Starting phenix.real_space_refine
on Wed Jan 14 09:15:40 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8e06_27818/01_2026/8e06_27818_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8e06_27818/01_2026/8e06_27818.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8e06_27818/01_2026/8e06_27818_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8e06_27818/01_2026/8e06_27818_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8e06_27818/01_2026/8e06_27818.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8e06_27818/01_2026/8e06_27818.map"
  }
  resolution = 4.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.023
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: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      88      5.16       5
     C    8841      2.51       5
     N    2387      2.21       5
     O    2552      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13870
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 13842
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1749, 13842
          Classifications: {'peptide': 1749}
          Link IDs: {'PCIS': 3, 'PTRANS': 88, 'TRANS': 1657}
          Chain breaks: 8
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'GDP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 3.06, per 1000 atoms: 0.22
  Number of scatterers: 13870
  At special positions: 0
  Unit cell: (154.28, 125.28, 106.72, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      88     16.00
     P       2     15.00
     O    2552      8.00
     N    2387      7.00
     C    8841      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.15
  Conformation dependent library (CDL) restraints added in 511.9 milliseconds
  

  3462 Ramachandran restraints generated.
    1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3308

  Finding SS restraints...
    Secondary structure from input PDB file:
      69 helices and 19 sheets defined
      39.2% alpha, 18.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.78
  Creating SS restraints...
    Processing helix  chain 'A' and resid 52 through 64
      removed outlier: 3.911A  pdb=" N   GLU A  56 " --> pdb=" O   SER A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 66 through 81
    Processing helix  chain 'A' and resid 83 through 98
      removed outlier: 3.856A  pdb=" N   ILE A  93 " --> pdb=" O   GLN A  89 " (cutoff:3.500A)
      Proline residue:  A  94  - end of helix
    Processing helix  chain 'A' and resid 99 through 109
    Processing helix  chain 'A' and resid 122 through 131
    Processing helix  chain 'A' and resid 132 through 142
    Processing helix  chain 'A' and resid 149 through 164
    Processing helix  chain 'A' and resid 165 through 177
    Processing helix  chain 'A' and resid 196 through 204
    Processing helix  chain 'A' and resid 206 through 216
    Processing helix  chain 'A' and resid 221 through 228
    Processing helix  chain 'A' and resid 228 through 240
      removed outlier: 3.554A  pdb=" N   SER A 232 " --> pdb=" O   SER A 228 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   PHE A 240 " --> pdb=" O   LEU A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 277
      removed outlier: 4.495A  pdb=" N   ILE A 274 " --> pdb=" O   ASP A 271 " (cutoff:3.500A)
      removed outlier: 5.846A  pdb=" N   ASP A 275 " --> pdb=" O   TRP A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 322 through 326
    Processing helix  chain 'A' and resid 345 through 351
      removed outlier: 3.502A  pdb=" N   PHE A 348 " --> pdb=" O   PRO A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 396 through 403
      removed outlier: 3.742A  pdb=" N   LEU A 400 " --> pdb=" O   PRO A 396 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 448
    Processing helix  chain 'A' and resid 466 through 471
      removed outlier: 4.218A  pdb=" N   PHE A 470 " --> pdb=" O   PRO A 466 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 490 through 494
    Processing helix  chain 'A' and resid 544 through 549
    Processing helix  chain 'A' and resid 564 through 570
    Processing helix  chain 'A' and resid 588 through 594
    Processing helix  chain 'A' and resid 611 through 618
    Processing helix  chain 'A' and resid 618 through 631
    Processing helix  chain 'A' and resid 650 through 661
    Processing helix  chain 'A' and resid 703 through 705
      No H-bonds generated for 'chain 'A' and resid 703 through 705'
    Processing helix  chain 'A' and resid 706 through 711
    Processing helix  chain 'A' and resid 712 through 714
      No H-bonds generated for 'chain 'A' and resid 712 through 714'
    Processing helix  chain 'A' and resid 728 through 747
      removed outlier: 3.536A  pdb=" N   ASN A 735 " --> pdb=" O   GLU A 731 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   GLN A 737 " --> pdb=" O   VAL A 733 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   PHE A 738 " --> pdb=" O   ALA A 734 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   TRP A 739 " --> pdb=" O   ASN A 735 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   LYS A 746 " --> pdb=" O   ASN A 742 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 758 through 762
    Processing helix  chain 'A' and resid 763 through 781
      removed outlier: 4.459A  pdb=" N   VAL A 768 " --> pdb=" O   ALA A 764 " (cutoff:3.500A)
      removed outlier: 5.314A  pdb=" N   GLU A 769 " --> pdb=" O   LYS A 765 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 797 through 799
      No H-bonds generated for 'chain 'A' and resid 797 through 799'
    Processing helix  chain 'A' and resid 811 through 826
    Processing helix  chain 'A' and resid 844 through 864
    Processing helix  chain 'A' and resid 871 through 881
    Processing helix  chain 'A' and resid 889 through 904
      removed outlier: 3.951A  pdb=" N   LEU A 893 " --> pdb=" O   ASP A 889 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 912 through 916
      removed outlier: 3.640A  pdb=" N   GLY A 915 " --> pdb=" O   THR A 912 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 923 through 936
    Processing helix  chain 'A' and resid 951 through 958
    Processing helix  chain 'A' and resid 964 through 978
      removed outlier: 4.629A  pdb=" N   GLU A 969 " --> pdb=" O   GLN A 965 " (cutoff:3.500A)
      removed outlier: 6.137A  pdb=" N   GLN A 970 " --> pdb=" O   GLN A 966 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   LYS A 977 " --> pdb=" O   GLN A 973 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 992 through 995
      removed outlier: 3.519A  pdb=" N   LEU A 995 " --> pdb=" O   PRO A 992 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 992 through 995'
    Processing helix  chain 'A' and resid 1002 through 1007
      removed outlier: 3.904A  pdb=" N   MET A1006 " --> pdb=" O   ASP A1002 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1026 through 1046
    Processing helix  chain 'A' and resid 1107 through 1111
    Processing helix  chain 'A' and resid 1127 through 1145
      removed outlier: 3.798A  pdb=" N   ALA A1131 " --> pdb=" O   PHE A1127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1146 through 1149
    Processing helix  chain 'A' and resid 1165 through 1173
    Processing helix  chain 'A' and resid 1190 through 1200
      removed outlier: 4.127A  pdb=" N   GLU A1199 " --> pdb=" O   LEU A1195 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1216 through 1218
      No H-bonds generated for 'chain 'A' and resid 1216 through 1218'
    Processing helix  chain 'A' and resid 1219 through 1224
      removed outlier: 3.702A  pdb=" N   MET A1224 " --> pdb=" O   GLU A1221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1228 through 1232
    Processing helix  chain 'A' and resid 1234 through 1236
      No H-bonds generated for 'chain 'A' and resid 1234 through 1236'
    Processing helix  chain 'A' and resid 1243 through 1245
      No H-bonds generated for 'chain 'A' and resid 1243 through 1245'
    Processing helix  chain 'A' and resid 1286 through 1313
      removed outlier: 3.702A  pdb=" N   ALA A1313 " --> pdb=" O   SER A1309 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1341 through 1351
      removed outlier: 3.500A  pdb=" N   VAL A1345 " --> pdb=" O   SER A1341 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   ARG A1351 " --> pdb=" O   SER A1347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1359 through 1380
    Processing helix  chain 'A' and resid 1442 through 1460
      removed outlier: 3.531A  pdb=" N   ASP A1446 " --> pdb=" O   ASP A1442 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1468 through 1478
    Processing helix  chain 'A' and resid 1486 through 1491
    Processing helix  chain 'A' and resid 1492 through 1503
      removed outlier: 3.749A  pdb=" N   TRP A1503 " --> pdb=" O   MET A1499 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1506 through 1510
    Processing helix  chain 'A' and resid 1512 through 1522
      removed outlier: 3.871A  pdb=" N   ASP A1522 " --> pdb=" O   SER A1518 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1523 through 1526
    Processing helix  chain 'A' and resid 1556 through 1559
    Processing helix  chain 'A' and resid 1609 through 1611
      No H-bonds generated for 'chain 'A' and resid 1609 through 1611'
    Processing helix  chain 'A' and resid 1670 through 1678
    Processing helix  chain 'A' and resid 1685 through 1689
      removed outlier: 3.584A  pdb=" N   GLN A1688 " --> pdb=" O   ASP A1685 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1950 through 1957
      Proline residue:  A1955  - end of helix
    Processing helix  chain 'A' and resid 1990 through 2006
    Processing sheet with id=AA1, first strand: chain 'A' and resid 241 through 242
    Processing sheet with id=AA2, first strand: chain 'A' and resid 306 through 308
      removed outlier: 7.053A  pdb=" N   ILE A 334 " --> pdb=" O   THR A 358 " (cutoff:3.500A)
      removed outlier: 6.912A  pdb=" N   LEU A 357 " --> pdb=" O   ASP A 386 " (cutoff:3.500A)
      removed outlier: 7.015A  pdb=" N   LEU A 385 " --> pdb=" O   ASN A 410 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   LEU A 409 " --> pdb=" O   LYS A 431 " (cutoff:3.500A)
      removed outlier: 6.888A  pdb=" N   CYS A 430 " --> pdb=" O   ASP A 456 " (cutoff:3.500A)
      removed outlier: 7.359A  pdb=" N   LEU A 502 " --> pdb=" O   CYS A 554 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 634 through 636
      removed outlier: 3.603A  pdb=" N   ARG A 841 " --> pdb=" O   CYS A 636 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 673 through 681
      removed outlier: 6.334A  pdb=" N   MET A 639 " --> pdb=" O   ASN A 696 " (cutoff:3.500A)
      removed outlier: 7.735A  pdb=" N   TRP A 698 " --> pdb=" O   MET A 639 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   MET A 641 " --> pdb=" O   TRP A 698 " (cutoff:3.500A)
      removed outlier: 7.663A  pdb=" N   ILE A 700 " --> pdb=" O   MET A 641 " (cutoff:3.500A)
      removed outlier: 6.370A  pdb=" N   ILE A 643 " --> pdb=" O   ILE A 700 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 869 through 870
    Processing sheet with id=AA6, first strand: chain 'A' and resid 944 through 945
      removed outlier: 3.724A  pdb=" N   VAL A 948 " --> pdb=" O   LYS A 945 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1082 through 1086
      removed outlier: 6.288A  pdb=" N   GLN A1015 " --> pdb=" O   PRO A1164 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1202 through 1205
      removed outlier: 4.785A  pdb=" N   CYS A1205 " --> pdb=" O   LEU A1211 " (cutoff:3.500A)
      removed outlier: 6.249A  pdb=" N   LEU A1211 " --> pdb=" O   CYS A1205 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 1238 through 1239
      removed outlier: 6.632A  pdb=" N   ILE A1257 " --> pdb=" O   LEU A1248 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 1238 through 1239
      removed outlier: 3.622A  pdb=" N   GLY A1324 " --> pdb=" O   ALA A1333 " (cutoff:3.500A)
      removed outlier: 6.529A  pdb=" N   GLU A1335 " --> pdb=" O   LEU A1322 " (cutoff:3.500A)
      removed outlier: 7.649A  pdb=" N   LEU A1322 " --> pdb=" O   GLU A1335 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 1392 through 1394
    Processing sheet with id=AB3, first strand: chain 'A' and resid 1528 through 1536
      removed outlier: 6.448A  pdb=" N   PHE A1528 " --> pdb=" O   ARG A1987 " (cutoff:3.500A)
      removed outlier: 6.032A  pdb=" N   ARG A1987 " --> pdb=" O   PHE A1528 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   TYR A1530 " --> pdb=" O   VAL A1985 " (cutoff:3.500A)
      removed outlier: 5.670A  pdb=" N   TRP A1981 " --> pdb=" O   CYS A1534 " (cutoff:3.500A)
      removed outlier: 7.878A  pdb=" N   THR A1969 " --> pdb=" O   VAL A1964 " (cutoff:3.500A)
      removed outlier: 5.419A  pdb=" N   VAL A1964 " --> pdb=" O   THR A1969 " (cutoff:3.500A)
      removed outlier: 7.084A  pdb=" N   VAL A1971 " --> pdb=" O   ALA A1962 " (cutoff:3.500A)
      removed outlier: 4.816A  pdb=" N   ALA A1962 " --> pdb=" O   VAL A1971 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   THR A1973 " --> pdb=" O   VAL A1960 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 1539 through 1541
      removed outlier: 7.245A  pdb=" N   VAL A1564 " --> pdb=" O   GLN A1575 " (cutoff:3.500A)
      removed outlier: 5.396A  pdb=" N   GLN A1575 " --> pdb=" O   VAL A1564 " (cutoff:3.500A)
      removed outlier: 7.719A  pdb=" N   ASN A1566 " --> pdb=" O   GLU A1573 " (cutoff:3.500A)
      removed outlier: 6.309A  pdb=" N   GLU A1573 " --> pdb=" O   ASN A1566 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 1584 through 1590
      removed outlier: 3.941A  pdb=" N   CYS A1586 " --> pdb=" O   ALA A1597 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   LYS A1602 " --> pdb=" O   THR A1598 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 1627 through 1635
      removed outlier: 6.724A  pdb=" N   GLY A1646 " --> pdb=" O   THR A1628 " (cutoff:3.500A)
      removed outlier: 4.387A  pdb=" N   PHE A1630 " --> pdb=" O   LEU A1644 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   LEU A1644 " --> pdb=" O   PHE A1630 " (cutoff:3.500A)
      removed outlier: 4.261A  pdb=" N   ALA A1632 " --> pdb=" O   LEU A1642 " (cutoff:3.500A)
      removed outlier: 6.481A  pdb=" N   LEU A1642 " --> pdb=" O   ALA A1632 " (cutoff:3.500A)
      removed outlier: 7.025A  pdb=" N   SER A1640 " --> pdb=" O   PRO A1634 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 1627 through 1635
      removed outlier: 6.724A  pdb=" N   GLY A1646 " --> pdb=" O   THR A1628 " (cutoff:3.500A)
      removed outlier: 4.387A  pdb=" N   PHE A1630 " --> pdb=" O   LEU A1644 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   LEU A1644 " --> pdb=" O   PHE A1630 " (cutoff:3.500A)
      removed outlier: 4.261A  pdb=" N   ALA A1632 " --> pdb=" O   LEU A1642 " (cutoff:3.500A)
      removed outlier: 6.481A  pdb=" N   LEU A1642 " --> pdb=" O   ALA A1632 " (cutoff:3.500A)
      removed outlier: 7.025A  pdb=" N   SER A1640 " --> pdb=" O   PRO A1634 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'A' and resid 1696 through 1699
      removed outlier: 6.426A  pdb=" N   ASP A1717 " --> pdb=" O   ILE A1723 " (cutoff:3.500A)
      removed outlier: 6.191A  pdb=" N   ILE A1723 " --> pdb=" O   ASP A1717 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'A' and resid 1736 through 1743
      removed outlier: 3.907A  pdb=" N   SER A1738 " --> pdb=" O   LEU A1754 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   VAL A1750 " --> pdb=" O   SER A1742 " (cutoff:3.500A)
      removed outlier: 4.362A  pdb=" N   SER A1760 " --> pdb=" O   ASP A1755 " (cutoff:3.500A)
      removed outlier: 6.928A  pdb=" N   LEU A1761 " --> pdb=" O   ARG A1774 " (cutoff:3.500A)
      removed outlier: 4.625A  pdb=" N   ARG A1774 " --> pdb=" O   LEU A1761 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   MET A1763 " --> pdb=" O   CYS A1772 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'A' and resid 1786 through 1789
      removed outlier: 7.075A  pdb=" N   VAL A1930 " --> pdb=" O   ILE A1945 " (cutoff:3.500A)
      removed outlier: 4.897A  pdb=" N   VAL A1947 " --> pdb=" O   VAL A1928 " (cutoff:3.500A)
      removed outlier: 6.754A  pdb=" N   VAL A1928 " --> pdb=" O   VAL A1947 " (cutoff:3.500A)

    600 hydrogen bonds defined for protein.
    1602 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: 4.59

  Time building geometry restraints manager: 1.54 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4540
        1.34 -     1.46: 3037
        1.46 -     1.58: 6465
        1.58 -     1.70: 3
        1.70 -     1.82: 126
  Bond restraints: 14171
  Sorted by residual:
  bond pdb=" N   ASP A 886 "
       pdb=" CA  ASP A 886 "
    ideal  model  delta    sigma   weight residual
    1.456  1.486 -0.030 1.26e-02 6.30e+03 5.81e+00
  bond pdb=" C   HIS A 343 "
       pdb=" N   LEU A 344 "
    ideal  model  delta    sigma   weight residual
    1.330  1.302  0.028 1.47e-02 4.63e+03 3.73e+00
  bond pdb=" N   GLU A1160 "
       pdb=" CA  GLU A1160 "
    ideal  model  delta    sigma   weight residual
    1.455  1.477 -0.022 1.29e-02 6.01e+03 2.95e+00
  bond pdb=" CB  TRP A 155 "
       pdb=" CG  TRP A 155 "
    ideal  model  delta    sigma   weight residual
    1.498  1.448  0.050 3.10e-02 1.04e+03 2.63e+00
  bond pdb=" C   GLU A1160 "
       pdb=" N   GLN A1161 "
    ideal  model  delta    sigma   weight residual
    1.332  1.312  0.020 1.26e-02 6.30e+03 2.40e+00
  ... (remaining 14166 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.63: 18555
        1.63 -     3.25: 515
        3.25 -     4.88: 137
        4.88 -     6.50: 14
        6.50 -     8.13: 2
  Bond angle restraints: 19223
  Sorted by residual:
  angle pdb=" C   ALA A 985 "
        pdb=" CA  ALA A 985 "
        pdb=" CB  ALA A 985 "
      ideal   model   delta    sigma   weight residual
     116.54  112.30    4.24 1.15e+00 7.56e-01 1.36e+01
  angle pdb=" N   VAL A 411 "
        pdb=" CA  VAL A 411 "
        pdb=" C   VAL A 411 "
      ideal   model   delta    sigma   weight residual
     111.91  109.03    2.88 8.90e-01 1.26e+00 1.05e+01
  angle pdb=" N   GLY A 595 "
        pdb=" CA  GLY A 595 "
        pdb=" C   GLY A 595 "
      ideal   model   delta    sigma   weight residual
     112.50  116.12   -3.62 1.16e+00 7.43e-01 9.77e+00
  angle pdb=" N   ASN A 749 "
        pdb=" CA  ASN A 749 "
        pdb=" C   ASN A 749 "
      ideal   model   delta    sigma   weight residual
     112.59  108.81    3.78 1.22e+00 6.72e-01 9.60e+00
  angle pdb=" C   GLN A1491 "
        pdb=" N   PHE A1492 "
        pdb=" CA  PHE A1492 "
      ideal   model   delta    sigma   weight residual
     122.62  117.71    4.91 1.63e+00 3.76e-01 9.06e+00
  ... (remaining 19218 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.90: 8050
       17.90 -    35.80: 439
       35.80 -    53.70: 63
       53.70 -    71.60: 23
       71.60 -    89.50: 11
  Dihedral angle restraints: 8586
    sinusoidal: 3491
      harmonic: 5095
  Sorted by residual:
  dihedral pdb=" CA  ALA A 985 "
           pdb=" C   ALA A 985 "
           pdb=" N   ASN A 986 "
           pdb=" CA  ASN A 986 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.13   23.87     0      5.00e+00 4.00e-02 2.28e+01
  dihedral pdb=" CA  LEU A 301 "
           pdb=" C   LEU A 301 "
           pdb=" N   ILE A 302 "
           pdb=" CA  ILE A 302 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.20  -20.80     0      5.00e+00 4.00e-02 1.73e+01
  dihedral pdb=" CA  CYS A1666 "
           pdb=" C   CYS A1666 "
           pdb=" N   SER A1667 "
           pdb=" CA  SER A1667 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.40   17.60     0      5.00e+00 4.00e-02 1.24e+01
  ... (remaining 8583 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 1332
       0.031 -    0.063: 552
       0.063 -    0.094: 156
       0.094 -    0.125: 103
       0.125 -    0.156: 29
  Chirality restraints: 2172
  Sorted by residual:
  chirality pdb=" CA  ILE A1716 "
            pdb=" N   ILE A1716 "
            pdb=" C   ILE A1716 "
            pdb=" CB  ILE A1716 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.11e-01
  chirality pdb=" CA  ILE A 843 "
            pdb=" N   ILE A 843 "
            pdb=" C   ILE A 843 "
            pdb=" CB  ILE A 843 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.86e-01
  chirality pdb=" CA  VAL A1970 "
            pdb=" N   VAL A1970 "
            pdb=" C   VAL A1970 "
            pdb=" CB  VAL A1970 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.58e-01
  ... (remaining 2169 not shown)

  Planarity restraints: 2462
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A1492 "    0.016 2.00e-02 2.50e+03   1.71e-02 5.14e+00
        pdb=" CG  PHE A1492 "   -0.039 2.00e-02 2.50e+03
        pdb=" CD1 PHE A1492 "    0.013 2.00e-02 2.50e+03
        pdb=" CD2 PHE A1492 "    0.005 2.00e-02 2.50e+03
        pdb=" CE1 PHE A1492 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE A1492 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ  PHE A1492 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 299 "    0.021 2.00e-02 2.50e+03   1.39e-02 4.84e+00
        pdb=" CG  TRP A 299 "   -0.035 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 299 "    0.008 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 299 "   -0.003 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 299 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 299 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 299 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 299 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 299 "   -0.008 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 299 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A1921 "    0.035 5.00e-02 4.00e+02   5.38e-02 4.62e+00
        pdb=" N   PRO A1922 "   -0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO A1922 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A1922 "    0.030 5.00e-02 4.00e+02
  ... (remaining 2459 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 381
        2.69 -     3.25: 14182
        3.25 -     3.80: 22134
        3.80 -     4.35: 29147
        4.35 -     4.90: 47406
  Nonbonded interactions: 113250
  Sorted by model distance:
  nonbonded pdb=" O   PHE A1065 "
            pdb=" OG1 THR A1066 "
     model   vdw
     2.143 3.040
  nonbonded pdb=" O   PRO A 683 "
            pdb=" OG  SER A 686 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" OE1 GLU A1160 "
            pdb=" OH  TYR A1162 "
     model   vdw
     2.246 3.040
  nonbonded pdb=" N   GLN A1486 "
            pdb=" OE2 GLU A1489 "
     model   vdw
     2.290 3.120
  nonbonded pdb=" O   CYS A1777 "
            pdb=" NH2 ARG A1923 "
     model   vdw
     2.330 3.120
  ... (remaining 113245 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.960
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     16.370
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  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:1.510
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.160
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7661
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      :  0.004   0.050  14171  Z= 0.167
  Angle     :  0.703   8.129  19223  Z= 0.386
  Chirality :  0.044   0.156   2172
  Planarity :  0.005   0.054   2462
  Dihedral  : 12.112  89.500   5278
  Min Nonbonded Distance : 2.143

Molprobity Statistics.
  All-atom Clashscore : 3.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.13 %
    Favored  : 99.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.30 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.12 (0.20), residues: 1731
  helix:  0.82 (0.22), residues: 545
  sheet: -0.79 (0.29), residues: 302
  loop : -0.28 (0.22), residues: 884

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 110 
 TYR   0.020   0.002   TYR A 105 
 PHE   0.039   0.002   PHE A1492 
 TRP   0.035   0.002   TRP A 299 
 HIS   0.004   0.001   HIS A1956 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 (14171)
  covalent geometry    : angle       0.70287 (19223)
  hydrogen bonds       : bond        0.15107 (  591)
  hydrogen bonds       : angle       7.16414 ( 1602)

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

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

  3462 Ramachandran restraints generated.
    1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3462 Ramachandran restraints generated.
    1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  345 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 345
  time to evaluate  : 0.552 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 VAL cc_start: 0.9128 (t) cc_final: 0.8853 (t)
REVERT: A  262 HIS cc_start: 0.8954 (m-70) cc_final: 0.8377 (m-70)
REVERT: A  290 LEU cc_start: 0.5740 (mt) cc_final: 0.5296 (mt)
REVERT: A  333 GLU cc_start: 0.8302 (tm-30) cc_final: 0.6970 (mp0)
REVERT: A  348 PHE cc_start: 0.8432 (m-10) cc_final: 0.8045 (m-80)
REVERT: A  387 ILE cc_start: 0.9201 (pt) cc_final: 0.8896 (mt)
REVERT: A  389 ASP cc_start: 0.8763 (m-30) cc_final: 0.8512 (m-30)
REVERT: A  500 LYS cc_start: 0.8410 (mmtt) cc_final: 0.8200 (mmtt)
REVERT: A  622 MET cc_start: 0.9398 (mmm) cc_final: 0.8775 (mmt)
REVERT: A  654 LEU cc_start: 0.9493 (tp) cc_final: 0.9262 (tt)
REVERT: A  658 LEU cc_start: 0.9336 (mt) cc_final: 0.8944 (mt)
REVERT: A  710 ASN cc_start: 0.8713 (m110) cc_final: 0.8012 (m110)
REVERT: A  877 GLN cc_start: 0.9089 (tt0) cc_final: 0.8716 (tp-100)
REVERT: A  891 GLU cc_start: 0.8186 (mp0) cc_final: 0.7897 (pm20)
REVERT: A 1091 LEU cc_start: 0.9219 (tp) cc_final: 0.8995 (tp)
REVERT: A 1127 PHE cc_start: 0.7678 (m-10) cc_final: 0.7412 (m-10)
REVERT: A 1239 GLU cc_start: 0.7534 (tm-30) cc_final: 0.7020 (tm-30)
REVERT: A 1405 ILE cc_start: 0.8582 (pt) cc_final: 0.8213 (mm)
REVERT: A 1502 CYS cc_start: 0.7519 (m) cc_final: 0.7253 (m)
REVERT: A 1521 LYS cc_start: 0.8336 (tttt) cc_final: 0.7764 (tptp)
REVERT: A 1529 MET cc_start: 0.8376 (mtm) cc_final: 0.7888 (mtm)
REVERT: A 1611 MET cc_start: 0.9178 (mmp) cc_final: 0.8800 (mmm)
REVERT: A 1707 TYR cc_start: 0.8279 (p90) cc_final: 0.8018 (p90)
REVERT: A 1763 MET cc_start: 0.8280 (tmm) cc_final: 0.7787 (tmm)
REVERT: A 1913 LEU cc_start: 0.9091 (mp) cc_final: 0.8809 (mm)
REVERT: A 1961 ASP cc_start: 0.8800 (t0) cc_final: 0.8356 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 345
  average time/residue: 0.1105
  time to fit residues: 57.2583
Evaluate side-chains
  264 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 264
  time to evaluate  : 0.534 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 98 optimal weight:    0.8980
   chunk 107 optimal weight:    6.9990
   chunk 10 optimal weight:    0.7980
   chunk 66 optimal weight:    3.9990
   chunk 130 optimal weight:    0.5980
   chunk 124 optimal weight:    0.9990
   chunk 103 optimal weight:    0.5980
   chunk 77 optimal weight:   10.0000
   chunk 122 optimal weight:    0.8980
   chunk 91 optimal weight:    6.9990
   chunk 149 optimal weight:    3.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 460 ASN
** A 993 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1008 HIS
A1328 HIS
** A1471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1999 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.105763 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.084161 restraints weight = 43485.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.087017 restraints weight = 26274.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.089076 restraints weight = 18491.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.090507 restraints weight = 14376.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.091475 restraints weight = 11982.591|
|-----------------------------------------------------------------------------|
r_work (final): 0.3454
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7769
moved from start:          0.1744

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.072  14171  Z= 0.133
  Angle     :  0.607   7.391  19223  Z= 0.309
  Chirality :  0.044   0.178   2172
  Planarity :  0.004   0.044   2462
  Dihedral  :  4.624  30.937   1895
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  2.28 %
    Favored  : 97.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.30 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.01 (0.20), residues: 1731
  helix:  0.96 (0.22), residues: 570
  sheet: -0.70 (0.28), residues: 316
  loop : -0.29 (0.22), residues: 845

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  67 
 TYR   0.021   0.001   TYR A 971 
 PHE   0.021   0.002   PHE A1492 
 TRP   0.043   0.002   TRP A1706 
 HIS   0.003   0.001   HIS A 821 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 (14171)
  covalent geometry    : angle       0.60650 (19223)
  hydrogen bonds       : bond        0.04083 (  591)
  hydrogen bonds       : angle       5.46866 ( 1602)

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

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

  3462 Ramachandran restraints generated.
    1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3462 Ramachandran restraints generated.
    1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  320 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 317
  time to evaluate  : 0.561 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  156 MET cc_start: 0.8152 (mtt) cc_final: 0.7933 (mtt)
REVERT: A  262 HIS cc_start: 0.8887 (m-70) cc_final: 0.8356 (m90)
REVERT: A  333 GLU cc_start: 0.8055 (tm-30) cc_final: 0.7178 (mp0)
REVERT: A  387 ILE cc_start: 0.9278 (pt) cc_final: 0.8917 (mt)
REVERT: A  389 ASP cc_start: 0.8532 (m-30) cc_final: 0.7938 (m-30)
REVERT: A  395 LEU cc_start: 0.9202 (mt) cc_final: 0.8954 (mt)
REVERT: A  413 ARG cc_start: 0.8502 (mtt180) cc_final: 0.7531 (tpm170)
REVERT: A  429 CYS cc_start: 0.8129 (t) cc_final: 0.7392 (m)
REVERT: A  500 LYS cc_start: 0.8740 (mmtt) cc_final: 0.8330 (mmtt)
REVERT: A  503 ASP cc_start: 0.8420 (t0) cc_final: 0.7980 (t0)
REVERT: A  584 LEU cc_start: 0.7723 (mt) cc_final: 0.7048 (tt)
REVERT: A  622 MET cc_start: 0.9331 (mmm) cc_final: 0.8768 (mmt)
REVERT: A  654 LEU cc_start: 0.9489 (tp) cc_final: 0.9212 (tt)
REVERT: A  658 LEU cc_start: 0.9244 (mt) cc_final: 0.8819 (mt)
REVERT: A  706 MET cc_start: 0.8658 (ptm) cc_final: 0.8279 (ppp)
REVERT: A  710 ASN cc_start: 0.8770 (m110) cc_final: 0.7336 (m110)
REVERT: A  749 ASN cc_start: 0.8308 (t0) cc_final: 0.8102 (t0)
REVERT: A  877 GLN cc_start: 0.9041 (tt0) cc_final: 0.8694 (tp-100)
REVERT: A  891 GLU cc_start: 0.8162 (mp0) cc_final: 0.7908 (pm20)
REVERT: A  905 THR cc_start: 0.9011 (m) cc_final: 0.8515 (m)
REVERT: A 1091 LEU cc_start: 0.9123 (tp) cc_final: 0.8895 (tp)
REVERT: A 1239 GLU cc_start: 0.7573 (tm-30) cc_final: 0.7115 (tm-30)
REVERT: A 1248 LEU cc_start: 0.9069 (mt) cc_final: 0.8597 (mt)
REVERT: A 1521 LYS cc_start: 0.8342 (tttt) cc_final: 0.7736 (tptp)
REVERT: A 1553 TRP cc_start: 0.6799 (m100) cc_final: 0.6276 (m100)
REVERT: A 1611 MET cc_start: 0.9004 (mmp) cc_final: 0.8517 (mmm)
REVERT: A 1735 MET cc_start: 0.8805 (pmm) cc_final: 0.8538 (pmm)
REVERT: A 1763 MET cc_start: 0.8523 (tmm) cc_final: 0.8285 (tmm)
REVERT: A 1913 LEU cc_start: 0.9174 (mp) cc_final: 0.8808 (mt)
REVERT: A 1959 LEU cc_start: 0.8338 (tp) cc_final: 0.8009 (tp)
REVERT: A 1995 ASP cc_start: 0.8501 (t70) cc_final: 0.7568 (t0)
REVERT: A 1999 GLN cc_start: 0.9103 (mt0) cc_final: 0.8822 (mt0)
  outliers start: 3
  outliers final: 1
  residues processed: 318
  average time/residue: 0.1092
  time to fit residues: 52.8032
Evaluate side-chains
  251 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 250
  time to evaluate  : 0.544 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 133 optimal weight:    5.9990
   chunk 58 optimal weight:    0.1980
   chunk 14 optimal weight:    2.9990
   chunk 17 optimal weight:    0.0980
   chunk 113 optimal weight:    6.9990
   chunk 99 optimal weight:    8.9990
   chunk 120 optimal weight:    5.9990
   chunk 131 optimal weight:    0.9980
   chunk 77 optimal weight:    7.9990
   chunk 156 optimal weight:    1.9990
   chunk 76 optimal weight:    0.9990
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
A 154 ASN
A 216 HIS
** A 993 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1008 HIS
A1300 ASN
A1591 GLN
** A1940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.105402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.083663 restraints weight = 44150.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.086424 restraints weight = 26910.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.088343 restraints weight = 19164.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.089719 restraints weight = 15110.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.090664 restraints weight = 12696.489|
|-----------------------------------------------------------------------------|
r_work (final): 0.3435
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7801
moved from start:          0.2288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  14171  Z= 0.124
  Angle     :  0.583   7.631  19223  Z= 0.295
  Chirality :  0.044   0.208   2172
  Planarity :  0.004   0.067   2462
  Dihedral  :  4.476  28.348   1895
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  2.60 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.30 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.02 (0.20), residues: 1731
  helix:  1.06 (0.22), residues: 571
  sheet: -0.72 (0.28), residues: 322
  loop : -0.31 (0.22), residues: 838

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1493 
 TYR   0.019   0.001   TYR A 890 
 PHE   0.017   0.002   PHE A 403 
 TRP   0.038   0.002   TRP A1503 
 HIS   0.004   0.001   HIS A 802 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 (14171)
  covalent geometry    : angle       0.58296 (19223)
  hydrogen bonds       : bond        0.03780 (  591)
  hydrogen bonds       : angle       5.22352 ( 1602)

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

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

  3462 Ramachandran restraints generated.
    1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3462 Ramachandran restraints generated.
    1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  304 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 304
  time to evaluate  : 0.559 
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  136 VAL cc_start: 0.9160 (t) cc_final: 0.8825 (t)
REVERT: A  214 LEU cc_start: 0.8713 (tp) cc_final: 0.8350 (tp)
REVERT: A  262 HIS cc_start: 0.8928 (m-70) cc_final: 0.8516 (m-70)
REVERT: A  333 GLU cc_start: 0.7578 (tm-30) cc_final: 0.7071 (mp0)
REVERT: A  387 ILE cc_start: 0.9235 (pt) cc_final: 0.8920 (mt)
REVERT: A  389 ASP cc_start: 0.8537 (m-30) cc_final: 0.7915 (m-30)
REVERT: A  413 ARG cc_start: 0.8472 (mtt180) cc_final: 0.7583 (tpm170)
REVERT: A  429 CYS cc_start: 0.8421 (t) cc_final: 0.7432 (m)
REVERT: A  434 ARG cc_start: 0.7070 (mtp85) cc_final: 0.6676 (tpm170)
REVERT: A  500 LYS cc_start: 0.8740 (mmtt) cc_final: 0.8365 (mmtt)
REVERT: A  503 ASP cc_start: 0.8379 (t0) cc_final: 0.7944 (t0)
REVERT: A  584 LEU cc_start: 0.7741 (mt) cc_final: 0.7376 (mt)
REVERT: A  654 LEU cc_start: 0.9465 (tp) cc_final: 0.9137 (tt)
REVERT: A  658 LEU cc_start: 0.9217 (mt) cc_final: 0.8928 (mt)
REVERT: A  706 MET cc_start: 0.8563 (ptm) cc_final: 0.8171 (ppp)
REVERT: A  710 ASN cc_start: 0.8649 (m110) cc_final: 0.7159 (m110)
REVERT: A  877 GLN cc_start: 0.9000 (tt0) cc_final: 0.8670 (tp-100)
REVERT: A  891 GLU cc_start: 0.8174 (mp0) cc_final: 0.7888 (pm20)
REVERT: A  905 THR cc_start: 0.9088 (m) cc_final: 0.8769 (m)
REVERT: A 1072 ARG cc_start: 0.7393 (tpp80) cc_final: 0.7184 (tpp80)
REVERT: A 1074 SER cc_start: 0.8662 (m) cc_final: 0.8146 (m)
REVERT: A 1091 LEU cc_start: 0.9107 (tp) cc_final: 0.8877 (tp)
REVERT: A 1130 MET cc_start: 0.8700 (tpp) cc_final: 0.8458 (tpp)
REVERT: A 1239 GLU cc_start: 0.7531 (tm-30) cc_final: 0.7154 (tm-30)
REVERT: A 1248 LEU cc_start: 0.9197 (mt) cc_final: 0.8985 (mt)
REVERT: A 1452 MET cc_start: 0.8574 (tpt) cc_final: 0.8067 (tmm)
REVERT: A 1476 LEU cc_start: 0.9120 (mt) cc_final: 0.8567 (pp)
REVERT: A 1501 GLU cc_start: 0.7881 (tp30) cc_final: 0.7553 (tp30)
REVERT: A 1521 LYS cc_start: 0.8402 (tttt) cc_final: 0.7917 (tptp)
REVERT: A 1529 MET cc_start: 0.8492 (mtm) cc_final: 0.8193 (mpp)
REVERT: A 1611 MET cc_start: 0.9012 (mmp) cc_final: 0.8676 (mmm)
REVERT: A 1707 TYR cc_start: 0.7981 (p90) cc_final: 0.7691 (p90)
REVERT: A 1735 MET cc_start: 0.8736 (pmm) cc_final: 0.8535 (pmm)
REVERT: A 1959 LEU cc_start: 0.8298 (tp) cc_final: 0.7950 (tp)
REVERT: A 1995 ASP cc_start: 0.8432 (t70) cc_final: 0.7330 (t0)
REVERT: A 1999 GLN cc_start: 0.9013 (mt0) cc_final: 0.8702 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 304
  average time/residue: 0.1073
  time to fit residues: 49.8189
Evaluate side-chains
  239 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 239
  time to evaluate  : 0.520 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 92 optimal weight:    0.6980
   chunk 66 optimal weight:    0.8980
   chunk 102 optimal weight:    0.7980
   chunk 128 optimal weight:    2.9990
   chunk 120 optimal weight:    6.9990
   chunk 46 optimal weight:    0.9990
   chunk 119 optimal weight:    0.9980
   chunk 34 optimal weight:    5.9990
   chunk 101 optimal weight:    0.9980
   chunk 117 optimal weight:    3.9990
   chunk 58 optimal weight:    7.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** A 993 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1008 HIS
A1591 GLN
** A1688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1940 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.105052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.083298 restraints weight = 44278.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.086101 restraints weight = 27250.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.088042 restraints weight = 19435.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.089371 restraints weight = 15277.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.090320 restraints weight = 12863.274|
|-----------------------------------------------------------------------------|
r_work (final): 0.3430
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7821
moved from start:          0.2776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  14171  Z= 0.117
  Angle     :  0.566   7.470  19223  Z= 0.286
  Chirality :  0.043   0.212   2172
  Planarity :  0.004   0.042   2462
  Dihedral  :  4.404  26.581   1895
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  2.60 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.30 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.13 (0.20), residues: 1731
  helix:  1.09 (0.22), residues: 566
  sheet: -0.47 (0.29), residues: 308
  loop : -0.29 (0.22), residues: 857

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1493 
 TYR   0.014   0.001   TYR A 219 
 PHE   0.025   0.002   PHE A1492 
 TRP   0.029   0.002   TRP A 448 
 HIS   0.007   0.001   HIS A 802 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 (14171)
  covalent geometry    : angle       0.56566 (19223)
  hydrogen bonds       : bond        0.03533 (  591)
  hydrogen bonds       : angle       5.09913 ( 1602)

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

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

  3462 Ramachandran restraints generated.
    1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3462 Ramachandran restraints generated.
    1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  295 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 295
  time to evaluate  : 0.539 
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  156 MET cc_start: 0.8192 (mtt) cc_final: 0.7897 (mtt)
REVERT: A  262 HIS cc_start: 0.8935 (m-70) cc_final: 0.8493 (m-70)
REVERT: A  333 GLU cc_start: 0.7713 (tm-30) cc_final: 0.7190 (mp0)
REVERT: A  361 LYS cc_start: 0.9321 (mttp) cc_final: 0.8884 (mmtp)
REVERT: A  387 ILE cc_start: 0.9381 (pt) cc_final: 0.8983 (mt)
REVERT: A  389 ASP cc_start: 0.8655 (m-30) cc_final: 0.7890 (m-30)
REVERT: A  413 ARG cc_start: 0.8499 (mtt180) cc_final: 0.7547 (tpm170)
REVERT: A  429 CYS cc_start: 0.8427 (t) cc_final: 0.7661 (m)
REVERT: A  434 ARG cc_start: 0.7157 (mtp85) cc_final: 0.6531 (tpm170)
REVERT: A  500 LYS cc_start: 0.8713 (mmtt) cc_final: 0.8342 (mmtt)
REVERT: A  503 ASP cc_start: 0.8568 (t0) cc_final: 0.8075 (t0)
REVERT: A  584 LEU cc_start: 0.7813 (mt) cc_final: 0.7486 (mt)
REVERT: A  622 MET cc_start: 0.9468 (mmm) cc_final: 0.9014 (mmt)
REVERT: A  706 MET cc_start: 0.8458 (ptm) cc_final: 0.8208 (ppp)
REVERT: A  710 ASN cc_start: 0.8673 (m110) cc_final: 0.7277 (m110)
REVERT: A  905 THR cc_start: 0.9050 (m) cc_final: 0.8753 (m)
REVERT: A 1074 SER cc_start: 0.8545 (m) cc_final: 0.7841 (m)
REVERT: A 1239 GLU cc_start: 0.7591 (tm-30) cc_final: 0.7200 (tm-30)
REVERT: A 1300 ASN cc_start: 0.8785 (m-40) cc_final: 0.8389 (m-40)
REVERT: A 1325 ILE cc_start: 0.8613 (pt) cc_final: 0.8343 (mt)
REVERT: A 1393 LEU cc_start: 0.8988 (mm) cc_final: 0.8765 (mm)
REVERT: A 1452 MET cc_start: 0.8702 (tpt) cc_final: 0.8162 (tmm)
REVERT: A 1501 GLU cc_start: 0.7698 (tp30) cc_final: 0.7390 (tp30)
REVERT: A 1611 MET cc_start: 0.8970 (mmp) cc_final: 0.8636 (mmm)
REVERT: A 1735 MET cc_start: 0.8769 (pmm) cc_final: 0.8567 (pmm)
REVERT: A 1754 LEU cc_start: 0.8973 (tp) cc_final: 0.8587 (mp)
REVERT: A 1959 LEU cc_start: 0.8318 (tp) cc_final: 0.7938 (tp)
REVERT: A 1995 ASP cc_start: 0.8409 (t70) cc_final: 0.7298 (t0)
REVERT: A 1999 GLN cc_start: 0.8983 (mt0) cc_final: 0.8680 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 295
  average time/residue: 0.1068
  time to fit residues: 47.9289
Evaluate side-chains
  233 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 233
  time to evaluate  : 0.569 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 47 optimal weight:    0.6980
   chunk 72 optimal weight:    0.7980
   chunk 157 optimal weight:    0.9990
   chunk 11 optimal weight:    5.9990
   chunk 65 optimal weight:    0.9980
   chunk 6 optimal weight:    2.9990
   chunk 19 optimal weight:    0.0070
   chunk 1 optimal weight:   10.0000
   chunk 3 optimal weight:    5.9990
   chunk 50 optimal weight:    3.9990
   chunk 64 optimal weight:    2.9990
   overall best weight:    0.7000

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

Flipped N/Q/H residues before XYZ refinement:
A 154 ASN
** A 993 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1688 GLN ** 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 = 0.3707 r_free = 0.3707 target = 0.105432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.083780 restraints weight = 44100.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.086544 restraints weight = 27323.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.088468 restraints weight = 19518.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.089835 restraints weight = 15359.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.090830 restraints weight = 12861.161|
|-----------------------------------------------------------------------------|
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
moved from start:          0.3132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  14171  Z= 0.105
  Angle     :  0.551   7.739  19223  Z= 0.277
  Chirality :  0.043   0.185   2172
  Planarity :  0.004   0.045   2462
  Dihedral  :  4.275  24.696   1895
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  2.43 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.30 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.25 (0.21), residues: 1731
  helix:  1.29 (0.22), residues: 557
  sheet: -0.47 (0.29), residues: 313
  loop : -0.25 (0.22), residues: 861

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1592 
 TYR   0.011   0.001   TYR A1707 
 PHE   0.026   0.002   PHE A1132 
 TRP   0.028   0.002   TRP A1503 
 HIS   0.007   0.001   HIS A 802 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 (14171)
  covalent geometry    : angle       0.55089 (19223)
  hydrogen bonds       : bond        0.03322 (  591)
  hydrogen bonds       : angle       4.96125 ( 1602)

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

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

  3462 Ramachandran restraints generated.
    1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3462 Ramachandran restraints generated.
    1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  298 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 298
  time to evaluate  : 0.629 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 VAL cc_start: 0.9124 (t) cc_final: 0.8791 (t)
REVERT: A  156 MET cc_start: 0.8167 (mtt) cc_final: 0.7893 (mtt)
REVERT: A  262 HIS cc_start: 0.8895 (m-70) cc_final: 0.8446 (m-70)
REVERT: A  333 GLU cc_start: 0.7686 (tm-30) cc_final: 0.7247 (mp0)
REVERT: A  361 LYS cc_start: 0.9374 (mttp) cc_final: 0.8898 (mmtp)
REVERT: A  389 ASP cc_start: 0.8643 (m-30) cc_final: 0.7892 (m-30)
REVERT: A  413 ARG cc_start: 0.8474 (mtt180) cc_final: 0.7535 (tpm170)
REVERT: A  429 CYS cc_start: 0.8468 (t) cc_final: 0.7889 (m)
REVERT: A  434 ARG cc_start: 0.7121 (mtp85) cc_final: 0.6490 (tpm170)
REVERT: A  500 LYS cc_start: 0.8639 (mmtt) cc_final: 0.8190 (mmtt)
REVERT: A  503 ASP cc_start: 0.8678 (t0) cc_final: 0.8232 (t0)
REVERT: A  570 LEU cc_start: 0.8354 (mt) cc_final: 0.8154 (mt)
REVERT: A  658 LEU cc_start: 0.9136 (mm) cc_final: 0.8933 (mm)
REVERT: A  706 MET cc_start: 0.8434 (ptm) cc_final: 0.8119 (ppp)
REVERT: A  710 ASN cc_start: 0.8680 (m110) cc_final: 0.7350 (m110)
REVERT: A  905 THR cc_start: 0.9106 (m) cc_final: 0.8831 (m)
REVERT: A  948 VAL cc_start: 0.8251 (m) cc_final: 0.7637 (m)
REVERT: A 1239 GLU cc_start: 0.7514 (tm-30) cc_final: 0.7215 (tm-30)
REVERT: A 1299 LYS cc_start: 0.9277 (tmmt) cc_final: 0.8971 (mmmt)
REVERT: A 1499 MET cc_start: 0.8998 (ttp) cc_final: 0.8701 (tmm)
REVERT: A 1501 GLU cc_start: 0.7646 (tp30) cc_final: 0.7317 (tp30)
REVERT: A 1529 MET cc_start: 0.8533 (mtm) cc_final: 0.8145 (mpp)
REVERT: A 1611 MET cc_start: 0.8873 (mmp) cc_final: 0.8523 (mmm)
REVERT: A 1707 TYR cc_start: 0.7832 (p90) cc_final: 0.7506 (p90)
REVERT: A 1735 MET cc_start: 0.8730 (pmm) cc_final: 0.8510 (pmm)
REVERT: A 1913 LEU cc_start: 0.9125 (mt) cc_final: 0.8856 (mp)
REVERT: A 1953 LEU cc_start: 0.9024 (mm) cc_final: 0.8786 (mm)
REVERT: A 1959 LEU cc_start: 0.8270 (tp) cc_final: 0.8000 (tp)
REVERT: A 1999 GLN cc_start: 0.8957 (mt0) cc_final: 0.8502 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 298
  average time/residue: 0.1048
  time to fit residues: 47.8088
Evaluate side-chains
  233 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 233
  time to evaluate  : 0.535 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 15 optimal weight:    5.9990
   chunk 81 optimal weight:    1.9990
   chunk 97 optimal weight:    7.9990
   chunk 121 optimal weight:    1.9990
   chunk 162 optimal weight:    9.9990
   chunk 36 optimal weight:    5.9990
   chunk 102 optimal weight:    0.8980
   chunk 33 optimal weight:    8.9990
   chunk 119 optimal weight:    0.0050
   chunk 169 optimal weight:    4.9990
   chunk 71 optimal weight:    6.9990
   overall best weight:    1.9800

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

Flipped N/Q/H residues before XYZ refinement:
** A  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 262 HIS
** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 993 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1672 HIS
** A1688 GLN ** 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 = 0.3660 r_free = 0.3660 target = 0.102567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.080689 restraints weight = 44192.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.083320 restraints weight = 27629.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.085159 restraints weight = 20003.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.086448 restraints weight = 15919.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.087375 restraints weight = 13495.092|
|-----------------------------------------------------------------------------|
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7910
moved from start:          0.3412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  14171  Z= 0.180
  Angle     :  0.612   7.249  19223  Z= 0.310
  Chirality :  0.044   0.195   2172
  Planarity :  0.004   0.048   2462
  Dihedral  :  4.428  26.558   1895
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 10.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.30 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.12 (0.21), residues: 1731
  helix:  1.05 (0.22), residues: 566
  sheet: -0.48 (0.29), residues: 305
  loop : -0.27 (0.22), residues: 860

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1784 
 TYR   0.013   0.001   TYR A1450 
 PHE   0.018   0.002   PHE A1332 
 TRP   0.052   0.002   TRP A1503 
 HIS   0.006   0.001   HIS A 802 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 (14171)
  covalent geometry    : angle       0.61191 (19223)
  hydrogen bonds       : bond        0.03657 (  591)
  hydrogen bonds       : angle       5.03706 ( 1602)

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

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

  3462 Ramachandran restraints generated.
    1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3462 Ramachandran restraints generated.
    1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 270
  time to evaluate  : 0.586 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 VAL cc_start: 0.9131 (t) cc_final: 0.8805 (t)
REVERT: A  156 MET cc_start: 0.8285 (mtt) cc_final: 0.8009 (mtt)
REVERT: A  262 HIS cc_start: 0.8848 (m90) cc_final: 0.8539 (m-70)
REVERT: A  333 GLU cc_start: 0.7808 (tm-30) cc_final: 0.7258 (mp0)
REVERT: A  389 ASP cc_start: 0.8815 (m-30) cc_final: 0.8251 (m-30)
REVERT: A  413 ARG cc_start: 0.8592 (mtt180) cc_final: 0.7643 (tpm170)
REVERT: A  434 ARG cc_start: 0.7243 (mtp85) cc_final: 0.6544 (tpm170)
REVERT: A  476 MET cc_start: 0.8405 (ppp) cc_final: 0.8074 (ppp)
REVERT: A  500 LYS cc_start: 0.8740 (mmtt) cc_final: 0.8348 (mmtt)
REVERT: A  716 ASP cc_start: 0.8977 (t0) cc_final: 0.8774 (t0)
REVERT: A  905 THR cc_start: 0.9192 (m) cc_final: 0.8937 (m)
REVERT: A 1239 GLU cc_start: 0.7509 (tm-30) cc_final: 0.7082 (tm-30)
REVERT: A 1299 LYS cc_start: 0.9306 (tmmt) cc_final: 0.9090 (tmtt)
REVERT: A 1300 ASN cc_start: 0.9046 (m-40) cc_final: 0.8690 (m-40)
REVERT: A 1325 ILE cc_start: 0.8626 (pt) cc_final: 0.8383 (mt)
REVERT: A 1501 GLU cc_start: 0.7718 (tp30) cc_final: 0.7481 (tp30)
REVERT: A 1529 MET cc_start: 0.8560 (mtm) cc_final: 0.8267 (mtm)
REVERT: A 1582 MET cc_start: 0.5774 (tmm) cc_final: 0.5537 (tmm)
REVERT: A 1611 MET cc_start: 0.8939 (mmp) cc_final: 0.8665 (mmm)
REVERT: A 1707 TYR cc_start: 0.7835 (p90) cc_final: 0.7404 (p90)
REVERT: A 1716 ILE cc_start: 0.8826 (mt) cc_final: 0.7539 (mt)
REVERT: A 1735 MET cc_start: 0.8734 (pmm) cc_final: 0.8504 (pmm)
REVERT: A 1913 LEU cc_start: 0.9150 (mt) cc_final: 0.8863 (mm)
REVERT: A 1953 LEU cc_start: 0.9117 (mm) cc_final: 0.8914 (mm)
REVERT: A 1959 LEU cc_start: 0.8244 (tp) cc_final: 0.7944 (tp)
REVERT: A 1995 ASP cc_start: 0.8518 (t70) cc_final: 0.7448 (t0)
REVERT: A 1999 GLN cc_start: 0.9024 (mt0) cc_final: 0.8657 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 270
  average time/residue: 0.1045
  time to fit residues: 43.2881
Evaluate side-chains
  217 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 217
  time to evaluate  : 0.524 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 120 optimal weight:    4.9990
   chunk 15 optimal weight:    2.9990
   chunk 146 optimal weight:    7.9990
   chunk 97 optimal weight:    0.9980
   chunk 39 optimal weight:    4.9990
   chunk 83 optimal weight:    0.9990
   chunk 145 optimal weight:    0.8980
   chunk 3 optimal weight:    0.0980
   chunk 32 optimal weight:    0.4980
   chunk 10 optimal weight:    3.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
** A  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 993 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.104907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.083993 restraints weight = 43866.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.087055 restraints weight = 26960.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.089474 restraints weight = 17356.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.089985 restraints weight = 13448.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.090184 restraints weight = 12131.594|
|-----------------------------------------------------------------------------|
r_work (final): 0.3421
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7850
moved from start:          0.3655

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  14171  Z= 0.109
  Angle     :  0.572   7.381  19223  Z= 0.286
  Chirality :  0.043   0.203   2172
  Planarity :  0.004   0.048   2462
  Dihedral  :  4.307  24.218   1895
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.30 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.25 (0.21), residues: 1731
  helix:  1.22 (0.22), residues: 560
  sheet: -0.39 (0.29), residues: 312
  loop : -0.24 (0.22), residues: 859

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1493 
 TYR   0.017   0.001   TYR A  62 
 PHE   0.018   0.002   PHE A 403 
 TRP   0.035   0.002   TRP A1503 
 HIS   0.007   0.001   HIS A 802 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 (14171)
  covalent geometry    : angle       0.57193 (19223)
  hydrogen bonds       : bond        0.03295 (  591)
  hydrogen bonds       : angle       4.98042 ( 1602)

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

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

  3462 Ramachandran restraints generated.
    1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3462 Ramachandran restraints generated.
    1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  278 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 278
  time to evaluate  : 0.554 
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  156 MET cc_start: 0.8213 (mtt) cc_final: 0.7979 (mtt)
REVERT: A  262 HIS cc_start: 0.8720 (m90) cc_final: 0.8432 (m-70)
REVERT: A  333 GLU cc_start: 0.7779 (tm-30) cc_final: 0.7398 (mp0)
REVERT: A  384 GLU cc_start: 0.8723 (tm-30) cc_final: 0.8425 (tm-30)
REVERT: A  387 ILE cc_start: 0.9415 (pt) cc_final: 0.8978 (mt)
REVERT: A  389 ASP cc_start: 0.8697 (m-30) cc_final: 0.8388 (m-30)
REVERT: A  413 ARG cc_start: 0.8480 (mtt180) cc_final: 0.7954 (mtm-85)
REVERT: A  434 ARG cc_start: 0.7134 (mtp85) cc_final: 0.6548 (tpm170)
REVERT: A  472 LEU cc_start: 0.8318 (mt) cc_final: 0.8110 (mt)
REVERT: A  476 MET cc_start: 0.8543 (ppp) cc_final: 0.8308 (ppp)
REVERT: A  503 ASP cc_start: 0.8633 (t0) cc_final: 0.7938 (t0)
REVERT: A  504 LEU cc_start: 0.9443 (mt) cc_final: 0.9187 (tp)
REVERT: A 1091 LEU cc_start: 0.8969 (tp) cc_final: 0.8501 (tp)
REVERT: A 1239 GLU cc_start: 0.7529 (tm-30) cc_final: 0.7106 (tm-30)
REVERT: A 1299 LYS cc_start: 0.9216 (tmmt) cc_final: 0.8969 (tmtt)
REVERT: A 1300 ASN cc_start: 0.8942 (m-40) cc_final: 0.8399 (m-40)
REVERT: A 1325 ILE cc_start: 0.8561 (pt) cc_final: 0.8328 (mt)
REVERT: A 1390 ASP cc_start: 0.9111 (p0) cc_final: 0.8842 (p0)
REVERT: A 1501 GLU cc_start: 0.7595 (tp30) cc_final: 0.7352 (tp30)
REVERT: A 1520 MET cc_start: 0.8874 (mtp) cc_final: 0.8434 (mtm)
REVERT: A 1521 LYS cc_start: 0.8454 (tttt) cc_final: 0.8020 (tptp)
REVERT: A 1525 PHE cc_start: 0.9372 (t80) cc_final: 0.8483 (t80)
REVERT: A 1582 MET cc_start: 0.5778 (tmm) cc_final: 0.5541 (tmm)
REVERT: A 1611 MET cc_start: 0.8778 (mmp) cc_final: 0.8552 (mmm)
REVERT: A 1707 TYR cc_start: 0.7848 (p90) cc_final: 0.7502 (p90)
REVERT: A 1716 ILE cc_start: 0.8745 (mt) cc_final: 0.7487 (mt)
REVERT: A 1735 MET cc_start: 0.8714 (pmm) cc_final: 0.8478 (pmm)
REVERT: A 1913 LEU cc_start: 0.9146 (mt) cc_final: 0.8879 (mm)
REVERT: A 1995 ASP cc_start: 0.8503 (t70) cc_final: 0.6974 (t0)
REVERT: A 1999 GLN cc_start: 0.9002 (mt0) cc_final: 0.8586 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 278
  average time/residue: 0.1030
  time to fit residues: 44.5604
Evaluate side-chains
  224 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 224
  time to evaluate  : 0.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 169 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   chunk 13 optimal weight:    9.9990
   chunk 108 optimal weight:    0.0970
   chunk 25 optimal weight:    0.9990
   chunk 109 optimal weight:    0.7980
   chunk 85 optimal weight:    5.9990
   chunk 41 optimal weight:    4.9990
   chunk 102 optimal weight:    0.9980
   chunk 155 optimal weight:    2.9990
   chunk 48 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A  84 GLN
A 313 HIS
** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1688 GLN ** 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 = 0.3704 r_free = 0.3704 target = 0.105239 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.083831 restraints weight = 43660.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.086523 restraints weight = 27186.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.088404 restraints weight = 19555.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.089734 restraints weight = 15475.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.090647 restraints weight = 13035.732|
|-----------------------------------------------------------------------------|
r_work (final): 0.3433
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7849
moved from start:          0.3840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  14171  Z= 0.112
  Angle     :  0.570   7.652  19223  Z= 0.286
  Chirality :  0.043   0.212   2172
  Planarity :  0.004   0.055   2462
  Dihedral  :  4.195  22.397   1895
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 9.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.26 %
    Favored  : 99.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.30 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.27 (0.21), residues: 1731
  helix:  1.25 (0.22), residues: 564
  sheet: -0.39 (0.29), residues: 312
  loop : -0.24 (0.22), residues: 855

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1784 
 TYR   0.010   0.001   TYR A 920 
 PHE   0.032   0.002   PHE A1301 
 TRP   0.036   0.001   TRP A1503 
 HIS   0.006   0.001   HIS A 802 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 (14171)
  covalent geometry    : angle       0.57023 (19223)
  hydrogen bonds       : bond        0.03287 (  591)
  hydrogen bonds       : angle       4.90283 ( 1602)

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

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

  3462 Ramachandran restraints generated.
    1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3462 Ramachandran restraints generated.
    1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  280 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 280
  time to evaluate  : 0.542 
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  136 VAL cc_start: 0.9074 (t) cc_final: 0.8688 (t)
REVERT: A  262 HIS cc_start: 0.8759 (m90) cc_final: 0.8459 (m-70)
REVERT: A  333 GLU cc_start: 0.7697 (tm-30) cc_final: 0.7432 (mp0)
REVERT: A  384 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8405 (tm-30)
REVERT: A  387 ILE cc_start: 0.9414 (pt) cc_final: 0.9081 (mt)
REVERT: A  389 ASP cc_start: 0.8726 (m-30) cc_final: 0.8350 (m-30)
REVERT: A  413 ARG cc_start: 0.8589 (mtt180) cc_final: 0.7728 (mtp85)
REVERT: A  429 CYS cc_start: 0.8326 (t) cc_final: 0.7879 (m)
REVERT: A  434 ARG cc_start: 0.7228 (mtp85) cc_final: 0.6639 (tpm170)
REVERT: A  458 SER cc_start: 0.8974 (p) cc_final: 0.8764 (m)
REVERT: A  503 ASP cc_start: 0.8774 (t0) cc_final: 0.8099 (t0)
REVERT: A  504 LEU cc_start: 0.9431 (mt) cc_final: 0.9193 (tp)
REVERT: A  742 ASN cc_start: 0.9137 (m-40) cc_final: 0.8821 (m-40)
REVERT: A 1239 GLU cc_start: 0.7562 (tm-30) cc_final: 0.7187 (tm-30)
REVERT: A 1300 ASN cc_start: 0.9010 (m-40) cc_final: 0.8777 (m-40)
REVERT: A 1325 ILE cc_start: 0.8521 (pt) cc_final: 0.8311 (mt)
REVERT: A 1390 ASP cc_start: 0.9102 (p0) cc_final: 0.8834 (p0)
REVERT: A 1484 LEU cc_start: 0.8844 (tp) cc_final: 0.8575 (tp)
REVERT: A 1499 MET cc_start: 0.8865 (ttp) cc_final: 0.8211 (tmm)
REVERT: A 1501 GLU cc_start: 0.7583 (tp30) cc_final: 0.7363 (tp30)
REVERT: A 1521 LYS cc_start: 0.8461 (tttt) cc_final: 0.8032 (tptp)
REVERT: A 1707 TYR cc_start: 0.7840 (p90) cc_final: 0.7447 (p90)
REVERT: A 1716 ILE cc_start: 0.8715 (mt) cc_final: 0.7390 (mt)
REVERT: A 1735 MET cc_start: 0.8615 (pmm) cc_final: 0.8400 (pmm)
REVERT: A 1913 LEU cc_start: 0.9207 (mt) cc_final: 0.8985 (mp)
REVERT: A 1953 LEU cc_start: 0.9035 (mm) cc_final: 0.8764 (mm)
REVERT: A 1995 ASP cc_start: 0.8467 (t70) cc_final: 0.6948 (t0)
REVERT: A 1999 GLN cc_start: 0.9009 (mt0) cc_final: 0.8564 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 280
  average time/residue: 0.1044
  time to fit residues: 45.0650
Evaluate side-chains
  224 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 224
  time to evaluate  : 0.653 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 81 optimal weight:    2.9990
   chunk 45 optimal weight:    0.6980
   chunk 39 optimal weight:    4.9990
   chunk 114 optimal weight:    3.9990
   chunk 139 optimal weight:    0.0170
   chunk 76 optimal weight:    0.8980
   chunk 25 optimal weight:    2.9990
   chunk 16 optimal weight:    0.2980
   chunk 118 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9990
   chunk 19 optimal weight:    4.9990
   overall best weight:    0.5820

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

Flipped N/Q/H residues before XYZ refinement:
A1136 HIS
** A1587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1688 GLN ** 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 = 0.3710 r_free = 0.3710 target = 0.105711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.084308 restraints weight = 43942.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.087018 restraints weight = 27175.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.088967 restraints weight = 19478.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.090266 restraints weight = 15285.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.091243 restraints weight = 12904.817|
|-----------------------------------------------------------------------------|
r_work (final): 0.3449
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7831
moved from start:          0.4018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  14171  Z= 0.103
  Angle     :  0.578   7.778  19223  Z= 0.287
  Chirality :  0.043   0.221   2172
  Planarity :  0.004   0.057   2462
  Dihedral  :  4.119  22.476   1895
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  0.39 %
    Favored  : 99.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.30 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.23 (0.21), residues: 1731
  helix:  1.20 (0.22), residues: 564
  sheet: -0.39 (0.29), residues: 313
  loop : -0.25 (0.22), residues: 854

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1493 
 TYR   0.011   0.001   TYR A  62 
 PHE   0.027   0.002   PHE A 921 
 TRP   0.034   0.001   TRP A1503 
 HIS   0.006   0.001   HIS A 802 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 (14171)
  covalent geometry    : angle       0.57788 (19223)
  hydrogen bonds       : bond        0.03252 (  591)
  hydrogen bonds       : angle       4.87934 ( 1602)

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

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

  3462 Ramachandran restraints generated.
    1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3462 Ramachandran restraints generated.
    1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  284 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 283
  time to evaluate  : 0.558 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 VAL cc_start: 0.9035 (t) cc_final: 0.8601 (t)
REVERT: A  262 HIS cc_start: 0.8732 (m90) cc_final: 0.8465 (m-70)
REVERT: A  340 LYS cc_start: 0.7996 (mmtt) cc_final: 0.7503 (ptmt)
REVERT: A  361 LYS cc_start: 0.9384 (mttp) cc_final: 0.8939 (mmtp)
REVERT: A  384 GLU cc_start: 0.8607 (tm-30) cc_final: 0.8321 (tm-30)
REVERT: A  387 ILE cc_start: 0.9397 (pt) cc_final: 0.9083 (mt)
REVERT: A  389 ASP cc_start: 0.8712 (m-30) cc_final: 0.8181 (m-30)
REVERT: A  413 ARG cc_start: 0.8579 (mtt180) cc_final: 0.7747 (mtp85)
REVERT: A  429 CYS cc_start: 0.8358 (t) cc_final: 0.7926 (m)
REVERT: A  434 ARG cc_start: 0.7214 (mtp85) cc_final: 0.6623 (tpm170)
REVERT: A  476 MET cc_start: 0.8460 (ppp) cc_final: 0.8252 (ppp)
REVERT: A  503 ASP cc_start: 0.8757 (t0) cc_final: 0.7971 (t0)
REVERT: A  504 LEU cc_start: 0.9427 (mt) cc_final: 0.9206 (tp)
REVERT: A  712 CYS cc_start: 0.8841 (p) cc_final: 0.8572 (p)
REVERT: A 1153 SER cc_start: 0.8633 (t) cc_final: 0.8365 (p)
REVERT: A 1239 GLU cc_start: 0.7596 (tm-30) cc_final: 0.7225 (tm-30)
REVERT: A 1390 ASP cc_start: 0.9053 (p0) cc_final: 0.8835 (p0)
REVERT: A 1452 MET cc_start: 0.8866 (tpp) cc_final: 0.8630 (tpp)
REVERT: A 1499 MET cc_start: 0.8878 (ttp) cc_final: 0.8285 (tmm)
REVERT: A 1501 GLU cc_start: 0.7564 (tp30) cc_final: 0.7321 (tp30)
REVERT: A 1521 LYS cc_start: 0.8429 (tttt) cc_final: 0.8075 (tptp)
REVERT: A 1707 TYR cc_start: 0.7832 (p90) cc_final: 0.7458 (p90)
REVERT: A 1716 ILE cc_start: 0.8691 (mt) cc_final: 0.7399 (mt)
REVERT: A 1735 MET cc_start: 0.8630 (pmm) cc_final: 0.8411 (pmm)
REVERT: A 1913 LEU cc_start: 0.9192 (mt) cc_final: 0.8983 (mp)
REVERT: A 1953 LEU cc_start: 0.9021 (mm) cc_final: 0.8776 (mm)
REVERT: A 1995 ASP cc_start: 0.8475 (t70) cc_final: 0.6943 (t0)
REVERT: A 1999 GLN cc_start: 0.8959 (mt0) cc_final: 0.8540 (mt0)
  outliers start: 1
  outliers final: 1
  residues processed: 284
  average time/residue: 0.1018
  time to fit residues: 44.6420
Evaluate side-chains
  232 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 231
  time to evaluate  : 0.559 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 60 optimal weight:    0.4980
   chunk 173 optimal weight:    0.9980
   chunk 168 optimal weight:    5.9990
   chunk 15 optimal weight:    0.9990
   chunk 103 optimal weight:    0.5980
   chunk 111 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9980
   chunk 27 optimal weight:    9.9990
   chunk 45 optimal weight:    5.9990
   chunk 94 optimal weight:    0.6980
   chunk 104 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A1300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.105955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.084091 restraints weight = 43954.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.086892 restraints weight = 27256.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.088847 restraints weight = 19509.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.090202 restraints weight = 15351.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.091189 restraints weight = 12911.092|
|-----------------------------------------------------------------------------|
r_work (final): 0.3446
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
moved from start:          0.4190

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  14171  Z= 0.112
  Angle     :  0.591   8.213  19223  Z= 0.294
  Chirality :  0.043   0.228   2172
  Planarity :  0.004   0.057   2462
  Dihedral  :  4.124  22.405   1895
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 9.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.20 %
    Favored  : 99.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.30 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.20 (0.21), residues: 1731
  helix:  1.10 (0.22), residues: 570
  sheet: -0.30 (0.30), residues: 308
  loop : -0.27 (0.22), residues: 853

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1493 
 TYR   0.017   0.001   TYR A 720 
 PHE   0.029   0.002   PHE A 978 
 TRP   0.033   0.001   TRP A1503 
 HIS   0.007   0.001   HIS A1765 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 (14171)
  covalent geometry    : angle       0.59083 (19223)
  hydrogen bonds       : bond        0.03260 (  591)
  hydrogen bonds       : angle       4.87349 ( 1602)

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

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

  3462 Ramachandran restraints generated.
    1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3462 Ramachandran restraints generated.
    1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  274 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 274
  time to evaluate  : 0.670 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 VAL cc_start: 0.8987 (t) cc_final: 0.8533 (t)
REVERT: A  262 HIS cc_start: 0.8780 (m90) cc_final: 0.8515 (m-70)
REVERT: A  340 LYS cc_start: 0.8109 (mmtt) cc_final: 0.7663 (ptmt)
REVERT: A  361 LYS cc_start: 0.9378 (mttp) cc_final: 0.8949 (mmtp)
REVERT: A  384 GLU cc_start: 0.8625 (tm-30) cc_final: 0.8374 (tm-30)
REVERT: A  387 ILE cc_start: 0.9398 (pt) cc_final: 0.9076 (mt)
REVERT: A  389 ASP cc_start: 0.8738 (m-30) cc_final: 0.8121 (m-30)
REVERT: A  413 ARG cc_start: 0.8547 (mtt180) cc_final: 0.7560 (tpm170)
REVERT: A  429 CYS cc_start: 0.8438 (t) cc_final: 0.7865 (m)
REVERT: A  434 ARG cc_start: 0.7226 (mtp85) cc_final: 0.6492 (tpm170)
REVERT: A  503 ASP cc_start: 0.8760 (t0) cc_final: 0.7965 (t0)
REVERT: A  504 LEU cc_start: 0.9417 (mt) cc_final: 0.9210 (tp)
REVERT: A  742 ASN cc_start: 0.9128 (m-40) cc_final: 0.8884 (m-40)
REVERT: A 1153 SER cc_start: 0.8552 (t) cc_final: 0.8290 (p)
REVERT: A 1239 GLU cc_start: 0.7624 (tm-30) cc_final: 0.7253 (tm-30)
REVERT: A 1325 ILE cc_start: 0.8413 (pt) cc_final: 0.8197 (mt)
REVERT: A 1398 ASP cc_start: 0.7643 (p0) cc_final: 0.6838 (p0)
REVERT: A 1484 LEU cc_start: 0.8770 (tp) cc_final: 0.8539 (tp)
REVERT: A 1499 MET cc_start: 0.8927 (ttp) cc_final: 0.8570 (tmm)
REVERT: A 1501 GLU cc_start: 0.7619 (tp30) cc_final: 0.7350 (tp30)
REVERT: A 1521 LYS cc_start: 0.8393 (tttt) cc_final: 0.8031 (tptp)
REVERT: A 1525 PHE cc_start: 0.8926 (t80) cc_final: 0.8671 (t80)
REVERT: A 1707 TYR cc_start: 0.7812 (p90) cc_final: 0.7452 (p90)
REVERT: A 1716 ILE cc_start: 0.8789 (mt) cc_final: 0.8047 (mp)
REVERT: A 1735 MET cc_start: 0.8582 (pmm) cc_final: 0.8330 (pmm)
REVERT: A 1913 LEU cc_start: 0.9212 (mt) cc_final: 0.8989 (mp)
REVERT: A 1953 LEU cc_start: 0.9033 (mm) cc_final: 0.8797 (mm)
REVERT: A 1995 ASP cc_start: 0.8436 (t70) cc_final: 0.6955 (t0)
REVERT: A 1999 GLN cc_start: 0.8981 (mt0) cc_final: 0.8540 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 274
  average time/residue: 0.1004
  time to fit residues: 42.6193
Evaluate side-chains
  228 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 228
  time to evaluate  : 0.603 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 174
   random chunks:
   chunk 36 optimal weight:   10.0000
   chunk 19 optimal weight:    0.0050
   chunk 2 optimal weight:    0.9980
   chunk 129 optimal weight:    0.5980
   chunk 34 optimal weight:    0.8980
   chunk 172 optimal weight:    5.9990
   chunk 3 optimal weight:    1.9990
   chunk 67 optimal weight:    0.0170
   chunk 160 optimal weight:    0.9980
   chunk 150 optimal weight:    6.9990
   chunk 28 optimal weight:    4.9990
   overall best weight:    0.5032

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

Flipped N/Q/H residues before XYZ refinement:
A1136 HIS
** A1300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1688 GLN ** 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 = 0.3732 r_free = 0.3732 target = 0.107023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.085585 restraints weight = 43648.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.088403 restraints weight = 26895.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.090372 restraints weight = 19106.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.091746 restraints weight = 14973.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.092670 restraints weight = 12524.567|
|-----------------------------------------------------------------------------|
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7809
moved from start:          0.4332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044  14171  Z= 0.108
  Angle     :  0.601   9.923  19223  Z= 0.298
  Chirality :  0.043   0.223   2172
  Planarity :  0.004   0.057   2462
  Dihedral  :  4.170  22.344   1895
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 9.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.26 %
    Favored  : 99.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.30 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.20 (0.21), residues: 1731
  helix:  1.14 (0.22), residues: 565
  sheet: -0.32 (0.31), residues: 295
  loop : -0.30 (0.22), residues: 871

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 941 
 TYR   0.010   0.001   TYR A  62 
 PHE   0.028   0.002   PHE A 978 
 TRP   0.032   0.001   TRP A1503 
 HIS   0.008   0.001   HIS A1765 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 (14171)
  covalent geometry    : angle       0.60134 (19223)
  hydrogen bonds       : bond        0.03272 (  591)
  hydrogen bonds       : angle       4.85582 ( 1602)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2246.65 seconds
wall clock time: 39 minutes 46.92 seconds (2386.92 seconds total)