Starting phenix.real_space_refine
on Sat Aug 23 15:24:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8kia_37256/08_2025/8kia_37256.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8kia_37256/08_2025/8kia_37256.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8kia_37256/08_2025/8kia_37256.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8kia_37256/08_2025/8kia_37256.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8kia_37256/08_2025/8kia_37256.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8kia_37256/08_2025/8kia_37256.cif"
  }
  resolution = 4.0
  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=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      90      5.16       5
     C    8140      2.51       5
     N    2090      2.21       5
     O    2397      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 56 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12717
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 12717
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1580, 12717
          Classifications: {'peptide': 1580}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 44, 'TRANS': 1535}
          Chain breaks: 11
          Unresolved non-hydrogen bonds: 39
          Unresolved non-hydrogen angles: 48
          Unresolved non-hydrogen dihedrals: 33
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 24
  Time building chain proxies: 2.13, per 1000 atoms: 0.17
  Number of scatterers: 12717
  At special positions: 0
  Unit cell: (112.32, 109.2, 114.4, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      90     16.00
     O    2397      8.00
     N    2090      7.00
     C    8140      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: 0.72
  Conformation dependent library (CDL) restraints added in 448.9 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  3112 Ramachandran restraints generated.
    1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3048

  Finding SS restraints...
    Secondary structure from input PDB file:
      75 helices and 7 sheets defined
      59.9% alpha, 5.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.48
  Creating SS restraints...
    Processing helix  chain 'A' and resid 337 through 347
      removed outlier: 4.575A  pdb=" N   ARG A 341 " --> pdb=" O   GLU A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 352 through 363
    Processing helix  chain 'A' and resid 364 through 367
    Processing helix  chain 'A' and resid 372 through 390
    Processing helix  chain 'A' and resid 397 through 413
      removed outlier: 4.856A  pdb=" N   GLN A 407 " --> pdb=" O   ASP A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 432
      removed outlier: 3.549A  pdb=" N   LYS A 418 " --> pdb=" O   SER A 414 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 439 through 455
    Processing helix  chain 'A' and resid 462 through 466
      removed outlier: 3.878A  pdb=" N   GLU A 465 " --> pdb=" O   ASP A 462 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 491 through 502
      removed outlier: 3.692A  pdb=" N   ASN A 495 " --> pdb=" O   ASN A 491 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 521 through 536
    Processing helix  chain 'A' and resid 591 through 605
    Processing helix  chain 'A' and resid 663 through 682
    Processing helix  chain 'A' and resid 690 through 700
    Processing helix  chain 'A' and resid 701 through 706
      removed outlier: 3.993A  pdb=" N   CYS A 704 " --> pdb=" O   ASN A 701 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 715 through 729
    Processing helix  chain 'A' and resid 730 through 749
    Processing helix  chain 'A' and resid 797 through 804
    Processing helix  chain 'A' and resid 828 through 837
    Processing helix  chain 'A' and resid 837 through 853
      Proline residue:  A 843  - end of helix
    Processing helix  chain 'A' and resid 853 through 863
    Processing helix  chain 'A' and resid 874 through 893
    Processing helix  chain 'A' and resid 896 through 908
    Processing helix  chain 'A' and resid 921 through 927
    Processing helix  chain 'A' and resid 937 through 953
    Processing helix  chain 'A' and resid 991 through 1005
      removed outlier: 3.933A  pdb=" N   LEU A 995 " --> pdb=" O   THR A 991 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   MET A1005 " --> pdb=" O   LEU A1001 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1012 through 1036
      removed outlier: 3.888A  pdb=" N   ASN A1016 " --> pdb=" O   ASN A1012 " (cutoff:3.500A)
      removed outlier: 5.067A  pdb=" N   THR A1018 " --> pdb=" O   VAL A1014 " (cutoff:3.500A)
      Proline residue:  A1024  - end of helix
    Processing helix  chain 'A' and resid 1062 through 1075
    Processing helix  chain 'A' and resid 1077 through 1089
    Processing helix  chain 'A' and resid 1094 through 1097
    Processing helix  chain 'A' and resid 1098 through 1103
    Processing helix  chain 'A' and resid 1114 through 1124
      removed outlier: 3.961A  pdb=" N   ILE A1118 " --> pdb=" O   SER A1114 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   ILE A1119 " --> pdb=" O   THR A1115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1126 through 1130
    Processing helix  chain 'A' and resid 1135 through 1151
      removed outlier: 3.764A  pdb=" N   ALA A1139 " --> pdb=" O   GLY A1135 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1151 through 1163
    Processing helix  chain 'A' and resid 1165 through 1178
    Processing helix  chain 'A' and resid 1190 through 1195
    Processing helix  chain 'A' and resid 1197 through 1209
      removed outlier: 3.759A  pdb=" N   VAL A1201 " --> pdb=" O   HIS A1197 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1223 through 1235
    Processing helix  chain 'A' and resid 1258 through 1272
      removed outlier: 3.860A  pdb=" N   ASN A1272 " --> pdb=" O   SER A1268 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1300 through 1314
    Processing helix  chain 'A' and resid 1331 through 1352
      removed outlier: 3.614A  pdb=" N   ARG A1335 " --> pdb=" O   ASP A1331 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1377 through 1385
      removed outlier: 3.751A  pdb=" N   VAL A1381 " --> pdb=" O   THR A1377 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   LEU A1382 " --> pdb=" O   TYR A1378 " (cutoff:3.500A)
      removed outlier: 4.044A  pdb=" N   ILE A1385 " --> pdb=" O   VAL A1381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1393 through 1408
    Processing helix  chain 'A' and resid 1414 through 1428
    Processing helix  chain 'A' and resid 1439 through 1443
    Processing helix  chain 'A' and resid 1458 through 1478
      removed outlier: 3.903A  pdb=" N   SER A1462 " --> pdb=" O   LEU A1458 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1505 through 1513
    Processing helix  chain 'A' and resid 1517 through 1533
    Processing helix  chain 'A' and resid 1565 through 1575
      removed outlier: 3.822A  pdb=" N   CYS A1573 " --> pdb=" O   LEU A1569 " (cutoff:3.500A)
      removed outlier: 4.060A  pdb=" N   GLU A1575 " --> pdb=" O   ASN A1571 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1580 through 1598
    Processing helix  chain 'A' and resid 1603 through 1620
      removed outlier: 4.639A  pdb=" N   PHE A1607 " --> pdb=" O   GLU A1603 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1630 through 1638
    Processing helix  chain 'A' and resid 1642 through 1646
      removed outlier: 3.614A  pdb=" N   GLU A1645 " --> pdb=" O   LYS A1642 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   ILE A1646 " --> pdb=" O   SER A1643 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1642 through 1646'
    Processing helix  chain 'A' and resid 1647 through 1651
    Processing helix  chain 'A' and resid 1657 through 1664
    Processing helix  chain 'A' and resid 1667 through 1682
    Processing helix  chain 'A' and resid 1686 through 1695
      removed outlier: 3.766A  pdb=" N   ASP A1692 " --> pdb=" O   GLU A1688 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1699 through 1714
    Processing helix  chain 'A' and resid 1717 through 1733
    Processing helix  chain 'A' and resid 1762 through 1769
      removed outlier: 4.050A  pdb=" N   ASN A1765 " --> pdb=" O   ILE A1762 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   LEU A1767 " --> pdb=" O   GLU A1764 " (cutoff:3.500A)
      removed outlier: 4.902A  pdb=" N   ASN A1768 " --> pdb=" O   ASN A1765 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1770 through 1780
    Processing helix  chain 'A' and resid 1781 through 1785
    Processing helix  chain 'A' and resid 1814 through 1829
      removed outlier: 3.569A  pdb=" N   ASN A1829 " --> pdb=" O   ILE A1825 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1830 through 1835
      removed outlier: 3.732A  pdb=" N   ILE A1835 " --> pdb=" O   GLU A1831 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1843 through 1850
    Processing helix  chain 'A' and resid 1870 through 1876
      removed outlier: 4.199A  pdb=" N   LEU A1874 " --> pdb=" O   LEU A1870 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1891 through 1905
      removed outlier: 4.410A  pdb=" N   LYS A1905 " --> pdb=" O   LEU A1901 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1910 through 1924
    Processing helix  chain 'A' and resid 1924 through 1936
      Proline residue:  A1932  - end of helix
    Processing helix  chain 'A' and resid 1954 through 1965
      Proline residue:  A1960  - end of helix
    Processing helix  chain 'A' and resid 1986 through 2008
    Processing helix  chain 'A' and resid 2018 through 2030
      removed outlier: 4.368A  pdb=" N   ASN A2030 " --> pdb=" O   PHE A2026 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2031 through 2043
      removed outlier: 4.619A  pdb=" N   MET A2042 " --> pdb=" O   ALA A2038 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2052 through 2058
      removed outlier: 3.671A  pdb=" N   PHE A2056 " --> pdb=" O   ILE A2052 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   ARG A2058 " --> pdb=" O   THR A2054 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2065 through 2069
      removed outlier: 3.536A  pdb=" N   LEU A2069 " --> pdb=" O   LYS A2066 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 508 through 509
      removed outlier: 3.568A  pdb=" N   HIS A 790 " --> pdb=" O   TYR A 820 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   MET A 822 " --> pdb=" O   ALA A 788 " (cutoff:3.500A)
      removed outlier: 4.787A  pdb=" N   ALA A 788 " --> pdb=" O   MET A 822 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 508 through 509
      removed outlier: 3.568A  pdb=" N   HIS A 790 " --> pdb=" O   TYR A 820 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   MET A 822 " --> pdb=" O   ALA A 788 " (cutoff:3.500A)
      removed outlier: 4.787A  pdb=" N   ALA A 788 " --> pdb=" O   MET A 822 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   TYR A 786 " --> pdb=" O   GLN A 825 " (cutoff:3.500A)
      removed outlier: 4.144A  pdb=" N   GLN A 825 " --> pdb=" O   TYR A 786 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1109 through 1110
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1298 through 1299
      removed outlier: 6.844A  pdb=" N   VAL A1281 " --> pdb=" O   CYS A1412 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1489 through 1492
      removed outlier: 3.711A  pdb=" N   HIS A1492 " --> pdb=" O   ASP A1495 " (cutoff:3.500A)
      removed outlier: 5.324A  pdb=" N   LYS A1541 " --> pdb=" O   ASP A1367 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1548 through 1549
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1973 through 1975
      removed outlier: 3.740A  pdb=" N   ILE A2084 " --> pdb=" O   VAL A1974 " (cutoff:3.500A)

    666 hydrogen bonds defined for protein.
    1920 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.82

  Time building geometry restraints manager: 1.07 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2888
        1.33 -     1.45: 2781
        1.45 -     1.58: 7134
        1.58 -     1.70: 2
        1.70 -     1.82: 147
  Bond restraints: 12952
  Sorted by residual:
  bond pdb=" C   LEU A 912 "
       pdb=" N   PRO A 913 "
    ideal  model  delta    sigma   weight residual
    1.337  1.387 -0.050 9.80e-03 1.04e+04 2.61e+01
  bond pdb=" CA  PHE A1953 "
       pdb=" C   PHE A1953 "
    ideal  model  delta    sigma   weight residual
    1.523  1.466  0.056 1.41e-02 5.03e+03 1.59e+01
  bond pdb=" CB  TRP A 859 "
       pdb=" CG  TRP A 859 "
    ideal  model  delta    sigma   weight residual
    1.498  1.596 -0.098 3.10e-02 1.04e+03 1.01e+01
  bond pdb=" CB  ILE A 882 "
       pdb=" CG2 ILE A 882 "
    ideal  model  delta    sigma   weight residual
    1.521  1.427  0.094 3.30e-02 9.18e+02 8.07e+00
  bond pdb=" CB  ASN A 919 "
       pdb=" CG  ASN A 919 "
    ideal  model  delta    sigma   weight residual
    1.516  1.581 -0.065 2.50e-02 1.60e+03 6.83e+00
  ... (remaining 12947 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.74: 17048
        3.74 -     7.48: 304
        7.48 -    11.22: 67
       11.22 -    14.97: 24
       14.97 -    18.71: 4
  Bond angle restraints: 17447
  Sorted by residual:
  angle pdb=" CA  LYS A1691 "
        pdb=" CB  LYS A1691 "
        pdb=" CG  LYS A1691 "
      ideal   model   delta    sigma   weight residual
     114.10  127.49  -13.39 2.00e+00 2.50e-01 4.48e+01
  angle pdb=" C   LYS A 432 "
        pdb=" N   LYS A 433 "
        pdb=" CA  LYS A 433 "
      ideal   model   delta    sigma   weight residual
     121.54  133.56  -12.02 1.91e+00 2.74e-01 3.96e+01
  angle pdb=" CA  MET A1509 "
        pdb=" CB  MET A1509 "
        pdb=" CG  MET A1509 "
      ideal   model   delta    sigma   weight residual
     114.10  126.44  -12.34 2.00e+00 2.50e-01 3.81e+01
  angle pdb=" CA  GLU A1202 "
        pdb=" CB  GLU A1202 "
        pdb=" CG  GLU A1202 "
      ideal   model   delta    sigma   weight residual
     114.10  125.81  -11.71 2.00e+00 2.50e-01 3.43e+01
  angle pdb=" CA  LYS A 433 "
        pdb=" CB  LYS A 433 "
        pdb=" CG  LYS A 433 "
      ideal   model   delta    sigma   weight residual
     114.10  125.45  -11.35 2.00e+00 2.50e-01 3.22e+01
  ... (remaining 17442 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.97: 6735
       17.97 -    35.95: 960
       35.95 -    53.92: 193
       53.92 -    71.90: 28
       71.90 -    89.87: 7
  Dihedral angle restraints: 7923
    sinusoidal: 3238
      harmonic: 4685
  Sorted by residual:
  dihedral pdb=" CA  VAL A1014 "
           pdb=" C   VAL A1014 "
           pdb=" N   HIS A1015 "
           pdb=" CA  HIS A1015 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  142.90   37.10     0      5.00e+00 4.00e-02 5.51e+01
  dihedral pdb=" CA  VAL A1962 "
           pdb=" C   VAL A1962 "
           pdb=" N   GLU A1963 "
           pdb=" CA  GLU A1963 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.10   26.90     0      5.00e+00 4.00e-02 2.89e+01
  dihedral pdb=" CA  ILE A1003 "
           pdb=" C   ILE A1003 "
           pdb=" N   TYR A1004 "
           pdb=" CA  TYR A1004 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.86  -26.14     0      5.00e+00 4.00e-02 2.73e+01
  ... (remaining 7920 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.091: 1723
       0.091 -    0.182: 236
       0.182 -    0.273: 21
       0.273 -    0.364: 2
       0.364 -    0.455: 1
  Chirality restraints: 1983
  Sorted by residual:
  chirality pdb=" CB  VAL A1604 "
            pdb=" CA  VAL A1604 "
            pdb=" CG1 VAL A1604 "
            pdb=" CG2 VAL A1604 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.17   -0.45 2.00e-01 2.50e+01 5.18e+00
  chirality pdb=" CB  ILE A1240 "
            pdb=" CA  ILE A1240 "
            pdb=" CG1 ILE A1240 "
            pdb=" CG2 ILE A1240 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.35    0.30 2.00e-01 2.50e+01 2.19e+00
  chirality pdb=" CB  VAL A1627 "
            pdb=" CA  VAL A1627 "
            pdb=" CG1 VAL A1627 "
            pdb=" CG2 VAL A1627 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.34   -0.29 2.00e-01 2.50e+01 2.09e+00
  ... (remaining 1980 not shown)

  Planarity restraints: 2182
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A1704 "    0.024 2.00e-02 2.50e+03   3.46e-02 2.09e+01
        pdb=" CG  PHE A1704 "   -0.079 2.00e-02 2.50e+03
        pdb=" CD1 PHE A1704 "    0.028 2.00e-02 2.50e+03
        pdb=" CD2 PHE A1704 "    0.029 2.00e-02 2.50e+03
        pdb=" CE1 PHE A1704 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE A1704 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE A1704 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 859 "   -0.027 2.00e-02 2.50e+03   2.34e-02 1.37e+01
        pdb=" CG  TRP A 859 "    0.061 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 859 "   -0.028 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 859 "    0.005 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 859 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 859 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 859 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 859 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 859 "    0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 859 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A1363 "   -0.000 2.00e-02 2.50e+03   2.39e-02 1.00e+01
        pdb=" CG  PHE A1363 "    0.040 2.00e-02 2.50e+03
        pdb=" CD1 PHE A1363 "   -0.016 2.00e-02 2.50e+03
        pdb=" CD2 PHE A1363 "   -0.041 2.00e-02 2.50e+03
        pdb=" CE1 PHE A1363 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE2 PHE A1363 "    0.018 2.00e-02 2.50e+03
        pdb=" CZ  PHE A1363 "    0.006 2.00e-02 2.50e+03
  ... (remaining 2179 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 660
        2.72 -     3.26: 12785
        3.26 -     3.81: 21629
        3.81 -     4.35: 25959
        4.35 -     4.90: 42704
  Nonbonded interactions: 103737
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 718 "
            pdb=" OE2 GLU A1603 "
     model   vdw
     2.171 3.040
  nonbonded pdb=" O   LYS A1440 "
            pdb=" OG1 THR A1443 "
     model   vdw
     2.190 3.040
  nonbonded pdb=" O   ASN A1538 "
            pdb=" OG  SER A1542 "
     model   vdw
     2.216 3.040
  nonbonded pdb=" O   VAL A 889 "
            pdb=" OG1 THR A 893 "
     model   vdw
     2.256 3.040
  nonbonded pdb=" OG  SER A 742 "
            pdb=" O   LEU A 832 "
     model   vdw
     2.268 3.040
  ... (remaining 103732 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.690
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.630
  Find NCS groups from input model:        0.040
  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:             0.000
  Load rotamer database and sin/cos tables:1.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7237
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      :  0.006   0.098  12952  Z= 0.279
  Angle     :  1.338  18.708  17447  Z= 0.679
  Chirality :  0.063   0.455   1983
  Planarity :  0.007   0.076   2182
  Dihedral  : 16.757  89.870   4875
  Min Nonbonded Distance : 2.171

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  7.58 %
    Favored  : 92.10 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 24.91 %
    Favored  : 72.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.64 (0.19), residues: 1556
  helix: -1.09 (0.16), residues: 869
  sheet: -0.49 (0.72), residues: 59
  loop : -2.79 (0.22), residues: 628

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A2034 
 TYR   0.050   0.003   TYR A2041 
 PHE   0.079   0.003   PHE A1704 
 TRP   0.061   0.003   TRP A 859 
 HIS   0.020   0.002   HIS A1312 

Details of bonding type rmsd
  covalent geometry    : bond        0.00600 (12952)
  covalent geometry    : angle       1.33771 (17447)
  hydrogen bonds       : bond        0.08465 (  655)
  hydrogen bonds       : angle       6.54821 ( 1920)

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

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

  3112 Ramachandran restraints generated.
    1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3112 Ramachandran restraints generated.
    1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  338 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 304
  time to evaluate  : 0.461 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  359 PHE cc_start: 0.8376 (t80) cc_final: 0.8152 (t80)
REVERT: A  371 MET cc_start: 0.7150 (mmm) cc_final: 0.6876 (mmm)
REVERT: A  402 LYS cc_start: 0.7517 (mmtm) cc_final: 0.7290 (tptp)
REVERT: A  481 ILE cc_start: 0.6036 (OUTLIER) cc_final: 0.5738 (mm)
REVERT: A  525 ASP cc_start: 0.8256 (m-30) cc_final: 0.7643 (t0)
REVERT: A  655 MET cc_start: 0.4136 (mtt) cc_final: 0.3782 (mtp)
REVERT: A  749 ASP cc_start: 0.8118 (m-30) cc_final: 0.7881 (p0)
REVERT: A  767 MET cc_start: 0.6948 (mmt) cc_final: 0.5236 (mmt)
REVERT: A  822 MET cc_start: 0.7665 (mtt) cc_final: 0.7246 (mtt)
REVERT: A  860 LEU cc_start: 0.8860 (mp) cc_final: 0.8624 (mp)
REVERT: A  890 MET cc_start: 0.8471 (mmm) cc_final: 0.8172 (mmm)
REVERT: A  946 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.8005 (mttp)
REVERT: A  997 ASN cc_start: 0.8757 (m-40) cc_final: 0.8190 (m110)
REVERT: A 1049 MET cc_start: 0.6608 (pmm) cc_final: 0.6372 (mpp)
REVERT: A 1173 LEU cc_start: -0.5699 (OUTLIER) cc_final: -0.6260 (mp)
REVERT: A 1238 MET cc_start: 0.7167 (pmm) cc_final: 0.5983 (tmm)
REVERT: A 1243 ASP cc_start: 0.8591 (t70) cc_final: 0.8325 (t70)
REVERT: A 1262 MET cc_start: 0.8060 (mmt) cc_final: 0.7585 (tpp)
REVERT: A 1311 GLU cc_start: 0.8272 (tt0) cc_final: 0.7769 (tt0)
REVERT: A 1315 LYS cc_start: 0.8879 (mtmt) cc_final: 0.8418 (mtmm)
REVERT: A 1348 TYR cc_start: 0.7891 (t80) cc_final: 0.7276 (t80)
REVERT: A 1447 TYR cc_start: 0.8341 (p90) cc_final: 0.8114 (p90)
REVERT: A 1564 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8073 (tt)
REVERT: A 1622 MET cc_start: 0.7965 (mmt) cc_final: 0.7577 (mmp)
REVERT: A 1664 LEU cc_start: 0.8724 (mt) cc_final: 0.8429 (mp)
REVERT: A 1671 GLN cc_start: 0.8819 (tt0) cc_final: 0.8577 (tt0)
REVERT: A 1770 MET cc_start: 0.8226 (mpp) cc_final: 0.7810 (mpp)
REVERT: A 1845 LEU cc_start: 0.8822 (pt) cc_final: 0.8167 (mt)
REVERT: A 1847 GLN cc_start: 0.8181 (mm-40) cc_final: 0.7820 (mm110)
REVERT: A 1875 ARG cc_start: 0.7033 (mmt-90) cc_final: 0.6538 (mmt-90)
REVERT: A 1962 VAL cc_start: 0.7131 (OUTLIER) cc_final: 0.6680 (t)
REVERT: A 2021 PHE cc_start: 0.8660 (m-10) cc_final: 0.8365 (m-10)
REVERT: A 2039 CYS cc_start: 0.9324 (m) cc_final: 0.9029 (t)
REVERT: A 2048 ARG cc_start: 0.8451 (tpm170) cc_final: 0.7741 (mtt180)
  outliers start: 34
  outliers final: 24
  residues processed: 322
  average time/residue: 0.0779
  time to fit residues: 38.3584
Evaluate side-chains
  310 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 281
  time to evaluate  : 0.464 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  321 TRP
Chi-restraints excluded: chain A residue  415 LEU
Chi-restraints excluded: chain A residue  470 PHE
Chi-restraints excluded: chain A residue  481 ILE
Chi-restraints excluded: chain A residue  725 LEU
Chi-restraints excluded: chain A residue  742 SER
Chi-restraints excluded: chain A residue  840 SER
Chi-restraints excluded: chain A residue  935 VAL
Chi-restraints excluded: chain A residue  937 ASP
Chi-restraints excluded: chain A residue  946 LYS
Chi-restraints excluded: chain A residue  982 CYS
Chi-restraints excluded: chain A residue  995 LEU
Chi-restraints excluded: chain A residue 1173 LEU
Chi-restraints excluded: chain A residue 1245 VAL
Chi-restraints excluded: chain A residue 1246 MET
Chi-restraints excluded: chain A residue 1415 THR
Chi-restraints excluded: chain A residue 1463 SER
Chi-restraints excluded: chain A residue 1541 LYS
Chi-restraints excluded: chain A residue 1545 SER
Chi-restraints excluded: chain A residue 1564 LEU
Chi-restraints excluded: chain A residue 1590 ILE
Chi-restraints excluded: chain A residue 1648 THR
Chi-restraints excluded: chain A residue 1897 GLU
Chi-restraints excluded: chain A residue 1908 LEU
Chi-restraints excluded: chain A residue 1917 CYS
Chi-restraints excluded: chain A residue 1962 VAL
Chi-restraints excluded: chain A residue 1998 LEU
Chi-restraints excluded: chain A residue 2026 PHE
Chi-restraints excluded: chain A residue 2052 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 98 optimal weight:    0.9990
   chunk 107 optimal weight:    0.5980
   chunk 10 optimal weight:    4.9990
   chunk 66 optimal weight:    0.1980
   chunk 130 optimal weight:    0.6980
   chunk 124 optimal weight:    0.8980
   chunk 103 optimal weight:    0.9990
   chunk 77 optimal weight:    0.6980
   chunk 122 optimal weight:    2.9990
   chunk 91 optimal weight:    0.9990
   chunk 149 optimal weight:    0.7980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 409 GLN
** A 790 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1496 ASN
** A1571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.121994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.099069 restraints weight = 35386.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.101677 restraints weight = 22182.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.103512 restraints weight = 15598.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.104673 restraints weight = 12050.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.105587 restraints weight = 10023.823|
|-----------------------------------------------------------------------------|
r_work (final): 0.3784
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7258
moved from start:          0.1213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065  12952  Z= 0.143
  Angle     :  0.741  11.499  17447  Z= 0.378
  Chirality :  0.045   0.190   1983
  Planarity :  0.004   0.046   2182
  Dihedral  :  7.311  59.923   1740
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 13.43
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  6.88 %
    Favored  : 92.80 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 20.85 %
    Favored  : 76.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.62 (0.21), residues: 1556
  helix: -0.07 (0.17), residues: 876
  sheet: -0.30 (0.68), residues: 64
  loop : -2.67 (0.23), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A2034 
 TYR   0.049   0.002   TYR A2041 
 PHE   0.030   0.002   PHE A 741 
 TRP   0.033   0.002   TRP A 859 
 HIS   0.011   0.001   HIS A1312 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 (12952)
  covalent geometry    : angle       0.74097 (17447)
  hydrogen bonds       : bond        0.04186 (  655)
  hydrogen bonds       : angle       5.15002 ( 1920)

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

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

  3112 Ramachandran restraints generated.
    1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3112 Ramachandran restraints generated.
    1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  341 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 298
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  402 LYS cc_start: 0.7392 (mmtm) cc_final: 0.7121 (tptp)
REVERT: A  525 ASP cc_start: 0.8180 (m-30) cc_final: 0.7762 (t0)
REVERT: A  655 MET cc_start: 0.4139 (mtt) cc_final: 0.3855 (mtp)
REVERT: A  738 MET cc_start: 0.7865 (mmt) cc_final: 0.7615 (mmt)
REVERT: A  767 MET cc_start: 0.7383 (mmt) cc_final: 0.5729 (mmt)
REVERT: A  768 MET cc_start: 0.6849 (mtp) cc_final: 0.6494 (mtp)
REVERT: A  890 MET cc_start: 0.8549 (mmm) cc_final: 0.8231 (mmm)
REVERT: A 1049 MET cc_start: 0.6617 (OUTLIER) cc_final: 0.6391 (mpp)
REVERT: A 1238 MET cc_start: 0.6940 (pmm) cc_final: 0.6128 (tmm)
REVERT: A 1262 MET cc_start: 0.8167 (mmt) cc_final: 0.7649 (tpp)
REVERT: A 1297 TYR cc_start: 0.3628 (m-80) cc_final: 0.3066 (m-80)
REVERT: A 1315 LYS cc_start: 0.8884 (mtmt) cc_final: 0.8237 (mtpt)
REVERT: A 1350 ASP cc_start: 0.8440 (m-30) cc_final: 0.8155 (p0)
REVERT: A 1389 ILE cc_start: 0.8681 (mt) cc_final: 0.8472 (mt)
REVERT: A 1418 PHE cc_start: 0.8203 (t80) cc_final: 0.7864 (t80)
REVERT: A 1461 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.7660 (tt)
REVERT: A 1509 MET cc_start: 0.7982 (ppp) cc_final: 0.7575 (ppp)
REVERT: A 1620 TYR cc_start: 0.6219 (OUTLIER) cc_final: 0.5266 (t80)
REVERT: A 1622 MET cc_start: 0.8085 (mmt) cc_final: 0.7683 (mmp)
REVERT: A 1770 MET cc_start: 0.8141 (mpp) cc_final: 0.7771 (mpp)
REVERT: A 1780 TYR cc_start: 0.8477 (m-10) cc_final: 0.8162 (m-10)
REVERT: A 1819 MET cc_start: 0.7978 (mmm) cc_final: 0.7740 (mmm)
REVERT: A 1845 LEU cc_start: 0.8683 (pt) cc_final: 0.8243 (mt)
REVERT: A 1851 TYR cc_start: 0.6570 (m-80) cc_final: 0.6240 (m-80)
REVERT: A 1875 ARG cc_start: 0.7207 (mmt-90) cc_final: 0.6763 (mmt-90)
REVERT: A 2008 MET cc_start: 0.5679 (pmm) cc_final: 0.4299 (ppp)
REVERT: A 2021 PHE cc_start: 0.8610 (m-10) cc_final: 0.8365 (t80)
REVERT: A 2048 ARG cc_start: 0.8487 (tpm170) cc_final: 0.7820 (mtt180)
  outliers start: 43
  outliers final: 23
  residues processed: 323
  average time/residue: 0.0764
  time to fit residues: 37.9169
Evaluate side-chains
  299 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 273
  time to evaluate  : 0.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  378 ASP
Chi-restraints excluded: chain A residue  470 PHE
Chi-restraints excluded: chain A residue  718 THR
Chi-restraints excluded: chain A residue  742 SER
Chi-restraints excluded: chain A residue  874 THR
Chi-restraints excluded: chain A residue  935 VAL
Chi-restraints excluded: chain A residue 1005 MET
Chi-restraints excluded: chain A residue 1049 MET
Chi-restraints excluded: chain A residue 1085 ILE
Chi-restraints excluded: chain A residue 1230 LEU
Chi-restraints excluded: chain A residue 1303 VAL
Chi-restraints excluded: chain A residue 1317 VAL
Chi-restraints excluded: chain A residue 1402 ILE
Chi-restraints excluded: chain A residue 1411 VAL
Chi-restraints excluded: chain A residue 1461 LEU
Chi-restraints excluded: chain A residue 1566 CYS
Chi-restraints excluded: chain A residue 1579 ILE
Chi-restraints excluded: chain A residue 1596 LEU
Chi-restraints excluded: chain A residue 1605 ILE
Chi-restraints excluded: chain A residue 1620 TYR
Chi-restraints excluded: chain A residue 1648 THR
Chi-restraints excluded: chain A residue 1661 LEU
Chi-restraints excluded: chain A residue 1908 LEU
Chi-restraints excluded: chain A residue 1998 LEU
Chi-restraints excluded: chain A residue 2026 PHE
Chi-restraints excluded: chain A residue 2056 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 123 optimal weight:    1.9990
   chunk 20 optimal weight:    8.9990
   chunk 110 optimal weight:    0.0270
   chunk 141 optimal weight:    4.9990
   chunk 65 optimal weight:    7.9990
   chunk 49 optimal weight:    5.9990
   chunk 48 optimal weight:    3.9990
   chunk 32 optimal weight:    0.8980
   chunk 39 optimal weight:    0.5980
   chunk 93 optimal weight:    0.7980
   chunk 124 optimal weight:    0.6980
   overall best weight:    0.6038

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

Flipped N/Q/H residues before XYZ refinement:
A 374 GLN
** A 790 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 997 ASN
** A1015 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1452 ASN
A1671 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.121190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.098270 restraints weight = 36037.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.100809 restraints weight = 22468.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 62)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.102668 restraints weight = 15883.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.103826 restraints weight = 12245.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.104759 restraints weight = 10166.770|
|-----------------------------------------------------------------------------|
r_work (final): 0.3776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7280
moved from start:          0.1617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  12952  Z= 0.134
  Angle     :  0.714  11.607  17447  Z= 0.361
  Chirality :  0.044   0.179   1983
  Planarity :  0.004   0.043   2182
  Dihedral  :  6.005  50.750   1698
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 13.28
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  7.01 %
    Favored  : 92.74 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 20.72 %
    Favored  : 75.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.13 (0.21), residues: 1556
  helix:  0.39 (0.18), residues: 869
  sheet: -0.15 (0.68), residues: 66
  loop : -2.53 (0.24), residues: 621

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A2034 
 TYR   0.035   0.002   TYR A1620 
 PHE   0.034   0.002   PHE A2002 
 TRP   0.022   0.002   TRP A 859 
 HIS   0.010   0.001   HIS A1312 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 (12952)
  covalent geometry    : angle       0.71428 (17447)
  hydrogen bonds       : bond        0.04020 (  655)
  hydrogen bonds       : angle       4.91759 ( 1920)

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

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

  3112 Ramachandran restraints generated.
    1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3112 Ramachandran restraints generated.
    1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  348 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 297
  time to evaluate  : 0.444 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  369 GLU cc_start: 0.7784 (pm20) cc_final: 0.7520 (pm20)
REVERT: A  374 GLN cc_start: 0.7218 (OUTLIER) cc_final: 0.6132 (tt0)
REVERT: A  525 ASP cc_start: 0.8217 (m-30) cc_final: 0.7750 (t0)
REVERT: A  655 MET cc_start: 0.4111 (mtt) cc_final: 0.3808 (mtp)
REVERT: A  738 MET cc_start: 0.7665 (mmt) cc_final: 0.7261 (mmt)
REVERT: A  767 MET cc_start: 0.7389 (mmt) cc_final: 0.5623 (mmt)
REVERT: A  875 MET cc_start: 0.8180 (tpp) cc_final: 0.7956 (tpp)
REVERT: A  890 MET cc_start: 0.8556 (mmm) cc_final: 0.8240 (mmm)
REVERT: A 1049 MET cc_start: 0.6643 (OUTLIER) cc_final: 0.6414 (mpp)
REVERT: A 1238 MET cc_start: 0.6919 (pmm) cc_final: 0.6088 (tmm)
REVERT: A 1262 MET cc_start: 0.8192 (mmt) cc_final: 0.7671 (tpp)
REVERT: A 1315 LYS cc_start: 0.8915 (mtmt) cc_final: 0.8444 (mtpt)
REVERT: A 1335 ARG cc_start: 0.8350 (mmm160) cc_final: 0.8074 (mmm160)
REVERT: A 1350 ASP cc_start: 0.8445 (m-30) cc_final: 0.8212 (p0)
REVERT: A 1455 GLN cc_start: 0.6850 (pm20) cc_final: 0.6215 (pm20)
REVERT: A 1461 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8462 (tp)
REVERT: A 1566 CYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7881 (m)
REVERT: A 1620 TYR cc_start: 0.6166 (OUTLIER) cc_final: 0.5241 (t80)
REVERT: A 1770 MET cc_start: 0.8104 (mpp) cc_final: 0.7875 (mpp)
REVERT: A 1845 LEU cc_start: 0.8713 (pt) cc_final: 0.8332 (mt)
REVERT: A 1875 ARG cc_start: 0.7181 (mmt-90) cc_final: 0.6757 (mmt-90)
REVERT: A 2008 MET cc_start: 0.5777 (pmm) cc_final: 0.4586 (ppp)
REVERT: A 2039 CYS cc_start: 0.9340 (m) cc_final: 0.8934 (t)
REVERT: A 2048 ARG cc_start: 0.8526 (tpm170) cc_final: 0.7842 (mtt180)
  outliers start: 51
  outliers final: 26
  residues processed: 326
  average time/residue: 0.0792
  time to fit residues: 39.2700
Evaluate side-chains
  304 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 273
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  321 TRP
Chi-restraints excluded: chain A residue  374 GLN
Chi-restraints excluded: chain A residue  378 ASP
Chi-restraints excluded: chain A residue  470 PHE
Chi-restraints excluded: chain A residue  680 LEU
Chi-restraints excluded: chain A residue  725 LEU
Chi-restraints excluded: chain A residue  791 ILE
Chi-restraints excluded: chain A residue  935 VAL
Chi-restraints excluded: chain A residue  982 CYS
Chi-restraints excluded: chain A residue  995 LEU
Chi-restraints excluded: chain A residue 1005 MET
Chi-restraints excluded: chain A residue 1049 MET
Chi-restraints excluded: chain A residue 1215 VAL
Chi-restraints excluded: chain A residue 1230 LEU
Chi-restraints excluded: chain A residue 1303 VAL
Chi-restraints excluded: chain A residue 1317 VAL
Chi-restraints excluded: chain A residue 1411 VAL
Chi-restraints excluded: chain A residue 1461 LEU
Chi-restraints excluded: chain A residue 1464 VAL
Chi-restraints excluded: chain A residue 1566 CYS
Chi-restraints excluded: chain A residue 1579 ILE
Chi-restraints excluded: chain A residue 1590 ILE
Chi-restraints excluded: chain A residue 1592 VAL
Chi-restraints excluded: chain A residue 1596 LEU
Chi-restraints excluded: chain A residue 1605 ILE
Chi-restraints excluded: chain A residue 1620 TYR
Chi-restraints excluded: chain A residue 1661 LEU
Chi-restraints excluded: chain A residue 1908 LEU
Chi-restraints excluded: chain A residue 1917 CYS
Chi-restraints excluded: chain A residue 1998 LEU
Chi-restraints excluded: chain A residue 2056 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 38 optimal weight:    4.9990
   chunk 34 optimal weight:    0.1980
   chunk 108 optimal weight:    2.9990
   chunk 113 optimal weight:    5.9990
   chunk 103 optimal weight:    3.9990
   chunk 85 optimal weight:    5.9990
   chunk 68 optimal weight:    0.0070
   chunk 141 optimal weight:    1.9990
   chunk 142 optimal weight:    0.8980
   chunk 125 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9990
   overall best weight:    0.8202

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

Flipped N/Q/H residues before XYZ refinement:
A 374 GLN
A 409 GLN
** A 790 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 997 ASN
** A1015 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1728 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.119929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.096679 restraints weight = 36249.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.099240 restraints weight = 22629.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.101026 restraints weight = 16046.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.102170 restraints weight = 12485.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.103078 restraints weight = 10415.482|
|-----------------------------------------------------------------------------|
r_work (final): 0.3748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7324
moved from start:          0.2012

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  12952  Z= 0.143
  Angle     :  0.732  13.687  17447  Z= 0.367
  Chirality :  0.045   0.201   1983
  Planarity :  0.004   0.039   2182
  Dihedral  :  5.741  52.252   1694
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 13.24
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  7.52 %
    Favored  : 92.22 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 22.64 %
    Favored  : 73.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.00 (0.22), residues: 1556
  helix:  0.54 (0.18), residues: 865
  sheet: -0.24 (0.64), residues: 71
  loop : -2.54 (0.24), residues: 620

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1872 
 TYR   0.034   0.002   TYR A1620 
 PHE   0.027   0.002   PHE A1363 
 TRP   0.018   0.002   TRP A 859 
 HIS   0.007   0.001   HIS A1015 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 (12952)
  covalent geometry    : angle       0.73174 (17447)
  hydrogen bonds       : bond        0.03961 (  655)
  hydrogen bonds       : angle       4.84841 ( 1920)

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

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

  3112 Ramachandran restraints generated.
    1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3112 Ramachandran restraints generated.
    1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  327 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 275
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  374 GLN cc_start: 0.7318 (OUTLIER) cc_final: 0.6661 (pt0)
REVERT: A  402 LYS cc_start: 0.7554 (tptp) cc_final: 0.6639 (tppt)
REVERT: A  481 ILE cc_start: 0.6076 (OUTLIER) cc_final: 0.5714 (mm)
REVERT: A  525 ASP cc_start: 0.8223 (m-30) cc_final: 0.7686 (t0)
REVERT: A  655 MET cc_start: 0.4154 (mtt) cc_final: 0.3845 (mtp)
REVERT: A  738 MET cc_start: 0.7760 (mmt) cc_final: 0.7327 (mmt)
REVERT: A  767 MET cc_start: 0.7535 (mmt) cc_final: 0.5747 (mmt)
REVERT: A  890 MET cc_start: 0.8602 (mmm) cc_final: 0.8292 (mmm)
REVERT: A 1105 LYS cc_start: 0.8536 (ptpt) cc_final: 0.8274 (ptpt)
REVERT: A 1173 LEU cc_start: -0.5555 (OUTLIER) cc_final: -0.6218 (mp)
REVERT: A 1238 MET cc_start: 0.6982 (pmm) cc_final: 0.6147 (tmm)
REVERT: A 1262 MET cc_start: 0.8193 (mmt) cc_final: 0.7654 (tpp)
REVERT: A 1315 LYS cc_start: 0.8951 (mtmt) cc_final: 0.8473 (mtpt)
REVERT: A 1335 ARG cc_start: 0.8352 (mmm160) cc_final: 0.8040 (mmm160)
REVERT: A 1350 ASP cc_start: 0.8461 (m-30) cc_final: 0.8221 (p0)
REVERT: A 1461 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8625 (tp)
REVERT: A 1620 TYR cc_start: 0.6161 (OUTLIER) cc_final: 0.5067 (t80)
REVERT: A 1770 MET cc_start: 0.8116 (mpp) cc_final: 0.7862 (mpp)
REVERT: A 1845 LEU cc_start: 0.8783 (pt) cc_final: 0.8331 (mt)
REVERT: A 1875 ARG cc_start: 0.7081 (mmt-90) cc_final: 0.6611 (mmt-90)
REVERT: A 2008 MET cc_start: 0.5847 (pmm) cc_final: 0.4810 (ppp)
REVERT: A 2039 CYS cc_start: 0.9360 (m) cc_final: 0.8969 (t)
REVERT: A 2048 ARG cc_start: 0.8488 (tpm170) cc_final: 0.8254 (tpp-160)
  outliers start: 52
  outliers final: 35
  residues processed: 304
  average time/residue: 0.0785
  time to fit residues: 36.7604
Evaluate side-chains
  302 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 262
  time to evaluate  : 0.468 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  321 TRP
Chi-restraints excluded: chain A residue  374 GLN
Chi-restraints excluded: chain A residue  378 ASP
Chi-restraints excluded: chain A residue  470 PHE
Chi-restraints excluded: chain A residue  481 ILE
Chi-restraints excluded: chain A residue  680 LEU
Chi-restraints excluded: chain A residue  718 THR
Chi-restraints excluded: chain A residue  725 LEU
Chi-restraints excluded: chain A residue  742 SER
Chi-restraints excluded: chain A residue  791 ILE
Chi-restraints excluded: chain A residue  821 ILE
Chi-restraints excluded: chain A residue  906 MET
Chi-restraints excluded: chain A residue  935 VAL
Chi-restraints excluded: chain A residue  982 CYS
Chi-restraints excluded: chain A residue  984 ILE
Chi-restraints excluded: chain A residue  995 LEU
Chi-restraints excluded: chain A residue 1005 MET
Chi-restraints excluded: chain A residue 1092 LEU
Chi-restraints excluded: chain A residue 1173 LEU
Chi-restraints excluded: chain A residue 1215 VAL
Chi-restraints excluded: chain A residue 1230 LEU
Chi-restraints excluded: chain A residue 1303 VAL
Chi-restraints excluded: chain A residue 1317 VAL
Chi-restraints excluded: chain A residue 1402 ILE
Chi-restraints excluded: chain A residue 1411 VAL
Chi-restraints excluded: chain A residue 1461 LEU
Chi-restraints excluded: chain A residue 1579 ILE
Chi-restraints excluded: chain A residue 1590 ILE
Chi-restraints excluded: chain A residue 1592 VAL
Chi-restraints excluded: chain A residue 1596 LEU
Chi-restraints excluded: chain A residue 1605 ILE
Chi-restraints excluded: chain A residue 1620 TYR
Chi-restraints excluded: chain A residue 1648 THR
Chi-restraints excluded: chain A residue 1661 LEU
Chi-restraints excluded: chain A residue 1908 LEU
Chi-restraints excluded: chain A residue 1917 CYS
Chi-restraints excluded: chain A residue 1985 LEU
Chi-restraints excluded: chain A residue 1998 LEU
Chi-restraints excluded: chain A residue 2052 ILE
Chi-restraints excluded: chain A residue 2056 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 65 optimal weight:    6.9990
   chunk 10 optimal weight:    4.9990
   chunk 153 optimal weight:    5.9990
   chunk 9 optimal weight:    0.7980
   chunk 93 optimal weight:    0.9980
   chunk 129 optimal weight:   10.0000
   chunk 105 optimal weight:    7.9990
   chunk 104 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
A 363 ASN
A 374 GLN
** A1015 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1452 ASN
A1628 ASN
A1829 ASN
A1996 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.118332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.095540 restraints weight = 36461.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.097983 restraints weight = 22789.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.099695 restraints weight = 16274.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 56)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.100988 restraints weight = 12680.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.101698 restraints weight = 10452.520|
|-----------------------------------------------------------------------------|
r_work (final): 0.3724
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7355
moved from start:          0.2331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  12952  Z= 0.149
  Angle     :  0.731  11.398  17447  Z= 0.368
  Chirality :  0.045   0.195   1983
  Planarity :  0.004   0.051   2182
  Dihedral  :  5.779  53.940   1694
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 13.75
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  7.90 %
    Favored  : 91.90 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 22.71 %
    Favored  : 73.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.93 (0.22), residues: 1556
  helix:  0.62 (0.18), residues: 860
  sheet: -0.24 (0.64), residues: 71
  loop : -2.52 (0.24), residues: 625

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1082 
 TYR   0.033   0.002   TYR A1620 
 PHE   0.031   0.002   PHE A1363 
 TRP   0.016   0.002   TRP A 859 
 HIS   0.007   0.001   HIS A1015 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 (12952)
  covalent geometry    : angle       0.73145 (17447)
  hydrogen bonds       : bond        0.03950 (  655)
  hydrogen bonds       : angle       4.80907 ( 1920)

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

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

  3112 Ramachandran restraints generated.
    1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3112 Ramachandran restraints generated.
    1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  334 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 272
  time to evaluate  : 0.483 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  374 GLN cc_start: 0.7471 (OUTLIER) cc_final: 0.6812 (pt0)
REVERT: A  525 ASP cc_start: 0.8215 (m-30) cc_final: 0.7651 (t0)
REVERT: A  527 THR cc_start: 0.8998 (m) cc_final: 0.8770 (p)
REVERT: A  655 MET cc_start: 0.4011 (mtt) cc_final: 0.3692 (mtp)
REVERT: A  742 SER cc_start: 0.9159 (OUTLIER) cc_final: 0.8935 (p)
REVERT: A  767 MET cc_start: 0.7384 (mmt) cc_final: 0.5799 (mmt)
REVERT: A  768 MET cc_start: 0.7185 (mtt) cc_final: 0.6934 (ttm)
REVERT: A  890 MET cc_start: 0.8609 (mmm) cc_final: 0.8376 (mmm)
REVERT: A 1105 LYS cc_start: 0.8533 (ptpt) cc_final: 0.8247 (ptpt)
REVERT: A 1173 LEU cc_start: -0.5404 (OUTLIER) cc_final: -0.6070 (mp)
REVERT: A 1238 MET cc_start: 0.6856 (pmm) cc_final: 0.6180 (tmm)
REVERT: A 1262 MET cc_start: 0.8179 (OUTLIER) cc_final: 0.7644 (tpp)
REVERT: A 1350 ASP cc_start: 0.8498 (m-30) cc_final: 0.8260 (p0)
REVERT: A 1461 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8618 (tp)
REVERT: A 1522 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8344 (tp)
REVERT: A 1620 TYR cc_start: 0.6164 (OUTLIER) cc_final: 0.5047 (t80)
REVERT: A 1845 LEU cc_start: 0.8841 (pt) cc_final: 0.8394 (mt)
REVERT: A 1963 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7537 (pp20)
REVERT: A 2008 MET cc_start: 0.5887 (pmm) cc_final: 0.4826 (ppp)
REVERT: A 2039 CYS cc_start: 0.9375 (m) cc_final: 0.9006 (t)
REVERT: A 2048 ARG cc_start: 0.8559 (tpm170) cc_final: 0.8313 (tpp-160)
  outliers start: 62
  outliers final: 43
  residues processed: 309
  average time/residue: 0.0825
  time to fit residues: 38.7952
Evaluate side-chains
  306 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 256
  time to evaluate  : 0.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  321 TRP
Chi-restraints excluded: chain A residue  332 GLU
Chi-restraints excluded: chain A residue  374 GLN
Chi-restraints excluded: chain A residue  378 ASP
Chi-restraints excluded: chain A residue  470 PHE
Chi-restraints excluded: chain A residue  680 LEU
Chi-restraints excluded: chain A residue  718 THR
Chi-restraints excluded: chain A residue  725 LEU
Chi-restraints excluded: chain A residue  742 SER
Chi-restraints excluded: chain A residue  749 ASP
Chi-restraints excluded: chain A residue  791 ILE
Chi-restraints excluded: chain A residue  821 ILE
Chi-restraints excluded: chain A residue  833 LEU
Chi-restraints excluded: chain A residue  906 MET
Chi-restraints excluded: chain A residue  935 VAL
Chi-restraints excluded: chain A residue  982 CYS
Chi-restraints excluded: chain A residue  984 ILE
Chi-restraints excluded: chain A residue  995 LEU
Chi-restraints excluded: chain A residue 1005 MET
Chi-restraints excluded: chain A residue 1037 PHE
Chi-restraints excluded: chain A residue 1085 ILE
Chi-restraints excluded: chain A residue 1173 LEU
Chi-restraints excluded: chain A residue 1230 LEU
Chi-restraints excluded: chain A residue 1262 MET
Chi-restraints excluded: chain A residue 1303 VAL
Chi-restraints excluded: chain A residue 1317 VAL
Chi-restraints excluded: chain A residue 1352 LEU
Chi-restraints excluded: chain A residue 1402 ILE
Chi-restraints excluded: chain A residue 1411 VAL
Chi-restraints excluded: chain A residue 1415 THR
Chi-restraints excluded: chain A residue 1452 ASN
Chi-restraints excluded: chain A residue 1461 LEU
Chi-restraints excluded: chain A residue 1482 ASP
Chi-restraints excluded: chain A residue 1522 LEU
Chi-restraints excluded: chain A residue 1541 LYS
Chi-restraints excluded: chain A residue 1579 ILE
Chi-restraints excluded: chain A residue 1590 ILE
Chi-restraints excluded: chain A residue 1592 VAL
Chi-restraints excluded: chain A residue 1596 LEU
Chi-restraints excluded: chain A residue 1605 ILE
Chi-restraints excluded: chain A residue 1620 TYR
Chi-restraints excluded: chain A residue 1648 THR
Chi-restraints excluded: chain A residue 1661 LEU
Chi-restraints excluded: chain A residue 1908 LEU
Chi-restraints excluded: chain A residue 1985 LEU
Chi-restraints excluded: chain A residue 1988 ILE
Chi-restraints excluded: chain A residue 1992 ASP
Chi-restraints excluded: chain A residue 1998 LEU
Chi-restraints excluded: chain A residue 2052 ILE
Chi-restraints excluded: chain A residue 2056 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 103 optimal weight:    5.9990
   chunk 23 optimal weight:    4.9990
   chunk 59 optimal weight:    0.9980
   chunk 55 optimal weight:    1.9990
   chunk 114 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 49 optimal weight:    6.9990
   chunk 29 optimal weight:    2.9990
   chunk 44 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
A 374 GLN
** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 681 HIS
A 997 ASN
** A1015 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1420 ASN
A1452 ASN
A1496 ASN
** A1954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.114544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.091887 restraints weight = 36591.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.094197 restraints weight = 23332.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.095741 restraints weight = 16933.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.096935 restraints weight = 13462.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.097654 restraints weight = 11297.955|
|-----------------------------------------------------------------------------|
r_work (final): 0.3654
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7468
moved from start:          0.2918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060  12952  Z= 0.219
  Angle     :  0.785  13.815  17447  Z= 0.403
  Chirality :  0.047   0.236   1983
  Planarity :  0.004   0.066   2182
  Dihedral  :  5.910  56.199   1694
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 17.58
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  8.35 %
    Favored  : 91.45 %
  Rotamer:
    Outliers :  4.89 %
    Allowed  : 22.71 %
    Favored  : 72.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.09 (0.21), residues: 1556
  helix:  0.53 (0.18), residues: 865
  sheet: -0.45 (0.58), residues: 81
  loop : -2.68 (0.24), residues: 610

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 899 
 TYR   0.031   0.002   TYR A1620 
 PHE   0.042   0.002   PHE A1363 
 TRP   0.019   0.002   TRP A 859 
 HIS   0.010   0.001   HIS A1312 

Details of bonding type rmsd
  covalent geometry    : bond        0.00484 (12952)
  covalent geometry    : angle       0.78517 (17447)
  hydrogen bonds       : bond        0.04326 (  655)
  hydrogen bonds       : angle       4.97250 ( 1920)

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

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

  3112 Ramachandran restraints generated.
    1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3112 Ramachandran restraints generated.
    1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  338 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 267
  time to evaluate  : 0.469 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  374 GLN cc_start: 0.7701 (OUTLIER) cc_final: 0.6882 (tt0)
REVERT: A  525 ASP cc_start: 0.8132 (m-30) cc_final: 0.7617 (t0)
REVERT: A  655 MET cc_start: 0.4228 (mtt) cc_final: 0.3904 (mtp)
REVERT: A  755 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7614 (pm20)
REVERT: A  767 MET cc_start: 0.7701 (mmt) cc_final: 0.6050 (mmt)
REVERT: A  768 MET cc_start: 0.7061 (mtt) cc_final: 0.6777 (ttm)
REVERT: A  809 TYR cc_start: 0.7334 (OUTLIER) cc_final: 0.6902 (t80)
REVERT: A 1105 LYS cc_start: 0.8621 (ptpt) cc_final: 0.7787 (tmtt)
REVERT: A 1238 MET cc_start: 0.6903 (pmm) cc_final: 0.6155 (tmm)
REVERT: A 1262 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.7717 (tpp)
REVERT: A 1311 GLU cc_start: 0.8290 (tp30) cc_final: 0.8090 (tp30)
REVERT: A 1315 LYS cc_start: 0.8869 (mtmt) cc_final: 0.8604 (mtpt)
REVERT: A 1350 ASP cc_start: 0.8626 (m-30) cc_final: 0.8348 (p0)
REVERT: A 1461 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.7864 (tt)
REVERT: A 1522 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8439 (tp)
REVERT: A 1620 TYR cc_start: 0.6653 (OUTLIER) cc_final: 0.5532 (t80)
REVERT: A 1770 MET cc_start: 0.8474 (mpp) cc_final: 0.7396 (ptm)
REVERT: A 1834 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8239 (tt)
REVERT: A 1875 ARG cc_start: 0.7212 (mmt-90) cc_final: 0.6857 (mmt-90)
REVERT: A 1992 ASP cc_start: 0.8431 (OUTLIER) cc_final: 0.8230 (t0)
REVERT: A 2008 MET cc_start: 0.5814 (pmm) cc_final: 0.4551 (ppp)
REVERT: A 2049 LEU cc_start: 0.8551 (tp) cc_final: 0.7631 (mp)
  outliers start: 71
  outliers final: 50
  residues processed: 308
  average time/residue: 0.0778
  time to fit residues: 36.6563
Evaluate side-chains
  311 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 252
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  332 GLU
Chi-restraints excluded: chain A residue  374 GLN
Chi-restraints excluded: chain A residue  378 ASP
Chi-restraints excluded: chain A residue  470 PHE
Chi-restraints excluded: chain A residue  680 LEU
Chi-restraints excluded: chain A residue  718 THR
Chi-restraints excluded: chain A residue  725 LEU
Chi-restraints excluded: chain A residue  742 SER
Chi-restraints excluded: chain A residue  749 ASP
Chi-restraints excluded: chain A residue  755 GLU
Chi-restraints excluded: chain A residue  766 SER
Chi-restraints excluded: chain A residue  770 LEU
Chi-restraints excluded: chain A residue  791 ILE
Chi-restraints excluded: chain A residue  809 TYR
Chi-restraints excluded: chain A residue  821 ILE
Chi-restraints excluded: chain A residue  833 LEU
Chi-restraints excluded: chain A residue  902 ILE
Chi-restraints excluded: chain A residue  906 MET
Chi-restraints excluded: chain A residue  935 VAL
Chi-restraints excluded: chain A residue  982 CYS
Chi-restraints excluded: chain A residue  984 ILE
Chi-restraints excluded: chain A residue  995 LEU
Chi-restraints excluded: chain A residue 1005 MET
Chi-restraints excluded: chain A residue 1037 PHE
Chi-restraints excluded: chain A residue 1064 VAL
Chi-restraints excluded: chain A residue 1085 ILE
Chi-restraints excluded: chain A residue 1090 ASP
Chi-restraints excluded: chain A residue 1173 LEU
Chi-restraints excluded: chain A residue 1230 LEU
Chi-restraints excluded: chain A residue 1262 MET
Chi-restraints excluded: chain A residue 1303 VAL
Chi-restraints excluded: chain A residue 1317 VAL
Chi-restraints excluded: chain A residue 1364 LEU
Chi-restraints excluded: chain A residue 1402 ILE
Chi-restraints excluded: chain A residue 1411 VAL
Chi-restraints excluded: chain A residue 1415 THR
Chi-restraints excluded: chain A residue 1452 ASN
Chi-restraints excluded: chain A residue 1454 LEU
Chi-restraints excluded: chain A residue 1461 LEU
Chi-restraints excluded: chain A residue 1482 ASP
Chi-restraints excluded: chain A residue 1522 LEU
Chi-restraints excluded: chain A residue 1541 LYS
Chi-restraints excluded: chain A residue 1579 ILE
Chi-restraints excluded: chain A residue 1590 ILE
Chi-restraints excluded: chain A residue 1596 LEU
Chi-restraints excluded: chain A residue 1605 ILE
Chi-restraints excluded: chain A residue 1620 TYR
Chi-restraints excluded: chain A residue 1648 THR
Chi-restraints excluded: chain A residue 1661 LEU
Chi-restraints excluded: chain A residue 1834 LEU
Chi-restraints excluded: chain A residue 1908 LEU
Chi-restraints excluded: chain A residue 1917 CYS
Chi-restraints excluded: chain A residue 1985 LEU
Chi-restraints excluded: chain A residue 1988 ILE
Chi-restraints excluded: chain A residue 1992 ASP
Chi-restraints excluded: chain A residue 1998 LEU
Chi-restraints excluded: chain A residue 2040 ASN
Chi-restraints excluded: chain A residue 2052 ILE
Chi-restraints excluded: chain A residue 2056 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 30 optimal weight:    0.8980
   chunk 108 optimal weight:    0.3980
   chunk 130 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9980
   chunk 37 optimal weight:    0.7980
   chunk 102 optimal weight:    0.7980
   chunk 14 optimal weight:    6.9990
   chunk 156 optimal weight:    7.9990
   chunk 25 optimal weight:    2.9990
   chunk 126 optimal weight:    2.9990
   chunk 82 optimal weight:    3.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 374 GLN
A 997 ASN
** A1015 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1628 ASN
A1919 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.116825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.093970 restraints weight = 36223.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.096533 restraints weight = 22453.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.098144 restraints weight = 15896.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.099324 restraints weight = 12520.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.100266 restraints weight = 10310.050|
|-----------------------------------------------------------------------------|
r_work (final): 0.3698
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7402
moved from start:          0.2959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  12952  Z= 0.150
  Angle     :  0.784  13.325  17447  Z= 0.389
  Chirality :  0.046   0.186   1983
  Planarity :  0.004   0.059   2182
  Dihedral  :  5.870  57.215   1694
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 15.70
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  7.84 %
    Favored  : 91.97 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 24.16 %
    Favored  : 71.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.04 (0.22), residues: 1556
  helix:  0.52 (0.18), residues: 868
  sheet: -0.33 (0.63), residues: 71
  loop : -2.56 (0.24), residues: 617

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1335 
 TYR   0.032   0.002   TYR A1620 
 PHE   0.041   0.002   PHE A2002 
 TRP   0.022   0.002   TRP A1952 
 HIS   0.007   0.001   HIS A1312 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 (12952)
  covalent geometry    : angle       0.78353 (17447)
  hydrogen bonds       : bond        0.04102 (  655)
  hydrogen bonds       : angle       4.88317 ( 1920)

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

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

  3112 Ramachandran restraints generated.
    1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3112 Ramachandran restraints generated.
    1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  336 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 274
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  374 GLN cc_start: 0.7598 (OUTLIER) cc_final: 0.7131 (pt0)
REVERT: A  402 LYS cc_start: 0.7335 (tptp) cc_final: 0.6632 (tppt)
REVERT: A  525 ASP cc_start: 0.8096 (m-30) cc_final: 0.7572 (t0)
REVERT: A  655 MET cc_start: 0.4222 (mtt) cc_final: 0.3908 (mtp)
REVERT: A  755 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7602 (pm20)
REVERT: A  767 MET cc_start: 0.7432 (mmt) cc_final: 0.5800 (mmt)
REVERT: A  890 MET cc_start: 0.8419 (mmm) cc_final: 0.7860 (mmm)
REVERT: A 1105 LYS cc_start: 0.8572 (ptpt) cc_final: 0.7706 (tmtt)
REVERT: A 1173 LEU cc_start: -0.5358 (OUTLIER) cc_final: -0.6026 (mp)
REVERT: A 1238 MET cc_start: 0.6800 (pmm) cc_final: 0.6073 (tmm)
REVERT: A 1262 MET cc_start: 0.8242 (OUTLIER) cc_final: 0.7685 (tpp)
REVERT: A 1311 GLU cc_start: 0.8199 (tp30) cc_final: 0.7731 (tp30)
REVERT: A 1315 LYS cc_start: 0.8897 (mtmt) cc_final: 0.8594 (mtpt)
REVERT: A 1335 ARG cc_start: 0.8415 (mmp80) cc_final: 0.8209 (mmp80)
REVERT: A 1350 ASP cc_start: 0.8545 (m-30) cc_final: 0.8337 (p0)
REVERT: A 1418 PHE cc_start: 0.8360 (t80) cc_final: 0.7846 (t80)
REVERT: A 1461 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8292 (tp)
REVERT: A 1509 MET cc_start: 0.8098 (ppp) cc_final: 0.7633 (ppp)
REVERT: A 1522 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8442 (tp)
REVERT: A 1620 TYR cc_start: 0.6440 (OUTLIER) cc_final: 0.4991 (t80)
REVERT: A 1770 MET cc_start: 0.8312 (mpp) cc_final: 0.7341 (ptm)
REVERT: A 1875 ARG cc_start: 0.7180 (mmt-90) cc_final: 0.6852 (mmt-90)
REVERT: A 1963 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7660 (pp20)
REVERT: A 2008 MET cc_start: 0.5951 (pmm) cc_final: 0.4662 (ppp)
REVERT: A 2022 GLU cc_start: 0.6899 (OUTLIER) cc_final: 0.6689 (mp0)
REVERT: A 2048 ARG cc_start: 0.8331 (tpp-160) cc_final: 0.7808 (mmt90)
REVERT: A 2049 LEU cc_start: 0.8639 (tp) cc_final: 0.7876 (mp)
  outliers start: 62
  outliers final: 45
  residues processed: 308
  average time/residue: 0.0840
  time to fit residues: 39.1247
Evaluate side-chains
  309 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 256
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  332 GLU
Chi-restraints excluded: chain A residue  374 GLN
Chi-restraints excluded: chain A residue  378 ASP
Chi-restraints excluded: chain A residue  470 PHE
Chi-restraints excluded: chain A residue  680 LEU
Chi-restraints excluded: chain A residue  690 LYS
Chi-restraints excluded: chain A residue  718 THR
Chi-restraints excluded: chain A residue  725 LEU
Chi-restraints excluded: chain A residue  742 SER
Chi-restraints excluded: chain A residue  749 ASP
Chi-restraints excluded: chain A residue  755 GLU
Chi-restraints excluded: chain A residue  770 LEU
Chi-restraints excluded: chain A residue  791 ILE
Chi-restraints excluded: chain A residue  821 ILE
Chi-restraints excluded: chain A residue  833 LEU
Chi-restraints excluded: chain A residue  902 ILE
Chi-restraints excluded: chain A residue  906 MET
Chi-restraints excluded: chain A residue  935 VAL
Chi-restraints excluded: chain A residue  982 CYS
Chi-restraints excluded: chain A residue  984 ILE
Chi-restraints excluded: chain A residue  995 LEU
Chi-restraints excluded: chain A residue 1005 MET
Chi-restraints excluded: chain A residue 1037 PHE
Chi-restraints excluded: chain A residue 1085 ILE
Chi-restraints excluded: chain A residue 1090 ASP
Chi-restraints excluded: chain A residue 1173 LEU
Chi-restraints excluded: chain A residue 1230 LEU
Chi-restraints excluded: chain A residue 1262 MET
Chi-restraints excluded: chain A residue 1303 VAL
Chi-restraints excluded: chain A residue 1317 VAL
Chi-restraints excluded: chain A residue 1402 ILE
Chi-restraints excluded: chain A residue 1415 THR
Chi-restraints excluded: chain A residue 1452 ASN
Chi-restraints excluded: chain A residue 1454 LEU
Chi-restraints excluded: chain A residue 1461 LEU
Chi-restraints excluded: chain A residue 1482 ASP
Chi-restraints excluded: chain A residue 1522 LEU
Chi-restraints excluded: chain A residue 1541 LYS
Chi-restraints excluded: chain A residue 1579 ILE
Chi-restraints excluded: chain A residue 1590 ILE
Chi-restraints excluded: chain A residue 1596 LEU
Chi-restraints excluded: chain A residue 1605 ILE
Chi-restraints excluded: chain A residue 1620 TYR
Chi-restraints excluded: chain A residue 1648 THR
Chi-restraints excluded: chain A residue 1661 LEU
Chi-restraints excluded: chain A residue 1908 LEU
Chi-restraints excluded: chain A residue 1917 CYS
Chi-restraints excluded: chain A residue 1988 ILE
Chi-restraints excluded: chain A residue 1992 ASP
Chi-restraints excluded: chain A residue 1998 LEU
Chi-restraints excluded: chain A residue 2022 GLU
Chi-restraints excluded: chain A residue 2052 ILE
Chi-restraints excluded: chain A residue 2056 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 148 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 135 optimal weight:    2.9990
   chunk 32 optimal weight:    0.5980
   chunk 157 optimal weight:    0.9980
   chunk 10 optimal weight:    4.9990
   chunk 127 optimal weight:    4.9990
   chunk 128 optimal weight:    1.9990
   chunk 26 optimal weight:    0.7980
   chunk 71 optimal weight:    0.9980
   chunk 12 optimal weight:    0.0370
   overall best weight:    0.6858

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

Flipped N/Q/H residues before XYZ refinement:
** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 848 GLN
** A1015 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1452 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.117539 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.094923 restraints weight = 36079.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.097421 restraints weight = 22948.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.099124 restraints weight = 16473.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.100203 restraints weight = 12940.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.100958 restraints weight = 10912.326|
|-----------------------------------------------------------------------------|
r_work (final): 0.3710
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7391
moved from start:          0.3092

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  12952  Z= 0.146
  Angle     :  0.775  12.750  17447  Z= 0.388
  Chirality :  0.047   0.214   1983
  Planarity :  0.004   0.055   2182
  Dihedral  :  5.827  56.947   1694
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 15.78
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  8.35 %
    Favored  : 91.45 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 24.50 %
    Favored  : 71.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.98 (0.22), residues: 1556
  helix:  0.56 (0.18), residues: 857
  sheet: -0.32 (0.62), residues: 71
  loop : -2.47 (0.24), residues: 628

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A1422 
 TYR   0.034   0.002   TYR A1620 
 PHE   0.041   0.002   PHE A1363 
 TRP   0.021   0.002   TRP A1952 
 HIS   0.009   0.001   HIS A1312 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 (12952)
  covalent geometry    : angle       0.77454 (17447)
  hydrogen bonds       : bond        0.04083 (  655)
  hydrogen bonds       : angle       4.85498 ( 1920)

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

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

  3112 Ramachandran restraints generated.
    1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3112 Ramachandran restraints generated.
    1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  330 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 271
  time to evaluate  : 0.448 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  402 LYS cc_start: 0.7318 (tptp) cc_final: 0.6582 (tppt)
REVERT: A  525 ASP cc_start: 0.8131 (m-30) cc_final: 0.7599 (t0)
REVERT: A  655 MET cc_start: 0.4210 (mtt) cc_final: 0.3908 (mtp)
REVERT: A  755 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7565 (pm20)
REVERT: A  767 MET cc_start: 0.7364 (mmt) cc_final: 0.5652 (mmt)
REVERT: A  809 TYR cc_start: 0.7308 (OUTLIER) cc_final: 0.6929 (t80)
REVERT: A  836 PHE cc_start: 0.9007 (t80) cc_final: 0.8666 (t80)
REVERT: A  890 MET cc_start: 0.8383 (mmm) cc_final: 0.7966 (mmm)
REVERT: A 1105 LYS cc_start: 0.8553 (ptpt) cc_final: 0.7670 (tmtt)
REVERT: A 1238 MET cc_start: 0.6841 (pmm) cc_final: 0.5954 (tmm)
REVERT: A 1262 MET cc_start: 0.8164 (OUTLIER) cc_final: 0.7595 (tpp)
REVERT: A 1267 MET cc_start: 0.9009 (mmm) cc_final: 0.8777 (mmm)
REVERT: A 1311 GLU cc_start: 0.8206 (tp30) cc_final: 0.7750 (tp30)
REVERT: A 1315 LYS cc_start: 0.8867 (mtmt) cc_final: 0.8574 (mtpt)
REVERT: A 1350 ASP cc_start: 0.8542 (m-30) cc_final: 0.8324 (p0)
REVERT: A 1404 MET cc_start: 0.7405 (mmt) cc_final: 0.7150 (mmp)
REVERT: A 1418 PHE cc_start: 0.8563 (t80) cc_final: 0.8331 (t80)
REVERT: A 1461 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8286 (tp)
REVERT: A 1509 MET cc_start: 0.8122 (ppp) cc_final: 0.7687 (ppp)
REVERT: A 1620 TYR cc_start: 0.6532 (OUTLIER) cc_final: 0.5018 (t80)
REVERT: A 1770 MET cc_start: 0.8310 (mpp) cc_final: 0.7343 (ptm)
REVERT: A 1820 GLU cc_start: 0.7943 (tp30) cc_final: 0.7694 (tp30)
REVERT: A 1875 ARG cc_start: 0.7171 (mmt-90) cc_final: 0.6840 (mmt-90)
REVERT: A 1927 PHE cc_start: 0.8884 (t80) cc_final: 0.8610 (t80)
REVERT: A 1963 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7715 (pp20)
REVERT: A 2008 MET cc_start: 0.5728 (pmm) cc_final: 0.4471 (ppp)
REVERT: A 2022 GLU cc_start: 0.6921 (OUTLIER) cc_final: 0.6691 (mp0)
REVERT: A 2049 LEU cc_start: 0.8605 (tp) cc_final: 0.7845 (mp)
REVERT: A 2088 GLU cc_start: 0.6314 (tp30) cc_final: 0.6052 (tp30)
  outliers start: 59
  outliers final: 43
  residues processed: 309
  average time/residue: 0.0772
  time to fit residues: 36.1989
Evaluate side-chains
  302 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 253
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  321 TRP
Chi-restraints excluded: chain A residue  332 GLU
Chi-restraints excluded: chain A residue  378 ASP
Chi-restraints excluded: chain A residue  470 PHE
Chi-restraints excluded: chain A residue  680 LEU
Chi-restraints excluded: chain A residue  690 LYS
Chi-restraints excluded: chain A residue  718 THR
Chi-restraints excluded: chain A residue  725 LEU
Chi-restraints excluded: chain A residue  742 SER
Chi-restraints excluded: chain A residue  749 ASP
Chi-restraints excluded: chain A residue  755 GLU
Chi-restraints excluded: chain A residue  791 ILE
Chi-restraints excluded: chain A residue  809 TYR
Chi-restraints excluded: chain A residue  821 ILE
Chi-restraints excluded: chain A residue  902 ILE
Chi-restraints excluded: chain A residue  906 MET
Chi-restraints excluded: chain A residue  935 VAL
Chi-restraints excluded: chain A residue  982 CYS
Chi-restraints excluded: chain A residue  984 ILE
Chi-restraints excluded: chain A residue  995 LEU
Chi-restraints excluded: chain A residue 1005 MET
Chi-restraints excluded: chain A residue 1037 PHE
Chi-restraints excluded: chain A residue 1085 ILE
Chi-restraints excluded: chain A residue 1173 LEU
Chi-restraints excluded: chain A residue 1230 LEU
Chi-restraints excluded: chain A residue 1262 MET
Chi-restraints excluded: chain A residue 1303 VAL
Chi-restraints excluded: chain A residue 1317 VAL
Chi-restraints excluded: chain A residue 1402 ILE
Chi-restraints excluded: chain A residue 1415 THR
Chi-restraints excluded: chain A residue 1461 LEU
Chi-restraints excluded: chain A residue 1482 ASP
Chi-restraints excluded: chain A residue 1541 LYS
Chi-restraints excluded: chain A residue 1579 ILE
Chi-restraints excluded: chain A residue 1590 ILE
Chi-restraints excluded: chain A residue 1596 LEU
Chi-restraints excluded: chain A residue 1605 ILE
Chi-restraints excluded: chain A residue 1620 TYR
Chi-restraints excluded: chain A residue 1648 THR
Chi-restraints excluded: chain A residue 1661 LEU
Chi-restraints excluded: chain A residue 1908 LEU
Chi-restraints excluded: chain A residue 1917 CYS
Chi-restraints excluded: chain A residue 1985 LEU
Chi-restraints excluded: chain A residue 1992 ASP
Chi-restraints excluded: chain A residue 1998 LEU
Chi-restraints excluded: chain A residue 2022 GLU
Chi-restraints excluded: chain A residue 2040 ASN
Chi-restraints excluded: chain A residue 2052 ILE
Chi-restraints excluded: chain A residue 2056 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 48 optimal weight:    3.9990
   chunk 149 optimal weight:    0.0570
   chunk 60 optimal weight:    3.9990
   chunk 11 optimal weight:    5.9990
   chunk 4 optimal weight:    0.7980
   chunk 18 optimal weight:    6.9990
   chunk 139 optimal weight:    0.0170
   chunk 116 optimal weight:    0.9990
   chunk 119 optimal weight:    6.9990
   chunk 27 optimal weight:    1.9990
   chunk 62 optimal weight:    4.9990
   overall best weight:    0.7740

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

Flipped N/Q/H residues before XYZ refinement:
** A1015 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1996 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.117503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.094846 restraints weight = 36675.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.097327 restraints weight = 23267.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.099057 restraints weight = 16709.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.100153 restraints weight = 13172.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.100970 restraints weight = 11098.158|
|-----------------------------------------------------------------------------|
r_work (final): 0.3711
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7392
moved from start:          0.3243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  12952  Z= 0.151
  Angle     :  0.815  12.966  17447  Z= 0.406
  Chirality :  0.047   0.246   1983
  Planarity :  0.004   0.054   2182
  Dihedral  :  5.834  58.593   1694
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 16.29
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  8.29 %
    Favored  : 91.52 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 25.12 %
    Favored  : 71.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.01 (0.21), residues: 1556
  helix:  0.47 (0.18), residues: 860
  sheet: -0.28 (0.61), residues: 71
  loop : -2.39 (0.24), residues: 625

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A1335 
 TYR   0.033   0.002   TYR A1620 
 PHE   0.043   0.002   PHE A1363 
 TRP   0.019   0.002   TRP A1952 
 HIS   0.009   0.001   HIS A1312 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 (12952)
  covalent geometry    : angle       0.81453 (17447)
  hydrogen bonds       : bond        0.04124 (  655)
  hydrogen bonds       : angle       4.87700 ( 1920)

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

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

  3112 Ramachandran restraints generated.
    1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3112 Ramachandran restraints generated.
    1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  321 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 267
  time to evaluate  : 0.454 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  402 LYS cc_start: 0.7161 (tptp) cc_final: 0.6850 (tppt)
REVERT: A  525 ASP cc_start: 0.8177 (m-30) cc_final: 0.7625 (t0)
REVERT: A  655 MET cc_start: 0.4182 (mtt) cc_final: 0.3875 (mtp)
REVERT: A  755 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7613 (pm20)
REVERT: A  767 MET cc_start: 0.7445 (mmt) cc_final: 0.5733 (mmt)
REVERT: A  809 TYR cc_start: 0.7283 (OUTLIER) cc_final: 0.6897 (t80)
REVERT: A  873 MET cc_start: 0.8040 (mpp) cc_final: 0.7617 (mpp)
REVERT: A  890 MET cc_start: 0.8423 (mmm) cc_final: 0.7902 (mmm)
REVERT: A 1011 HIS cc_start: 0.5058 (OUTLIER) cc_final: 0.4617 (p-80)
REVERT: A 1105 LYS cc_start: 0.8544 (ptpt) cc_final: 0.7657 (tmtt)
REVERT: A 1238 MET cc_start: 0.6707 (pmm) cc_final: 0.6277 (tmm)
REVERT: A 1262 MET cc_start: 0.8125 (OUTLIER) cc_final: 0.7556 (tpp)
REVERT: A 1311 GLU cc_start: 0.8216 (tp30) cc_final: 0.7720 (tp30)
REVERT: A 1315 LYS cc_start: 0.8873 (mtmt) cc_final: 0.8552 (mtpt)
REVERT: A 1335 ARG cc_start: 0.8613 (mmp-170) cc_final: 0.8223 (mmp-170)
REVERT: A 1350 ASP cc_start: 0.8532 (m-30) cc_final: 0.8318 (p0)
REVERT: A 1418 PHE cc_start: 0.8615 (t80) cc_final: 0.8190 (t80)
REVERT: A 1461 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8299 (tp)
REVERT: A 1509 MET cc_start: 0.8179 (ppp) cc_final: 0.7804 (ppp)
REVERT: A 1620 TYR cc_start: 0.6372 (OUTLIER) cc_final: 0.4769 (t80)
REVERT: A 1645 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8078 (pm20)
REVERT: A 1770 MET cc_start: 0.8234 (mpp) cc_final: 0.7324 (ptm)
REVERT: A 1831 GLU cc_start: 0.8521 (pm20) cc_final: 0.7490 (pm20)
REVERT: A 1927 PHE cc_start: 0.8890 (t80) cc_final: 0.8653 (t80)
REVERT: A 1963 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7736 (pp20)
REVERT: A 1992 ASP cc_start: 0.8388 (OUTLIER) cc_final: 0.8113 (t0)
REVERT: A 2008 MET cc_start: 0.5841 (pmm) cc_final: 0.4704 (ppp)
REVERT: A 2022 GLU cc_start: 0.6932 (OUTLIER) cc_final: 0.6697 (mp0)
REVERT: A 2049 LEU cc_start: 0.8608 (tp) cc_final: 0.7876 (mp)
REVERT: A 2088 GLU cc_start: 0.6273 (tp30) cc_final: 0.5976 (tp30)
  outliers start: 54
  outliers final: 40
  residues processed: 298
  average time/residue: 0.0785
  time to fit residues: 35.8927
Evaluate side-chains
  306 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 257
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  321 TRP
Chi-restraints excluded: chain A residue  332 GLU
Chi-restraints excluded: chain A residue  378 ASP
Chi-restraints excluded: chain A residue  470 PHE
Chi-restraints excluded: chain A residue  680 LEU
Chi-restraints excluded: chain A residue  718 THR
Chi-restraints excluded: chain A residue  725 LEU
Chi-restraints excluded: chain A residue  742 SER
Chi-restraints excluded: chain A residue  749 ASP
Chi-restraints excluded: chain A residue  755 GLU
Chi-restraints excluded: chain A residue  791 ILE
Chi-restraints excluded: chain A residue  809 TYR
Chi-restraints excluded: chain A residue  821 ILE
Chi-restraints excluded: chain A residue  833 LEU
Chi-restraints excluded: chain A residue  906 MET
Chi-restraints excluded: chain A residue  935 VAL
Chi-restraints excluded: chain A residue  982 CYS
Chi-restraints excluded: chain A residue  984 ILE
Chi-restraints excluded: chain A residue  995 LEU
Chi-restraints excluded: chain A residue 1005 MET
Chi-restraints excluded: chain A residue 1011 HIS
Chi-restraints excluded: chain A residue 1037 PHE
Chi-restraints excluded: chain A residue 1173 LEU
Chi-restraints excluded: chain A residue 1230 LEU
Chi-restraints excluded: chain A residue 1262 MET
Chi-restraints excluded: chain A residue 1303 VAL
Chi-restraints excluded: chain A residue 1317 VAL
Chi-restraints excluded: chain A residue 1402 ILE
Chi-restraints excluded: chain A residue 1415 THR
Chi-restraints excluded: chain A residue 1461 LEU
Chi-restraints excluded: chain A residue 1482 ASP
Chi-restraints excluded: chain A residue 1579 ILE
Chi-restraints excluded: chain A residue 1590 ILE
Chi-restraints excluded: chain A residue 1596 LEU
Chi-restraints excluded: chain A residue 1605 ILE
Chi-restraints excluded: chain A residue 1620 TYR
Chi-restraints excluded: chain A residue 1645 GLU
Chi-restraints excluded: chain A residue 1648 THR
Chi-restraints excluded: chain A residue 1661 LEU
Chi-restraints excluded: chain A residue 1825 ILE
Chi-restraints excluded: chain A residue 1908 LEU
Chi-restraints excluded: chain A residue 1917 CYS
Chi-restraints excluded: chain A residue 1985 LEU
Chi-restraints excluded: chain A residue 1992 ASP
Chi-restraints excluded: chain A residue 1998 LEU
Chi-restraints excluded: chain A residue 2022 GLU
Chi-restraints excluded: chain A residue 2040 ASN
Chi-restraints excluded: chain A residue 2052 ILE
Chi-restraints excluded: chain A residue 2056 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 27 optimal weight:    0.4980
   chunk 13 optimal weight:    2.9990
   chunk 125 optimal weight:    0.9990
   chunk 145 optimal weight:    0.0170
   chunk 102 optimal weight:    4.9990
   chunk 112 optimal weight:    0.9980
   chunk 121 optimal weight:    0.6980
   chunk 59 optimal weight:    0.9990
   chunk 139 optimal weight:    0.0870
   chunk 80 optimal weight:    1.9990
   overall best weight:    0.4596

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

Flipped N/Q/H residues before XYZ refinement:
A 848 GLN
** A1015 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 = 0.4002 r_free = 0.4002 target = 0.119188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.095910 restraints weight = 36777.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.098274 restraints weight = 23472.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.099896 restraints weight = 16928.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.101129 restraints weight = 13424.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.101910 restraints weight = 11332.170|
|-----------------------------------------------------------------------------|
r_work (final): 0.3732
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7363
moved from start:          0.3352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  12952  Z= 0.144
  Angle     :  0.811  13.253  17447  Z= 0.404
  Chirality :  0.047   0.215   1983
  Planarity :  0.004   0.065   2182
  Dihedral  :  5.792  58.462   1694
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 15.59
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  7.78 %
    Favored  : 92.03 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 25.81 %
    Favored  : 70.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.93 (0.22), residues: 1556
  helix:  0.55 (0.18), residues: 856
  sheet: -0.27 (0.61), residues: 71
  loop : -2.35 (0.24), residues: 629

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 531 
 TYR   0.033   0.001   TYR A1620 
 PHE   0.041   0.002   PHE A1363 
 TRP   0.018   0.002   TRP A1952 
 HIS   0.007   0.001   HIS A1823 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 (12952)
  covalent geometry    : angle       0.81129 (17447)
  hydrogen bonds       : bond        0.04096 (  655)
  hydrogen bonds       : angle       4.82477 ( 1920)

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

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

  3112 Ramachandran restraints generated.
    1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3112 Ramachandran restraints generated.
    1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  316 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 269
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  402 LYS cc_start: 0.7027 (tptp) cc_final: 0.6726 (tppt)
REVERT: A  525 ASP cc_start: 0.8178 (m-30) cc_final: 0.7622 (t0)
REVERT: A  655 MET cc_start: 0.4009 (mtt) cc_final: 0.3712 (mtp)
REVERT: A  767 MET cc_start: 0.7441 (mmt) cc_final: 0.5716 (mmt)
REVERT: A  809 TYR cc_start: 0.7204 (OUTLIER) cc_final: 0.6905 (t80)
REVERT: A  873 MET cc_start: 0.7975 (mpp) cc_final: 0.7570 (mpp)
REVERT: A  890 MET cc_start: 0.8478 (mmm) cc_final: 0.8055 (mmm)
REVERT: A 1011 HIS cc_start: 0.5128 (OUTLIER) cc_final: 0.4729 (p-80)
REVERT: A 1049 MET cc_start: 0.7017 (pmm) cc_final: 0.6797 (pmm)
REVERT: A 1105 LYS cc_start: 0.8518 (ptpt) cc_final: 0.7675 (tmtt)
REVERT: A 1238 MET cc_start: 0.6779 (pmm) cc_final: 0.6131 (tmm)
REVERT: A 1262 MET cc_start: 0.8157 (OUTLIER) cc_final: 0.7607 (tpp)
REVERT: A 1267 MET cc_start: 0.8935 (mmm) cc_final: 0.8672 (mmm)
REVERT: A 1311 GLU cc_start: 0.8158 (tp30) cc_final: 0.7719 (tp30)
REVERT: A 1315 LYS cc_start: 0.8877 (mtmt) cc_final: 0.8546 (mtpt)
REVERT: A 1335 ARG cc_start: 0.8746 (mmp-170) cc_final: 0.8325 (mmp-170)
REVERT: A 1350 ASP cc_start: 0.8525 (m-30) cc_final: 0.8296 (p0)
REVERT: A 1404 MET cc_start: 0.7402 (mmt) cc_final: 0.7137 (mmp)
REVERT: A 1418 PHE cc_start: 0.8623 (t80) cc_final: 0.8220 (t80)
REVERT: A 1461 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8272 (tp)
REVERT: A 1509 MET cc_start: 0.8113 (ppp) cc_final: 0.7787 (ppp)
REVERT: A 1620 TYR cc_start: 0.6404 (OUTLIER) cc_final: 0.4729 (t80)
REVERT: A 1645 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8036 (pm20)
REVERT: A 1770 MET cc_start: 0.8260 (mpp) cc_final: 0.7377 (ptm)
REVERT: A 1820 GLU cc_start: 0.7875 (tp30) cc_final: 0.7555 (tp30)
REVERT: A 1831 GLU cc_start: 0.8590 (pm20) cc_final: 0.7678 (pm20)
REVERT: A 1927 PHE cc_start: 0.8842 (t80) cc_final: 0.8612 (t80)
REVERT: A 2008 MET cc_start: 0.5855 (pmm) cc_final: 0.4696 (ppp)
REVERT: A 2049 LEU cc_start: 0.8655 (tp) cc_final: 0.7948 (mp)
REVERT: A 2088 GLU cc_start: 0.6202 (tp30) cc_final: 0.5873 (tp30)
  outliers start: 47
  outliers final: 36
  residues processed: 296
  average time/residue: 0.0758
  time to fit residues: 34.4163
Evaluate side-chains
  292 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 250
  time to evaluate  : 0.466 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  321 TRP
Chi-restraints excluded: chain A residue  378 ASP
Chi-restraints excluded: chain A residue  429 GLU
Chi-restraints excluded: chain A residue  680 LEU
Chi-restraints excluded: chain A residue  718 THR
Chi-restraints excluded: chain A residue  725 LEU
Chi-restraints excluded: chain A residue  742 SER
Chi-restraints excluded: chain A residue  749 ASP
Chi-restraints excluded: chain A residue  791 ILE
Chi-restraints excluded: chain A residue  809 TYR
Chi-restraints excluded: chain A residue  821 ILE
Chi-restraints excluded: chain A residue  848 GLN
Chi-restraints excluded: chain A residue  906 MET
Chi-restraints excluded: chain A residue  935 VAL
Chi-restraints excluded: chain A residue  982 CYS
Chi-restraints excluded: chain A residue  995 LEU
Chi-restraints excluded: chain A residue 1005 MET
Chi-restraints excluded: chain A residue 1011 HIS
Chi-restraints excluded: chain A residue 1173 LEU
Chi-restraints excluded: chain A residue 1230 LEU
Chi-restraints excluded: chain A residue 1262 MET
Chi-restraints excluded: chain A residue 1303 VAL
Chi-restraints excluded: chain A residue 1317 VAL
Chi-restraints excluded: chain A residue 1402 ILE
Chi-restraints excluded: chain A residue 1415 THR
Chi-restraints excluded: chain A residue 1461 LEU
Chi-restraints excluded: chain A residue 1482 ASP
Chi-restraints excluded: chain A residue 1579 ILE
Chi-restraints excluded: chain A residue 1590 ILE
Chi-restraints excluded: chain A residue 1596 LEU
Chi-restraints excluded: chain A residue 1605 ILE
Chi-restraints excluded: chain A residue 1620 TYR
Chi-restraints excluded: chain A residue 1645 GLU
Chi-restraints excluded: chain A residue 1661 LEU
Chi-restraints excluded: chain A residue 1825 ILE
Chi-restraints excluded: chain A residue 1908 LEU
Chi-restraints excluded: chain A residue 1917 CYS
Chi-restraints excluded: chain A residue 1985 LEU
Chi-restraints excluded: chain A residue 1998 LEU
Chi-restraints excluded: chain A residue 2040 ASN
Chi-restraints excluded: chain A residue 2052 ILE
Chi-restraints excluded: chain A residue 2056 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 103 optimal weight:    1.9990
   chunk 141 optimal weight:    0.7980
   chunk 14 optimal weight:    0.2980
   chunk 40 optimal weight:    0.0060
   chunk 144 optimal weight:    0.6980
   chunk 42 optimal weight:    0.6980
   chunk 154 optimal weight:    0.9980
   chunk 48 optimal weight:    3.9990
   chunk 34 optimal weight:    4.9990
   chunk 24 optimal weight:    1.9990
   chunk 138 optimal weight:    4.9990
   overall best weight:    0.4996

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

Flipped N/Q/H residues before XYZ refinement:
A 848 GLN
** A1015 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 = 0.4005 r_free = 0.4005 target = 0.119198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.096279 restraints weight = 36268.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.098755 restraints weight = 22587.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.100436 restraints weight = 16070.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.101703 restraints weight = 12593.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.102483 restraints weight = 10515.073|
|-----------------------------------------------------------------------------|
r_work (final): 0.3744
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7350
moved from start:          0.3440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  12952  Z= 0.146
  Angle     :  0.813  13.301  17447  Z= 0.406
  Chirality :  0.047   0.196   1983
  Planarity :  0.004   0.063   2182
  Dihedral  :  5.625  56.060   1692
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 15.90
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  7.84 %
    Favored  : 91.97 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 26.29 %
    Favored  : 70.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.91 (0.22), residues: 1556
  helix:  0.56 (0.18), residues: 853
  sheet: -0.22 (0.62), residues: 71
  loop : -2.35 (0.24), residues: 632

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 531 
 TYR   0.030   0.002   TYR A1620 
 PHE   0.039   0.002   PHE A1363 
 TRP   0.016   0.002   TRP A1958 
 HIS   0.007   0.001   HIS A1015 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 (12952)
  covalent geometry    : angle       0.81285 (17447)
  hydrogen bonds       : bond        0.04106 (  655)
  hydrogen bonds       : angle       4.82064 ( 1920)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1825.27 seconds
wall clock time: 32 minutes 37.49 seconds (1957.49 seconds total)