.86 -     3.37: 11952
        3.37 -     3.88: 23461
        3.88 -     4.39: 26444
        4.39 -     4.90: 45415
  Nonbonded interactions: 111601
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP D1155 "
            pdb="CA    CA D2004 "
     model   vdw
     2.351 3.250
  nonbonded pdb=" OG1 THR D 449 "
            pdb="CA    CA D2008 "
     model   vdw
     2.361 3.250
  nonbonded pdb=" O   ASN D1218 "
            pdb="CA    CA D2004 "
     model   vdw
     2.363 3.250
  nonbonded pdb=" O4  PSF D2001 "
            pdb="CA    CA D2003 "
     model   vdw
     2.365 3.250
  nonbonded pdb=" O   TYR D1625 "
            pdb="CA    CA D2006 "
     model   vdw
     2.367 3.250
  ... (remaining 111596 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=0.78 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:             4.380
  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:          0.360
  Check model and map are aligned:         0.060
  Set scattering table:                    0.030
  Process input model:                     13.570
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:6.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.590
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8599
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   0.063  14098  Z= 0.220
  Angle     :  0.902  21.872  19099  Z= 0.444
  Chirality :  0.054   0.508   2035
  Planarity :  0.007   0.066   2472
  Dihedral  : 15.714  89.787   5366
  Min Nonbonded Distance : 2.351

Molprobity Statistics.
  All-atom Clashscore : 1.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 16.94 %
    Favored  : 81.73 %
  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: -1.56 (0.19), residues: 1673
  helix: -1.92 (0.27), residues: 234
  sheet: -0.57 (0.22), residues: 528
  loop : -1.00 (0.19), residues: 911

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG D1630 
 TYR   0.018   0.002   TYR D1558 
 PHE   0.017   0.002   PHE D1192 
 TRP   0.055   0.002   TRP D1076 
 HIS   0.005   0.001   HIS D1868 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00502 /  0.22 (14098)
  covalent geometry    : angle       0.90180 /  0.44 (19099)
  hydrogen bonds       : bond        0.19054 / 12.79 (  382)
  hydrogen bonds       : angle       8.63502 /  5.99 ( 1029)

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

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

  3346 Ramachandran restraints generated.
    1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3346 Ramachandran restraints generated.
    1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 96
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
REVERT: D  187 ASN cc_start: 0.8892 (p0) cc_final: 0.8460 (m110)
REVERT: D  227 GLN cc_start: 0.7855 (mp10) cc_final: 0.7611 (mp10)
REVERT: D  230 ARG cc_start: 0.8680 (tmt90) cc_final: 0.8451 (tmt90)
REVERT: D  243 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8306 (mm-30)
REVERT: D  289 ASP cc_start: 0.8647 (m-30) cc_final: 0.8382 (m-30)
REVERT: D  296 MET cc_start: 0.8508 (mmm) cc_final: 0.8223 (mmm)
REVERT: D  824 LYS cc_start: 0.9156 (tttt) cc_final: 0.8509 (pmtt)
REVERT: D  911 TRP cc_start: 0.7501 (m100) cc_final: 0.7065 (m100)
REVERT: D  934 VAL cc_start: 0.6691 (OUTLIER) cc_final: 0.6391 (m)
REVERT: D 1242 MET cc_start: 0.6805 (ppp) cc_final: 0.6578 (pp-130)
REVERT: D 1289 ASN cc_start: 0.8785 (t0) cc_final: 0.8534 (t0)
REVERT: D 1475 TYR cc_start: 0.7555 (m-80) cc_final: 0.7283 (m-80)
REVERT: D 1795 TRP cc_start: 0.8010 (m100) cc_final: 0.6820 (m100)
REVERT: D 1859 GLN cc_start: 0.7034 (OUTLIER) cc_final: 0.6290 (mp10)
REVERT: D 1888 TRP cc_start: 0.8066 (m-90) cc_final: 0.7831 (m-90)
REVERT: D 1901 PHE cc_start: 0.6964 (p90) cc_final: 0.6759 (p90)
REVERT: D 1922 ASP cc_start: 0.8589 (m-30) cc_final: 0.7816 (t70)
REVERT: D 1943 GLN cc_start: 0.8331 (tm-30) cc_final: 0.8129 (tp-100)
REVERT: D 1946 MET cc_start: 0.6071 (ptm) cc_final: 0.5863 (ptt)
  outliers start: 20
  outliers final: 8
  residues processed: 116
  average time/residue: 0.4760
  time to fit residues: 61.8565
Evaluate side-chains
  105 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 95
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  424 VAL
Chi-restraints excluded: chain D residue  496 VAL
Chi-restraints excluded: chain D residue  498 THR
Chi-restraints excluded: chain D residue  934 VAL
Chi-restraints excluded: chain D residue 1555 VAL
Chi-restraints excluded: chain D residue 1581 THR
Chi-restraints excluded: chain D residue 1597 THR
Chi-restraints excluded: chain D residue 1671 LEU
Chi-restraints excluded: chain D residue 1859 GLN
Chi-restraints excluded: chain D residue 1915 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 107 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 66 optimal weight:   20.0000
   chunk 130 optimal weight:    5.9990
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9980
   chunk 122 optimal weight:    9.9990
   chunk 91 optimal weight:    1.9990
   chunk 149 optimal weight:    6.9990
   overall best weight:    1.5988

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.137811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.087785 restraints weight = 27946.891|
|-----------------------------------------------------------------------------|
r_work (start): 0.3266 rms_B_bonded: 3.37
r_work: 0.3123 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3159
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3159 r_free = 0.3159    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3159 r_free = 0.3159    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.79   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3159
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8253
moved from start:          0.0980

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  14098  Z= 0.174
  Angle     :  0.559   9.729  19099  Z= 0.281
  Chirality :  0.044   0.222   2035
  Planarity :  0.004   0.051   2472
  Dihedral  :  6.122  52.846   1921
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 15.48 %
    Favored  : 82.13 %
  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: -0.83 (0.20), residues: 1673
  helix: -0.45 (0.32), residues: 236
  sheet: -0.30 (0.21), residues: 532
  loop : -0.65 (0.20), residues: 905

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 204 
 TYR   0.018   0.001   TYR D1816 
 PHE   0.023   0.001   PHE D 280 
 TRP   0.024   0.001   TRP D1076 
 HIS   0.003   0.001   HIS D1717 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00402 /  0.17 (14098)
  covalent geometry    : angle       0.55853 /  0.28 (19099)
  hydrogen bonds       : bond        0.03534 /  2.36 (  382)
  hydrogen bonds       : angle       6.11525 /  4.28 ( 1029)

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

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

  3346 Ramachandran restraints generated.
    1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3346 Ramachandran restraints generated.
    1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 96
  time to evaluate  : 0.548 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  187 ASN cc_start: 0.8851 (p0) cc_final: 0.8562 (p0)
REVERT: D  230 ARG cc_start: 0.8436 (tmt90) cc_final: 0.8046 (tmt90)
REVERT: D  281 LYS cc_start: 0.8612 (mttt) cc_final: 0.7967 (mttm)
REVERT: D  296 MET cc_start: 0.8676 (mmm) cc_final: 0.8399 (mmm)
REVERT: D  377 PHE cc_start: 0.7854 (m-80) cc_final: 0.7354 (m-10)
REVERT: D  391 LYS cc_start: 0.8949 (mmtt) cc_final: 0.8727 (mmpt)
REVERT: D  783 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8450 (tp30)
REVERT: D  829 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8393 (mptm)
REVERT: D  863 MET cc_start: 0.2436 (tpp) cc_final: 0.1846 (tpp)
REVERT: D 1014 MET cc_start: 0.3943 (ptm) cc_final: 0.3240 (pmt)
REVERT: D 1076 TRP cc_start: 0.7068 (t60) cc_final: 0.6784 (t60)
REVERT: D 1289 ASN cc_start: 0.8994 (t0) cc_final: 0.8771 (t0)
REVERT: D 1475 TYR cc_start: 0.7817 (m-80) cc_final: 0.7424 (m-80)
REVERT: D 1547 ASP cc_start: 0.8926 (t0) cc_final: 0.8725 (t0)
REVERT: D 1751 PHE cc_start: 0.8397 (t80) cc_final: 0.7805 (t80)
REVERT: D 1795 TRP cc_start: 0.8020 (m100) cc_final: 0.7220 (m100)
REVERT: D 1888 TRP cc_start: 0.8263 (m-90) cc_final: 0.7907 (m-90)
REVERT: D 1906 LEU cc_start: 0.6500 (OUTLIER) cc_final: 0.6267 (mm)
REVERT: D 1922 ASP cc_start: 0.8691 (m-30) cc_final: 0.7877 (t70)
REVERT: D 1943 GLN cc_start: 0.8140 (tm-30) cc_final: 0.7885 (tp-100)
  outliers start: 36
  outliers final: 14
  residues processed: 129
  average time/residue: 0.4498
  time to fit residues: 65.0232
Evaluate side-chains
  109 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 92
  time to evaluate  : 0.528 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  286 PHE
Chi-restraints excluded: chain D residue  394 LEU
Chi-restraints excluded: chain D residue  424 VAL
Chi-restraints excluded: chain D residue  448 LEU
Chi-restraints excluded: chain D residue  457 THR
Chi-restraints excluded: chain D residue  498 THR
Chi-restraints excluded: chain D residue  772 MET
Chi-restraints excluded: chain D residue  783 GLU
Chi-restraints excluded: chain D residue  829 LYS
Chi-restraints excluded: chain D residue  859 VAL
Chi-restraints excluded: chain D residue  938 GLU
Chi-restraints excluded: chain D residue 1290 LEU
Chi-restraints excluded: chain D residue 1555 VAL
Chi-restraints excluded: chain D residue 1655 ILE
Chi-restraints excluded: chain D residue 1901 PHE
Chi-restraints excluded: chain D residue 1902 LEU
Chi-restraints excluded: chain D residue 1906 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 105 optimal weight:    4.9990
   chunk 53 optimal weight:    3.9990
   chunk 73 optimal weight:    9.9990
   chunk 83 optimal weight:   20.0000
   chunk 152 optimal weight:    3.9990
   chunk 120 optimal weight:    4.9990
   chunk 47 optimal weight:    3.9990
   chunk 158 optimal weight:    1.9990
   chunk 63 optimal weight:    0.8980
   chunk 129 optimal weight:    0.7980
   chunk 5 optimal weight:    6.9990
   overall best weight:    2.3386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D 428 GLN
D1754 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.136213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.085949 restraints weight = 28295.806|
|-----------------------------------------------------------------------------|
r_work (start): 0.3223 rms_B_bonded: 3.42
r_work: 0.3082 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.3082
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3120
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3120 r_free = 0.3120    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.79   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3120 r_free = 0.3120    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.79   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3120
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8283
moved from start:          0.1459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  14098  Z= 0.236
  Angle     :  0.580   9.888  19099  Z= 0.291
  Chirality :  0.046   0.225   2035
  Planarity :  0.004   0.045   2472
  Dihedral  :  5.493  35.436   1911
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 14.62 %
    Favored  : 81.66 %
  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: -0.50 (0.20), residues: 1673
  helix:  0.24 (0.33), residues: 234
  sheet: -0.18 (0.21), residues: 559
  loop : -0.49 (0.21), residues: 880

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D1644 
 TYR   0.016   0.001   TYR D 533 
 PHE   0.016   0.001   PHE D1192 
 TRP   0.018   0.001   TRP D1076 
 HIS   0.003   0.001   HIS D 734 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00548 /  0.24 (14098)
  covalent geometry    : angle       0.57977 /  0.29 (19099)
  hydrogen bonds       : bond        0.03434 /  2.29 (  382)
  hydrogen bonds       : angle       5.67818 /  4.03 ( 1029)

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

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

  3346 Ramachandran restraints generated.
    1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3346 Ramachandran restraints generated.
    1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 92
  time to evaluate  : 0.405 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  187 ASN cc_start: 0.8841 (p0) cc_final: 0.8522 (p0)
REVERT: D  230 ARG cc_start: 0.8466 (tmt90) cc_final: 0.8209 (tmt90)
REVERT: D  281 LYS cc_start: 0.8605 (mttt) cc_final: 0.7982 (mttm)
REVERT: D  296 MET cc_start: 0.8722 (mmm) cc_final: 0.8416 (mmm)
REVERT: D  377 PHE cc_start: 0.7883 (m-80) cc_final: 0.7322 (m-10)
REVERT: D  829 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8033 (mptm)
REVERT: D  863 MET cc_start: 0.2990 (tpp) cc_final: 0.2326 (tpp)
REVERT: D 1014 MET cc_start: 0.3785 (ptm) cc_final: 0.3168 (pmt)
REVERT: D 1076 TRP cc_start: 0.7205 (t60) cc_final: 0.6250 (t60)
REVERT: D 1289 ASN cc_start: 0.9054 (t0) cc_final: 0.8824 (t0)
REVERT: D 1475 TYR cc_start: 0.7870 (m-80) cc_final: 0.7486 (m-80)
REVERT: D 1859 GLN cc_start: 0.6959 (OUTLIER) cc_final: 0.6595 (tp40)
REVERT: D 1888 TRP cc_start: 0.8250 (m-90) cc_final: 0.7863 (m-90)
REVERT: D 1898 TYR cc_start: 0.6091 (t80) cc_final: 0.5879 (t80)
REVERT: D 1906 LEU cc_start: 0.6599 (OUTLIER) cc_final: 0.6375 (mm)
REVERT: D 1922 ASP cc_start: 0.8733 (m-30) cc_final: 0.7927 (t70)
  outliers start: 56
  outliers final: 21
  residues processed: 137
  average time/residue: 0.4729
  time to fit residues: 72.1350
Evaluate side-chains
  111 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 87
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  286 PHE
Chi-restraints excluded: chain D residue  295 VAL
Chi-restraints excluded: chain D residue  307 ASP
Chi-restraints excluded: chain D residue  394 LEU
Chi-restraints excluded: chain D residue  424 VAL
Chi-restraints excluded: chain D residue  448 LEU
Chi-restraints excluded: chain D residue  457 THR
Chi-restraints excluded: chain D residue  498 THR
Chi-restraints excluded: chain D residue  585 MET
Chi-restraints excluded: chain D residue  772 MET
Chi-restraints excluded: chain D residue  825 ASN
Chi-restraints excluded: chain D residue  829 LYS
Chi-restraints excluded: chain D residue  834 LEU
Chi-restraints excluded: chain D residue  859 VAL
Chi-restraints excluded: chain D residue  938 GLU
Chi-restraints excluded: chain D residue 1290 LEU
Chi-restraints excluded: chain D residue 1555 VAL
Chi-restraints excluded: chain D residue 1561 ARG
Chi-restraints excluded: chain D residue 1581 THR
Chi-restraints excluded: chain D residue 1671 LEU
Chi-restraints excluded: chain D residue 1746 THR
Chi-restraints excluded: chain D residue 1797 THR
Chi-restraints excluded: chain D residue 1859 GLN
Chi-restraints excluded: chain D residue 1906 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 72 optimal weight:    8.9990
   chunk 131 optimal weight:    5.9990
   chunk 54 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9990
   chunk 103 optimal weight:    0.9990
   chunk 157 optimal weight:    7.9990
   chunk 97 optimal weight:    0.0570
   chunk 44 optimal weight:    2.9990
   chunk 87 optimal weight:    3.9990
   chunk 55 optimal weight:    0.6980
   overall best weight:    0.7302

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D 177 GLN
D 936 GLN
D1754 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.137018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.086804 restraints weight = 27864.624|
|-----------------------------------------------------------------------------|
r_work (start): 0.3272 rms_B_bonded: 3.46
r_work: 0.3128 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.3128
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3169
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3169 r_free = 0.3169    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.79   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3169 r_free = 0.3169    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.80   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3169
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8235
moved from start:          0.1509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043  14098  Z= 0.108
  Angle     :  0.520   9.765  19099  Z= 0.259
  Chirality :  0.044   0.263   2035
  Planarity :  0.004   0.057   2472
  Dihedral  :  5.158  36.091   1911
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 16.08 %
    Favored  : 80.60 %
  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: -0.29 (0.20), residues: 1673
  helix:  0.69 (0.35), residues: 234
  sheet: -0.13 (0.21), residues: 536
  loop : -0.39 (0.21), residues: 903

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D1298 
 TYR   0.016   0.001   TYR D1558 
 PHE   0.011   0.001   PHE D1192 
 TRP   0.016   0.001   TRP D1076 
 HIS   0.003   0.000   HIS D1717 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00246 /  0.11 (14098)
  covalent geometry    : angle       0.51962 /  0.26 (19099)
  hydrogen bonds       : bond        0.02845 /  1.88 (  382)
  hydrogen bonds       : angle       5.32985 /  3.77 ( 1029)

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

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

  3346 Ramachandran restraints generated.
    1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3346 Ramachandran restraints generated.
    1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 94
  time to evaluate  : 0.557 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  187 ASN cc_start: 0.8865 (p0) cc_final: 0.8545 (p0)
REVERT: D  230 ARG cc_start: 0.8447 (tmt90) cc_final: 0.8191 (tmt90)
REVERT: D  281 LYS cc_start: 0.8604 (mttt) cc_final: 0.8020 (mttp)
REVERT: D  296 MET cc_start: 0.8685 (mmm) cc_final: 0.8407 (mmm)
REVERT: D  377 PHE cc_start: 0.7872 (m-80) cc_final: 0.7281 (m-10)
REVERT: D  763 GLN cc_start: 0.8945 (mm110) cc_final: 0.8681 (mm110)
REVERT: D  863 MET cc_start: 0.2910 (tpp) cc_final: 0.2325 (tpp)
REVERT: D 1014 MET cc_start: 0.3763 (ptm) cc_final: 0.3144 (pmt)
REVERT: D 1076 TRP cc_start: 0.7203 (t60) cc_final: 0.6784 (t60)
REVERT: D 1242 MET cc_start: 0.6957 (ppp) cc_final: 0.6739 (ppp)
REVERT: D 1289 ASN cc_start: 0.8978 (t0) cc_final: 0.8757 (t0)
REVERT: D 1475 TYR cc_start: 0.7846 (m-80) cc_final: 0.7469 (m-80)
REVERT: D 1751 PHE cc_start: 0.8352 (t80) cc_final: 0.7737 (t80)
REVERT: D 1859 GLN cc_start: 0.6884 (OUTLIER) cc_final: 0.6543 (tp40)
REVERT: D 1888 TRP cc_start: 0.8234 (m-90) cc_final: 0.7821 (m-90)
REVERT: D 1898 TYR cc_start: 0.5595 (t80) cc_final: 0.5325 (t80)
REVERT: D 1922 ASP cc_start: 0.8709 (m-30) cc_final: 0.7960 (t70)
REVERT: D 1962 MET cc_start: 0.8391 (tpt) cc_final: 0.8052 (tpp)
  outliers start: 50
  outliers final: 19
  residues processed: 139
  average time/residue: 0.4864
  time to fit residues: 75.9837
Evaluate side-chains
  107 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 87
  time to evaluate  : 0.554 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  173 VAL
Chi-restraints excluded: chain D residue  260 ILE
Chi-restraints excluded: chain D residue  286 PHE
Chi-restraints excluded: chain D residue  295 VAL
Chi-restraints excluded: chain D residue  394 LEU
Chi-restraints excluded: chain D residue  448 LEU
Chi-restraints excluded: chain D residue  457 THR
Chi-restraints excluded: chain D residue  496 VAL
Chi-restraints excluded: chain D residue  825 ASN
Chi-restraints excluded: chain D residue  842 LEU
Chi-restraints excluded: chain D residue  859 VAL
Chi-restraints excluded: chain D residue  938 GLU
Chi-restraints excluded: chain D residue 1290 LEU
Chi-restraints excluded: chain D residue 1478 LEU
Chi-restraints excluded: chain D residue 1555 VAL
Chi-restraints excluded: chain D residue 1581 THR
Chi-restraints excluded: chain D residue 1746 THR
Chi-restraints excluded: chain D residue 1792 VAL
Chi-restraints excluded: chain D residue 1797 THR
Chi-restraints excluded: chain D residue 1859 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 108 optimal weight:    5.9990
   chunk 137 optimal weight:    0.7980
   chunk 93 optimal weight:    3.9990
   chunk 83 optimal weight:    7.9990
   chunk 110 optimal weight:    0.7980
   chunk 105 optimal weight:    2.9990
   chunk 63 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9990
   chunk 117 optimal weight:    9.9990
   chunk 84 optimal weight:   20.0000
   chunk 102 optimal weight:    0.7980
   overall best weight:    0.8382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D1754 ASN
** D1868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.136976 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.086849 restraints weight = 28145.381|
|-----------------------------------------------------------------------------|
r_work (start): 0.3275 rms_B_bonded: 3.44
r_work: 0.3130 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.3130
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3167
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3167 r_free = 0.3167    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.80   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3167 r_free = 0.3167    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.80   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3167
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8237
moved from start:          0.1598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  14098  Z= 0.113
  Angle     :  0.513   9.501  19099  Z= 0.254
  Chirality :  0.044   0.270   2035
  Planarity :  0.003   0.053   2472
  Dihedral  :  4.936  36.884   1909
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 16.94 %
    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: -0.13 (0.20), residues: 1673
  helix:  0.96 (0.35), residues: 234
  sheet:  0.01 (0.21), residues: 551
  loop : -0.35 (0.21), residues: 888

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 235 
 TYR   0.013   0.001   TYR D1558 
 PHE   0.013   0.001   PHE D1192 
 TRP   0.014   0.001   TRP D1076 
 HIS   0.005   0.000   HIS D1868 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00258 /  0.11 (14098)
  covalent geometry    : angle       0.51319 /  0.25 (19099)
  hydrogen bonds       : bond        0.02779 /  1.83 (  382)
  hydrogen bonds       : angle       5.14521 /  3.64 ( 1029)

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

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

  3346 Ramachandran restraints generated.
    1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3346 Ramachandran restraints generated.
    1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 90
  time to evaluate  : 0.551 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  230 ARG cc_start: 0.8468 (tmt90) cc_final: 0.8209 (tmt90)
REVERT: D  281 LYS cc_start: 0.8597 (mttt) cc_final: 0.7948 (mttm)
REVERT: D  296 MET cc_start: 0.8650 (mmm) cc_final: 0.8357 (mmm)
REVERT: D  377 PHE cc_start: 0.7900 (m-80) cc_final: 0.7293 (m-10)
REVERT: D  763 GLN cc_start: 0.8869 (mm110) cc_final: 0.8664 (mm110)
REVERT: D  786 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.9073 (tt)
REVERT: D  863 MET cc_start: 0.3086 (tpp) cc_final: 0.2616 (tpp)
REVERT: D  870 MET cc_start: 0.0680 (mmt) cc_final: 0.0199 (mpt)
REVERT: D 1014 MET cc_start: 0.3833 (ptm) cc_final: 0.3182 (pmt)
REVERT: D 1076 TRP cc_start: 0.7260 (t60) cc_final: 0.6820 (t60)
REVERT: D 1242 MET cc_start: 0.7080 (ppp) cc_final: 0.6771 (ppp)
REVERT: D 1289 ASN cc_start: 0.9033 (t0) cc_final: 0.8824 (t0)
REVERT: D 1475 TYR cc_start: 0.7842 (m-80) cc_final: 0.7480 (m-80)
REVERT: D 1751 PHE cc_start: 0.8345 (t80) cc_final: 0.7762 (t80)
REVERT: D 1859 GLN cc_start: 0.6866 (OUTLIER) cc_final: 0.6578 (tp40)
REVERT: D 1888 TRP cc_start: 0.8232 (m-90) cc_final: 0.7863 (m-90)
REVERT: D 1898 TYR cc_start: 0.5515 (t80) cc_final: 0.5280 (t80)
REVERT: D 1922 ASP cc_start: 0.8702 (m-30) cc_final: 0.7972 (t70)
REVERT: D 1962 MET cc_start: 0.8462 (tpt) cc_final: 0.8186 (tpp)
  outliers start: 35
  outliers final: 22
  residues processed: 122
  average time/residue: 0.4931
  time to fit residues: 67.4098
Evaluate side-chains
  111 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 87
  time to evaluate  : 0.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  260 ILE
Chi-restraints excluded: chain D residue  295 VAL
Chi-restraints excluded: chain D residue  394 LEU
Chi-restraints excluded: chain D residue  396 ASP
Chi-restraints excluded: chain D residue  448 LEU
Chi-restraints excluded: chain D residue  457 THR
Chi-restraints excluded: chain D residue  496 VAL
Chi-restraints excluded: chain D residue  754 ILE
Chi-restraints excluded: chain D residue  786 LEU
Chi-restraints excluded: chain D residue  825 ASN
Chi-restraints excluded: chain D residue  842 LEU
Chi-restraints excluded: chain D residue  859 VAL
Chi-restraints excluded: chain D residue  938 GLU
Chi-restraints excluded: chain D residue 1223 LYS
Chi-restraints excluded: chain D residue 1290 LEU
Chi-restraints excluded: chain D residue 1323 SER
Chi-restraints excluded: chain D residue 1555 VAL
Chi-restraints excluded: chain D residue 1581 THR
Chi-restraints excluded: chain D residue 1746 THR
Chi-restraints excluded: chain D residue 1792 VAL
Chi-restraints excluded: chain D residue 1797 THR
Chi-restraints excluded: chain D residue 1859 GLN
Chi-restraints excluded: chain D residue 1868 HIS
Chi-restraints excluded: chain D residue 1902 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 85 optimal weight:    6.9990
   chunk 80 optimal weight:   50.0000
   chunk 112 optimal weight:    0.0050
   chunk 118 optimal weight:    1.9990
   chunk 11 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9980
   chunk 138 optimal weight:   10.0000
   chunk 39 optimal weight:    2.9990
   chunk 32 optimal weight:    0.6980
   chunk 26 optimal weight:    0.6980
   chunk 91 optimal weight:    0.9990
   overall best weight:    0.6796

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.140775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.091490 restraints weight = 28039.449|
|-----------------------------------------------------------------------------|
r_work (start): 0.3298 rms_B_bonded: 3.41
r_work: 0.3151 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3182
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3182 r_free = 0.3182    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.80   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3182 r_free = 0.3182    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.80   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3182
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8219
moved from start:          0.1684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  14098  Z= 0.101
  Angle     :  0.511   9.605  19099  Z= 0.252
  Chirality :  0.044   0.280   2035
  Planarity :  0.003   0.052   2472
  Dihedral  :  4.812  37.573   1909
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 16.88 %
    Favored  : 80.33 %
  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: -0.02 (0.21), residues: 1673
  helix:  1.10 (0.35), residues: 234
  sheet:  0.04 (0.21), residues: 550
  loop : -0.26 (0.21), residues: 889

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 209 
 TYR   0.015   0.001   TYR D1558 
 PHE   0.012   0.001   PHE D1192 
 TRP   0.014   0.001   TRP D1076 
 HIS   0.004   0.000   HIS D1868 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00230 /  0.10 (14098)
  covalent geometry    : angle       0.51086 /  0.25 (19099)
  hydrogen bonds       : bond        0.02645 /  1.74 (  382)
  hydrogen bonds       : angle       5.01481 /  3.54 ( 1029)

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

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

  3346 Ramachandran restraints generated.
    1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3346 Ramachandran restraints generated.
    1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 91
  time to evaluate  : 0.568 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  195 LYS cc_start: 0.9272 (tppt) cc_final: 0.9072 (mmmm)
REVERT: D  204 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.7846 (ptm-80)
REVERT: D  230 ARG cc_start: 0.8501 (tmt90) cc_final: 0.8247 (tmt90)
REVERT: D  281 LYS cc_start: 0.8575 (mttt) cc_final: 0.7911 (mttm)
REVERT: D  296 MET cc_start: 0.8635 (mmm) cc_final: 0.8345 (mmm)
REVERT: D  377 PHE cc_start: 0.7886 (m-80) cc_final: 0.7270 (m-10)
REVERT: D  763 GLN cc_start: 0.8844 (mm110) cc_final: 0.8643 (mm110)
REVERT: D  786 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.9061 (tt)
REVERT: D  863 MET cc_start: 0.3153 (tpp) cc_final: 0.2557 (tpp)
REVERT: D  870 MET cc_start: 0.0359 (mmt) cc_final: 0.0033 (mpt)
REVERT: D 1014 MET cc_start: 0.3910 (ptm) cc_final: 0.3217 (pmt)
REVERT: D 1076 TRP cc_start: 0.7266 (t60) cc_final: 0.6826 (t60)
REVERT: D 1242 MET cc_start: 0.7124 (ppp) cc_final: 0.6890 (ppp)
REVERT: D 1475 TYR cc_start: 0.7824 (m-80) cc_final: 0.7380 (m-80)
REVERT: D 1561 ARG cc_start: 0.8660 (OUTLIER) cc_final: 0.8381 (ptt180)
REVERT: D 1751 PHE cc_start: 0.8321 (t80) cc_final: 0.7717 (t80)
REVERT: D 1859 GLN cc_start: 0.6842 (OUTLIER) cc_final: 0.6576 (tp40)
REVERT: D 1888 TRP cc_start: 0.8228 (m-90) cc_final: 0.7873 (m-90)
REVERT: D 1898 TYR cc_start: 0.5369 (t80) cc_final: 0.5095 (t80)
REVERT: D 1922 ASP cc_start: 0.8723 (m-30) cc_final: 0.7876 (t0)
REVERT: D 1962 MET cc_start: 0.8459 (tpt) cc_final: 0.8211 (tpp)
  outliers start: 42
  outliers final: 21
  residues processed: 128
  average time/residue: 0.4713
  time to fit residues: 67.1400
Evaluate side-chains
  112 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 87
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  173 VAL
Chi-restraints excluded: chain D residue  204 ARG
Chi-restraints excluded: chain D residue  260 ILE
Chi-restraints excluded: chain D residue  286 PHE
Chi-restraints excluded: chain D residue  394 LEU
Chi-restraints excluded: chain D residue  396 ASP
Chi-restraints excluded: chain D residue  424 VAL
Chi-restraints excluded: chain D residue  448 LEU
Chi-restraints excluded: chain D residue  457 THR
Chi-restraints excluded: chain D residue  496 VAL
Chi-restraints excluded: chain D residue  786 LEU
Chi-restraints excluded: chain D residue  825 ASN
Chi-restraints excluded: chain D residue  842 LEU
Chi-restraints excluded: chain D residue  859 VAL
Chi-restraints excluded: chain D residue  938 GLU
Chi-restraints excluded: chain D residue 1223 LYS
Chi-restraints excluded: chain D residue 1290 LEU
Chi-restraints excluded: chain D residue 1555 VAL
Chi-restraints excluded: chain D residue 1561 ARG
Chi-restraints excluded: chain D residue 1581 THR
Chi-restraints excluded: chain D residue 1746 THR
Chi-restraints excluded: chain D residue 1792 VAL
Chi-restraints excluded: chain D residue 1797 THR
Chi-restraints excluded: chain D residue 1859 GLN
Chi-restraints excluded: chain D residue 1868 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 36 optimal weight:    0.7980
   chunk 133 optimal weight:   10.0000
   chunk 102 optimal weight:    5.9990
   chunk 2 optimal weight:    8.9990
   chunk 35 optimal weight:    0.9980
   chunk 125 optimal weight:    4.9990
   chunk 137 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9990
   chunk 146 optimal weight:    0.8980
   chunk 128 optimal weight:    1.9990
   chunk 114 optimal weight:    0.0050
   overall best weight:    0.6794

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.141352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.092032 restraints weight = 28099.170|
|-----------------------------------------------------------------------------|
r_work (start): 0.3302 rms_B_bonded: 3.43
r_work: 0.3155 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.3155
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3185
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3185 r_free = 0.3185    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.80   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3185 r_free = 0.3185    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3185
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8216
moved from start:          0.1758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  14098  Z= 0.102
  Angle     :  0.520  10.472  19099  Z= 0.254
  Chirality :  0.044   0.288   2035
  Planarity :  0.003   0.051   2472
  Dihedral  :  4.711  38.159   1909
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 17.14 %
    Favored  : 80.07 %
  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:  0.06 (0.21), residues: 1673
  helix:  1.21 (0.36), residues: 234
  sheet:  0.11 (0.21), residues: 557
  loop : -0.24 (0.22), residues: 882

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 209 
 TYR   0.014   0.001   TYR D1558 
 PHE   0.012   0.001   PHE D1192 
 TRP   0.013   0.001   TRP D1076 
 HIS   0.004   0.000   HIS D1868 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00233 /  0.10 (14098)
  covalent geometry    : angle       0.52044 /  0.25 (19099)
  hydrogen bonds       : bond        0.02604 /  1.72 (  382)
  hydrogen bonds       : angle       4.94285 /  3.48 ( 1029)

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

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

  3346 Ramachandran restraints generated.
    1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3346 Ramachandran restraints generated.
    1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 91
  time to evaluate  : 0.488 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  187 ASN cc_start: 0.8886 (p0) cc_final: 0.8567 (p0)
REVERT: D  204 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.8214 (ptm-80)
REVERT: D  230 ARG cc_start: 0.8514 (tmt90) cc_final: 0.8268 (tmt90)
REVERT: D  281 LYS cc_start: 0.8553 (mttt) cc_final: 0.7896 (mttp)
REVERT: D  296 MET cc_start: 0.8620 (mmm) cc_final: 0.8326 (mmm)
REVERT: D  377 PHE cc_start: 0.7889 (m-80) cc_final: 0.7256 (m-10)
REVERT: D  763 GLN cc_start: 0.8836 (mm110) cc_final: 0.8631 (mm110)
REVERT: D  786 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.9067 (tt)
REVERT: D  863 MET cc_start: 0.3141 (tpp) cc_final: 0.2686 (tpp)
REVERT: D  870 MET cc_start: 0.0318 (mmt) cc_final: 0.0055 (mpt)
REVERT: D 1014 MET cc_start: 0.3929 (ptm) cc_final: 0.3233 (pmt)
REVERT: D 1076 TRP cc_start: 0.7243 (t60) cc_final: 0.6806 (t60)
REVERT: D 1242 MET cc_start: 0.7128 (ppp) cc_final: 0.6866 (ppp)
REVERT: D 1475 TYR cc_start: 0.7742 (m-80) cc_final: 0.7405 (m-80)
REVERT: D 1561 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.8378 (ptt180)
REVERT: D 1751 PHE cc_start: 0.8330 (t80) cc_final: 0.7724 (t80)
REVERT: D 1843 ASN cc_start: 0.9067 (p0) cc_final: 0.8801 (m-40)
REVERT: D 1859 GLN cc_start: 0.6822 (OUTLIER) cc_final: 0.6559 (tp40)
REVERT: D 1888 TRP cc_start: 0.8206 (m-90) cc_final: 0.7984 (m-90)
REVERT: D 1898 TYR cc_start: 0.5367 (t80) cc_final: 0.5167 (t80)
REVERT: D 1922 ASP cc_start: 0.8730 (m-30) cc_final: 0.7868 (t0)
  outliers start: 42
  outliers final: 26
  residues processed: 130
  average time/residue: 0.4574
  time to fit residues: 66.6805
Evaluate side-chains
  121 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 91
  time to evaluate  : 0.532 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  173 VAL
Chi-restraints excluded: chain D residue  204 ARG
Chi-restraints excluded: chain D residue  260 ILE
Chi-restraints excluded: chain D residue  286 PHE
Chi-restraints excluded: chain D residue  295 VAL
Chi-restraints excluded: chain D residue  394 LEU
Chi-restraints excluded: chain D residue  396 ASP
Chi-restraints excluded: chain D residue  408 VAL
Chi-restraints excluded: chain D residue  424 VAL
Chi-restraints excluded: chain D residue  448 LEU
Chi-restraints excluded: chain D residue  457 THR
Chi-restraints excluded: chain D residue  496 VAL
Chi-restraints excluded: chain D residue  498 THR
Chi-restraints excluded: chain D residue  529 GLU
Chi-restraints excluded: chain D residue  786 LEU
Chi-restraints excluded: chain D residue  825 ASN
Chi-restraints excluded: chain D residue  842 LEU
Chi-restraints excluded: chain D residue  859 VAL
Chi-restraints excluded: chain D residue  938 GLU
Chi-restraints excluded: chain D residue 1223 LYS
Chi-restraints excluded: chain D residue 1290 LEU
Chi-restraints excluded: chain D residue 1323 SER
Chi-restraints excluded: chain D residue 1555 VAL
Chi-restraints excluded: chain D residue 1561 ARG
Chi-restraints excluded: chain D residue 1581 THR
Chi-restraints excluded: chain D residue 1655 ILE
Chi-restraints excluded: chain D residue 1746 THR
Chi-restraints excluded: chain D residue 1792 VAL
Chi-restraints excluded: chain D residue 1797 THR
Chi-restraints excluded: chain D residue 1859 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 155 optimal weight:    0.0980
   chunk 149 optimal weight:    5.9990
   chunk 146 optimal weight:    1.9990
   chunk 166 optimal weight:    6.9990
   chunk 77 optimal weight:   20.0000
   chunk 15 optimal weight:    0.9990
   chunk 76 optimal weight:    6.9990
   chunk 58 optimal weight:    0.9980
   chunk 59 optimal weight:    0.9980
   chunk 109 optimal weight:    0.9980
   chunk 23 optimal weight:    6.9990
   overall best weight:    0.8182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D 428 GLN
D1754 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.140979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.091640 restraints weight = 27818.770|
|-----------------------------------------------------------------------------|
r_work (start): 0.3301 rms_B_bonded: 3.41
r_work: 0.3154 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.3154
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3170
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3170 r_free = 0.3170    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3170 r_free = 0.3170    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3170
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8221
moved from start:          0.1812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  14098  Z= 0.110
  Angle     :  0.529   9.945  19099  Z= 0.258
  Chirality :  0.044   0.287   2035
  Planarity :  0.003   0.050   2472
  Dihedral  :  4.675  38.631   1909
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 17.54 %
    Favored  : 79.87 %
  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:  0.09 (0.21), residues: 1673
  helix:  1.24 (0.36), residues: 234
  sheet:  0.12 (0.21), residues: 558
  loop : -0.21 (0.22), residues: 881

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 209 
 TYR   0.013   0.001   TYR D1558 
 PHE   0.012   0.001   PHE D1192 
 TRP   0.013   0.001   TRP D1076 
 HIS   0.004   0.000   HIS D1868 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00253 /  0.11 (14098)
  covalent geometry    : angle       0.52908 /  0.26 (19099)
  hydrogen bonds       : bond        0.02612 /  1.72 (  382)
  hydrogen bonds       : angle       4.91003 /  3.45 ( 1029)

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

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

  3346 Ramachandran restraints generated.
    1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3346 Ramachandran restraints generated.
    1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 89
  time to evaluate  : 0.534 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  204 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.8197 (ptm-80)
REVERT: D  230 ARG cc_start: 0.8511 (tmt90) cc_final: 0.8264 (tmt90)
REVERT: D  281 LYS cc_start: 0.8555 (mttt) cc_final: 0.7904 (mttp)
REVERT: D  296 MET cc_start: 0.8614 (mmm) cc_final: 0.8306 (mmm)
REVERT: D  377 PHE cc_start: 0.7890 (m-80) cc_final: 0.7257 (m-10)
REVERT: D  763 GLN cc_start: 0.8838 (mm110) cc_final: 0.8634 (mm110)
REVERT: D  786 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9088 (tt)
REVERT: D  863 MET cc_start: 0.3224 (tpp) cc_final: 0.2776 (tpp)
REVERT: D 1014 MET cc_start: 0.3883 (ptm) cc_final: 0.3219 (pmt)
REVERT: D 1076 TRP cc_start: 0.7238 (t60) cc_final: 0.6780 (t60)
REVERT: D 1242 MET cc_start: 0.7112 (ppp) cc_final: 0.6836 (ppp)
REVERT: D 1475 TYR cc_start: 0.7743 (m-80) cc_final: 0.7377 (m-80)
REVERT: D 1561 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.8369 (ptt180)
REVERT: D 1751 PHE cc_start: 0.8319 (t80) cc_final: 0.7703 (t80)
REVERT: D 1812 MET cc_start: 0.6385 (tmm) cc_final: 0.5359 (tpt)
REVERT: D 1843 ASN cc_start: 0.9087 (p0) cc_final: 0.8799 (t0)
REVERT: D 1859 GLN cc_start: 0.6822 (OUTLIER) cc_final: 0.6573 (tp40)
REVERT: D 1898 TYR cc_start: 0.5353 (t80) cc_final: 0.5148 (t80)
REVERT: D 1922 ASP cc_start: 0.8724 (m-30) cc_final: 0.7872 (t0)
  outliers start: 39
  outliers final: 25
  residues processed: 125
  average time/residue: 0.4639
  time to fit residues: 64.7674
Evaluate side-chains
  117 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 88
  time to evaluate  : 0.541 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  173 VAL
Chi-restraints excluded: chain D residue  204 ARG
Chi-restraints excluded: chain D residue  260 ILE
Chi-restraints excluded: chain D residue  286 PHE
Chi-restraints excluded: chain D residue  295 VAL
Chi-restraints excluded: chain D residue  394 LEU
Chi-restraints excluded: chain D residue  408 VAL
Chi-restraints excluded: chain D residue  424 VAL
Chi-restraints excluded: chain D residue  448 LEU
Chi-restraints excluded: chain D residue  457 THR
Chi-restraints excluded: chain D residue  496 VAL
Chi-restraints excluded: chain D residue  498 THR
Chi-restraints excluded: chain D residue  786 LEU
Chi-restraints excluded: chain D residue  825 ASN
Chi-restraints excluded: chain D residue  842 LEU
Chi-restraints excluded: chain D residue  859 VAL
Chi-restraints excluded: chain D residue  938 GLU
Chi-restraints excluded: chain D residue 1223 LYS
Chi-restraints excluded: chain D residue 1290 LEU
Chi-restraints excluded: chain D residue 1323 SER
Chi-restraints excluded: chain D residue 1555 VAL
Chi-restraints excluded: chain D residue 1561 ARG
Chi-restraints excluded: chain D residue 1581 THR
Chi-restraints excluded: chain D residue 1655 ILE
Chi-restraints excluded: chain D residue 1746 THR
Chi-restraints excluded: chain D residue 1792 VAL
Chi-restraints excluded: chain D residue 1797 THR
Chi-restraints excluded: chain D residue 1859 GLN
Chi-restraints excluded: chain D residue 1902 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 26 optimal weight:    0.8980
   chunk 122 optimal weight:    1.9990
   chunk 130 optimal weight:    0.4980
   chunk 2 optimal weight:    5.9990
   chunk 118 optimal weight:    0.9990
   chunk 57 optimal weight:    1.9990
   chunk 9 optimal weight:    4.9990
   chunk 102 optimal weight:    4.9990
   chunk 54 optimal weight:    2.9990
   chunk 140 optimal weight:    0.5980
   chunk 65 optimal weight:    4.9990
   overall best weight:    0.9984

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.137331 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.087115 restraints weight = 27923.189|
|-----------------------------------------------------------------------------|
r_work (start): 0.3279 rms_B_bonded: 3.48
r_work: 0.3136 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.3136
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3177
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3177 r_free = 0.3177    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3177 r_free = 0.3177    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3177
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8240
moved from start:          0.1854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  14098  Z= 0.124
  Angle     :  0.533   9.902  19099  Z= 0.261
  Chirality :  0.044   0.296   2035
  Planarity :  0.003   0.050   2472
  Dihedral  :  4.661  38.862   1909
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 17.34 %
    Favored  : 80.20 %
  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:  0.09 (0.21), residues: 1673
  helix:  1.22 (0.35), residues: 234
  sheet:  0.13 (0.21), residues: 563
  loop : -0.20 (0.22), residues: 876

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 209 
 TYR   0.013   0.001   TYR D1558 
 PHE   0.012   0.001   PHE D1192 
 TRP   0.013   0.001   TRP D1763 
 HIS   0.004   0.000   HIS D1868 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00288 /  0.12 (14098)
  covalent geometry    : angle       0.53333 /  0.26 (19099)
  hydrogen bonds       : bond        0.02639 /  1.75 (  382)
  hydrogen bonds       : angle       4.89518 /  3.45 ( 1029)

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

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

  3346 Ramachandran restraints generated.
    1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3346 Ramachandran restraints generated.
    1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 88
  time to evaluate  : 0.458 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  204 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.7850 (ptm-80)
REVERT: D  230 ARG cc_start: 0.8485 (tmt90) cc_final: 0.8233 (tmt90)
REVERT: D  281 LYS cc_start: 0.8552 (mttt) cc_final: 0.7879 (mttm)
REVERT: D  296 MET cc_start: 0.8617 (mmm) cc_final: 0.8307 (mmm)
REVERT: D  377 PHE cc_start: 0.7905 (m-80) cc_final: 0.7272 (m-10)
REVERT: D  863 MET cc_start: 0.3226 (tpp) cc_final: 0.2793 (tpp)
REVERT: D 1014 MET cc_start: 0.3848 (ptm) cc_final: 0.3221 (pmt)
REVERT: D 1076 TRP cc_start: 0.7242 (t60) cc_final: 0.6803 (t60)
REVERT: D 1242 MET cc_start: 0.7105 (ppp) cc_final: 0.6818 (ppp)
REVERT: D 1475 TYR cc_start: 0.7779 (m-80) cc_final: 0.7439 (m-80)
REVERT: D 1561 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.7955 (ptp-170)
REVERT: D 1619 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8268 (ttmm)
REVERT: D 1751 PHE cc_start: 0.8317 (t80) cc_final: 0.7691 (t80)
REVERT: D 1812 MET cc_start: 0.6243 (tmm) cc_final: 0.5353 (tpt)
REVERT: D 1859 GLN cc_start: 0.6830 (OUTLIER) cc_final: 0.6586 (tp40)
REVERT: D 1888 TRP cc_start: 0.8089 (m-90) cc_final: 0.7863 (m-90)
REVERT: D 1922 ASP cc_start: 0.8688 (m-30) cc_final: 0.7858 (t0)
  outliers start: 37
  outliers final: 27
  residues processed: 123
  average time/residue: 0.4336
  time to fit residues: 60.0305
Evaluate side-chains
  119 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 88
  time to evaluate  : 0.528 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  173 VAL
Chi-restraints excluded: chain D residue  204 ARG
Chi-restraints excluded: chain D residue  260 ILE
Chi-restraints excluded: chain D residue  394 LEU
Chi-restraints excluded: chain D residue  396 ASP
Chi-restraints excluded: chain D residue  408 VAL
Chi-restraints excluded: chain D residue  424 VAL
Chi-restraints excluded: chain D residue  448 LEU
Chi-restraints excluded: chain D residue  457 THR
Chi-restraints excluded: chain D residue  496 VAL
Chi-restraints excluded: chain D residue  498 THR
Chi-restraints excluded: chain D residue  825 ASN
Chi-restraints excluded: chain D residue  842 LEU
Chi-restraints excluded: chain D residue  859 VAL
Chi-restraints excluded: chain D residue  938 GLU
Chi-restraints excluded: chain D residue 1223 LYS
Chi-restraints excluded: chain D residue 1290 LEU
Chi-restraints excluded: chain D residue 1323 SER
Chi-restraints excluded: chain D residue 1392 CYS
Chi-restraints excluded: chain D residue 1478 LEU
Chi-restraints excluded: chain D residue 1555 VAL
Chi-restraints excluded: chain D residue 1561 ARG
Chi-restraints excluded: chain D residue 1581 THR
Chi-restraints excluded: chain D residue 1619 LYS
Chi-restraints excluded: chain D residue 1655 ILE
Chi-restraints excluded: chain D residue 1746 THR
Chi-restraints excluded: chain D residue 1792 VAL
Chi-restraints excluded: chain D residue 1797 THR
Chi-restraints excluded: chain D residue 1859 GLN
Chi-restraints excluded: chain D residue 1868 HIS
Chi-restraints excluded: chain D residue 1902 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 52 optimal weight:    5.9990
   chunk 73 optimal weight:    9.9990
   chunk 25 optimal weight:    2.9990
   chunk 89 optimal weight:    3.9990
   chunk 45 optimal weight:    2.9990
   chunk 95 optimal weight:    0.6980
   chunk 93 optimal weight:    0.4980
   chunk 143 optimal weight:    0.5980
   chunk 113 optimal weight:    3.9990
   chunk 53 optimal weight:    3.9990
   chunk 1 optimal weight:    3.9990
   overall best weight:    1.5584

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.136236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.085755 restraints weight = 27903.190|
|-----------------------------------------------------------------------------|
r_work (start): 0.3256 rms_B_bonded: 3.42
r_work: 0.3111 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3137
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3137 r_free = 0.3137    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3137 r_free = 0.3137    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3137
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8247
moved from start:          0.1947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  14098  Z= 0.170
  Angle     :  0.564  11.130  19099  Z= 0.277
  Chirality :  0.045   0.294   2035
  Planarity :  0.004   0.049   2472
  Dihedral  :  4.753  39.008   1909
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 17.67 %
    Favored  : 80.07 %
  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:  0.05 (0.21), residues: 1673
  helix:  1.11 (0.35), residues: 233
  sheet:  0.07 (0.21), residues: 577
  loop : -0.19 (0.22), residues: 863

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 209 
 TYR   0.015   0.001   TYR D1558 
 PHE   0.014   0.001   PHE D1192 
 TRP   0.012   0.001   TRP D1763 
 HIS   0.005   0.001   HIS D1868 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00397 /  0.17 (14098)
  covalent geometry    : angle       0.56411 /  0.28 (19099)
  hydrogen bonds       : bond        0.02828 /  1.88 (  382)
  hydrogen bonds       : angle       5.01230 /  3.53 ( 1029)

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

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

  3346 Ramachandran restraints generated.
    1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3346 Ramachandran restraints generated.
    1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 90
  time to evaluate  : 0.534 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  187 ASN cc_start: 0.8892 (p0) cc_final: 0.8580 (p0)
REVERT: D  230 ARG cc_start: 0.8480 (tmt90) cc_final: 0.8221 (tmt90)
REVERT: D  281 LYS cc_start: 0.8544 (mttt) cc_final: 0.7899 (mttp)
REVERT: D  296 MET cc_start: 0.8639 (mmm) cc_final: 0.8331 (mmm)
REVERT: D  377 PHE cc_start: 0.7895 (m-80) cc_final: 0.7265 (m-10)
REVERT: D  863 MET cc_start: 0.3236 (tpp) cc_final: 0.2696 (tpp)
REVERT: D 1014 MET cc_start: 0.3893 (ptm) cc_final: 0.3221 (pmt)
REVERT: D 1076 TRP cc_start: 0.7318 (t60) cc_final: 0.6539 (t60)
REVERT: D 1242 MET cc_start: 0.7150 (ppp) cc_final: 0.6848 (ppp)
REVERT: D 1475 TYR cc_start: 0.7844 (m-80) cc_final: 0.7488 (m-80)
REVERT: D 1561 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.7936 (ptp-170)
REVERT: D 1619 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8331 (ttmm)
REVERT: D 1751 PHE cc_start: 0.8285 (t80) cc_final: 0.7635 (t80)
REVERT: D 1812 MET cc_start: 0.6516 (tmm) cc_final: 0.5713 (tpt)
REVERT: D 1859 GLN cc_start: 0.6871 (OUTLIER) cc_final: 0.6637 (tp40)
REVERT: D 1888 TRP cc_start: 0.8032 (OUTLIER) cc_final: 0.7688 (m-90)
REVERT: D 1898 TYR cc_start: 0.6169 (t80) cc_final: 0.5959 (t80)
REVERT: D 1922 ASP cc_start: 0.8720 (m-30) cc_final: 0.7887 (t0)
  outliers start: 34
  outliers final: 25
  residues processed: 120
  average time/residue: 0.4804
  time to fit residues: 64.7070
Evaluate side-chains
  118 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 89
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  173 VAL
Chi-restraints excluded: chain D residue  260 ILE
Chi-restraints excluded: chain D residue  295 VAL
Chi-restraints excluded: chain D residue  394 LEU
Chi-restraints excluded: chain D residue  396 ASP
Chi-restraints excluded: chain D residue  408 VAL
Chi-restraints excluded: chain D residue  424 VAL
Chi-restraints excluded: chain D residue  448 LEU
Chi-restraints excluded: chain D residue  457 THR
Chi-restraints excluded: chain D residue  496 VAL
Chi-restraints excluded: chain D residue  498 THR
Chi-restraints excluded: chain D residue  825 ASN
Chi-restraints excluded: chain D residue  842 LEU
Chi-restraints excluded: chain D residue  859 VAL
Chi-restraints excluded: chain D residue  870 MET
Chi-restraints excluded: chain D residue  938 GLU
Chi-restraints excluded: chain D residue 1223 LYS
Chi-restraints excluded: chain D residue 1290 LEU
Chi-restraints excluded: chain D residue 1323 SER
Chi-restraints excluded: chain D residue 1555 VAL
Chi-restraints excluded: chain D residue 1561 ARG
Chi-restraints excluded: chain D residue 1581 THR
Chi-restraints excluded: chain D residue 1619 LYS
Chi-restraints excluded: chain D residue 1746 THR
Chi-restraints excluded: chain D residue 1792 VAL
Chi-restraints excluded: chain D residue 1797 THR
Chi-restraints excluded: chain D residue 1859 GLN
Chi-restraints excluded: chain D residue 1868 HIS
Chi-restraints excluded: chain D residue 1888 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 99 optimal weight:    0.9990
   chunk 84 optimal weight:    6.9990
   chunk 56 optimal weight:    4.9990
   chunk 20 optimal weight:    0.8980
   chunk 55 optimal weight:    0.8980
   chunk 52 optimal weight:    4.9990
   chunk 12 optimal weight:    2.9990
   chunk 150 optimal weight:    0.0270
   chunk 151 optimal weight:   20.0000
   chunk 123 optimal weight:    5.9990
   chunk 137 optimal weight:    0.5980
   overall best weight:    0.6840

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D 825 ASN
D1754 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.141082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.091608 restraints weight = 28104.180|
|-----------------------------------------------------------------------------|
r_work (start): 0.3301 rms_B_bonded: 3.43
r_work: 0.3154 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.3154
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3168
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3168 r_free = 0.3168    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3168 r_free = 0.3168    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3168
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8217
moved from start:          0.1949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  14098  Z= 0.105
  Angle     :  0.535  10.294  19099  Z= 0.262
  Chirality :  0.044   0.301   2035
  Planarity :  0.003   0.050   2472
  Dihedral  :  4.657  38.874   1909
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 18.07 %
    Favored  : 80.00 %
  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:  0.12 (0.21), residues: 1673
  helix:  1.23 (0.35), residues: 235
  sheet:  0.13 (0.21), residues: 558
  loop : -0.18 (0.22), residues: 880

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 209 
 TYR   0.015   0.001   TYR D1558 
 PHE   0.011   0.001   PHE D1192 
 TRP   0.014   0.001   TRP D1076 
 HIS   0.004   0.000   HIS D1868 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00243 /  0.11 (14098)
  covalent geometry    : angle       0.53547 /  0.26 (19099)
  hydrogen bonds       : bond        0.02609 /  1.71 (  382)
  hydrogen bonds       : angle       4.89998 /  3.44 ( 1029)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5376.00 seconds
wall clock time: 92 minutes 8.60 seconds (5528.60 seconds total)