Starting phenix.real_space_refine
on Wed Sep 17 20:57:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9gkm_51429/09_2025/9gkm_51429.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9gkm_51429/09_2025/9gkm_51429.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.69
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9gkm_51429/09_2025/9gkm_51429.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9gkm_51429/09_2025/9gkm_51429.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9gkm_51429/09_2025/9gkm_51429.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9gkm_51429/09_2025/9gkm_51429.cif"
  }
  resolution = 3.69
  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: 4
    Type Number    sf(0)   Gaussians
     S      66      5.16       5
     C    7197      2.51       5
     N    1911      2.21       5
     O    2057      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11231
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "B"
      Number of atoms: 573
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 573
          Classifications: {'peptide': 75}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 27
          Unresolved non-hydrogen dihedrals: 21
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 12
    Chain: "C"
      Number of atoms: 579
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 579
          Classifications: {'peptide': 73}
          Link IDs: {'PTRANS': 3, 'TRANS': 69}
    Chain: "D"
      Number of atoms: 591
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 591
          Classifications: {'peptide': 76}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 10
    Chain: "A"
      Number of atoms: 9481
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1222, 9481
          Classifications: {'peptide': 1222}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 73}
          Link IDs: {'PCIS': 1, 'PTRANS': 58, 'TRANS': 1162}
          Chain breaks: 11
          Unresolved non-hydrogen bonds: 291
          Unresolved non-hydrogen angles: 347
          Unresolved non-hydrogen dihedrals: 241
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 22, 'HIS:plan': 3, 'ARG:plan': 9, 'ASP:plan': 9}
          Unresolved non-hydrogen planarities: 195
    Chain: "B"
      Number of atoms: 7
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 7
          Unusual residues: {'SY8': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.78, per 1000 atoms: 0.25
  Number of scatterers: 11231
  At special positions: 0
  Unit cell: (105.549, 142.15, 130.234, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      66     16.00
     O    2057      8.00
     N    1911      7.00
     C    7197      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 additional links: simple=1, symmetry=0
    Simple link:   pdb=" C   GLY B  75 " - pdb=" N   SY8 B2101 "
  Number of custom bonds: simple=3, symmetry=0
  Number of additional bonds: simple=3, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.01
  Conformation dependent library (CDL) restraints added in 582.4 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2754

  Finding SS restraints...
    Secondary structure from input PDB file:
      68 helices and 8 sheets defined
      51.7% alpha, 9.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.44
  Creating SS restraints...
    Processing helix  chain 'B' and resid 23 through 34
    Processing helix  chain 'C' and resid 23 through 34
    Processing helix  chain 'C' and resid 56 through 59
    Processing helix  chain 'D' and resid 23 through 34
    Processing helix  chain 'A' and resid 484 through 495
      removed outlier: 3.645A  pdb=" N   GLN A 489 " --> pdb=" O   SER A 485 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 499 through 514
    Processing helix  chain 'A' and resid 526 through 538
      Proline residue:  A 531  - end of helix
    Processing helix  chain 'A' and resid 543 through 559
      removed outlier: 4.436A  pdb=" N   ASN A 547 " --> pdb=" O   PHE A 543 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   HIS A 548 " --> pdb=" O   ASP A 544 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 563 through 568
      removed outlier: 5.305A  pdb=" N   VAL A 568 " --> pdb=" O   SER A 564 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 570 through 579
    Processing helix  chain 'A' and resid 584 through 599
      removed outlier: 3.993A  pdb=" N   ARG A 599 " --> pdb=" O   GLU A 595 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 602 through 608
    Processing helix  chain 'A' and resid 610 through 615
      removed outlier: 4.964A  pdb=" N   LEU A 615 " --> pdb=" O   LEU A 611 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 623 through 638
      removed outlier: 4.065A  pdb=" N   ARG A 627 " --> pdb=" O   ILE A 623 " (cutoff:3.500A)
      removed outlier: 4.308A  pdb=" N   ASN A 628 " --> pdb=" O   ASN A 624 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 645 through 649
    Processing helix  chain 'A' and resid 651 through 659
    Processing helix  chain 'A' and resid 664 through 681
    Processing helix  chain 'A' and resid 685 through 692
    Processing helix  chain 'A' and resid 694 through 705
      removed outlier: 4.160A  pdb=" N   THR A 698 " --> pdb=" O   LYS A 694 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 713 through 729
    Processing helix  chain 'A' and resid 731 through 739
    Processing helix  chain 'A' and resid 742 through 751
    Processing helix  chain 'A' and resid 769 through 782
    Processing helix  chain 'A' and resid 793 through 798
      removed outlier: 4.270A  pdb=" N   MET A 797 " --> pdb=" O   ALA A 793 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 867 through 874
    Processing helix  chain 'A' and resid 876 through 895
      removed outlier: 5.151A  pdb=" N   GLY A 888 " --> pdb=" O   LYS A 884 " (cutoff:3.500A)
      removed outlier: 4.872A  pdb=" N   VAL A 889 " --> pdb=" O   THR A 885 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 900 through 916
      removed outlier: 3.717A  pdb=" N   HIS A 904 " --> pdb=" O   PRO A 900 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 919 through 926
    Processing helix  chain 'A' and resid 931 through 939
    Processing helix  chain 'A' and resid 944 through 960
      removed outlier: 5.179A  pdb=" N   VAL A 948 " --> pdb=" O   LEU A 944 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 963 through 966
      removed outlier: 3.778A  pdb=" N   SER A 966 " --> pdb=" O   ASP A 963 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 963 through 966'
    Processing helix  chain 'A' and resid 967 through 972
    Processing helix  chain 'A' and resid 974 through 983
    Processing helix  chain 'A' and resid 1132 through 1152
    Processing helix  chain 'A' and resid 1167 through 1178
      removed outlier: 3.654A  pdb=" N   GLN A1177 " --> pdb=" O   ALA A1173 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   LEU A1178 " --> pdb=" O   ALA A1174 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1187 through 1198
    Processing helix  chain 'A' and resid 1204 through 1209
    Processing helix  chain 'A' and resid 1211 through 1220
    Processing helix  chain 'A' and resid 1230 through 1241
    Processing helix  chain 'A' and resid 1261 through 1277
    Processing helix  chain 'A' and resid 1306 through 1312
    Processing helix  chain 'A' and resid 1343 through 1351
    Processing helix  chain 'A' and resid 1406 through 1414
    Processing helix  chain 'A' and resid 1435 through 1440
    Processing helix  chain 'A' and resid 1484 through 1488
    Processing helix  chain 'A' and resid 1498 through 1502
    Processing helix  chain 'A' and resid 1517 through 1532
    Processing helix  chain 'A' and resid 1555 through 1564
    Processing helix  chain 'A' and resid 1567 through 1572
    Processing helix  chain 'A' and resid 1577 through 1586
    Processing helix  chain 'A' and resid 1592 through 1603
    Processing helix  chain 'A' and resid 1606 through 1616
    Processing helix  chain 'A' and resid 1646 through 1657
    Processing helix  chain 'A' and resid 1676 through 1691
      removed outlier: 4.307A  pdb=" N   GLN A1691 " --> pdb=" O   SER A1687 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1735 through 1757
      removed outlier: 3.524A  pdb=" N   MET A1757 " --> pdb=" O   ALA A1753 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1768 through 1775
    Processing helix  chain 'A' and resid 1783 through 1789
      removed outlier: 3.832A  pdb=" N   PHE A1787 " --> pdb=" O   HIS A1784 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   ASP A1788 " --> pdb=" O   ASP A1785 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1792 through 1812
      removed outlier: 3.925A  pdb=" N   SER A1796 " --> pdb=" O   VAL A1792 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1818 through 1827
    Processing helix  chain 'A' and resid 1834 through 1838
    Processing helix  chain 'A' and resid 1866 through 1879
    Processing helix  chain 'A' and resid 1883 through 1893
    Processing helix  chain 'A' and resid 1907 through 1915
      removed outlier: 5.117A  pdb=" N   ASP A1911 " --> pdb=" O   PRO A1907 " (cutoff:3.500A)
      removed outlier: 5.524A  pdb=" N   GLN A1912 " --> pdb=" O   GLU A1908 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   LEU A1913 " --> pdb=" O   GLU A1909 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1924 through 1930
      removed outlier: 4.694A  pdb=" N   GLU A1929 " --> pdb=" O   LYS A1925 " (cutoff:3.500A)
      removed outlier: 4.647A  pdb=" N   CYS A1930 " --> pdb=" O   THR A1926 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1942 through 1953
      removed outlier: 3.888A  pdb=" N   SER A1952 " --> pdb=" O   PHE A1948 " (cutoff:3.500A)
      removed outlier: 4.464A  pdb=" N   SER A1953 " --> pdb=" O   GLU A1949 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1956 through 1967
    Processing helix  chain 'A' and resid 1976 through 1979
    Processing helix  chain 'A' and resid 2019 through 2032
      removed outlier: 3.975A  pdb=" N   ILE A2028 " --> pdb=" O   GLU A2024 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 11 through 17
      removed outlier: 5.107A  pdb=" N   LYS B  11 " --> pdb=" O   THR B   7 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   VAL B  17 " --> pdb=" O   MET B   1 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   MET B   1 " --> pdb=" O   VAL B  17 " (cutoff:3.500A)
      removed outlier: 5.750A  pdb=" N   SER B  65 " --> pdb=" O   GLN B   2 " (cutoff:3.500A)
      removed outlier: 8.042A  pdb=" N   HIS B  68 " --> pdb=" O   PHE B  45 " (cutoff:3.500A)
      removed outlier: 5.741A  pdb=" N   PHE B  45 " --> pdb=" O   HIS B  68 " (cutoff:3.500A)
      removed outlier: 7.139A  pdb=" N   VAL B  70 " --> pdb=" O   LEU B  43 " (cutoff:3.500A)
      removed outlier: 5.219A  pdb=" N   LEU B  43 " --> pdb=" O   VAL B  70 " (cutoff:3.500A)
      removed outlier: 6.203A  pdb=" N   ARG B  72 " --> pdb=" O   GLN B  41 " (cutoff:3.500A)
      removed outlier: 5.695A  pdb=" N   GLN B  41 " --> pdb=" O   ARG B  72 " (cutoff:3.500A)
      removed outlier: 5.179A  pdb=" N   LEU B  43 " --> pdb=" O   LEU B  50 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 10 through 17
      removed outlier: 4.631A  pdb=" N   LYS C  11 " --> pdb=" O   THR C   7 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   THR C   7 " --> pdb=" O   LYS C  11 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   GLU C  64 " --> pdb=" O   GLN C   2 " (cutoff:3.500A)
      removed outlier: 7.205A  pdb=" N   PHE C   4 " --> pdb=" O   GLU C  64 " (cutoff:3.500A)
      removed outlier: 4.663A  pdb=" N   THR C  66 " --> pdb=" O   PHE C   4 " (cutoff:3.500A)
      removed outlier: 7.612A  pdb=" N   LYS C   6 " --> pdb=" O   THR C  66 " (cutoff:3.500A)
      removed outlier: 4.993A  pdb=" N   HIS C  68 " --> pdb=" O   LYS C   6 " (cutoff:3.500A)
      removed outlier: 8.047A  pdb=" N   HIS C  68 " --> pdb=" O   PHE C  45 " (cutoff:3.500A)
      removed outlier: 5.541A  pdb=" N   PHE C  45 " --> pdb=" O   HIS C  68 " (cutoff:3.500A)
      removed outlier: 7.177A  pdb=" N   VAL C  70 " --> pdb=" O   LEU C  43 " (cutoff:3.500A)
      removed outlier: 5.223A  pdb=" N   LEU C  43 " --> pdb=" O   VAL C  70 " (cutoff:3.500A)
      removed outlier: 6.867A  pdb=" N   ARG C  72 " --> pdb=" O   GLN C  41 " (cutoff:3.500A)
      removed outlier: 6.542A  pdb=" N   GLN C  41 " --> pdb=" O   ARG C  72 " (cutoff:3.500A)
      removed outlier: 4.969A  pdb=" N   LEU C  43 " --> pdb=" O   LEU C  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 10 through 17
      removed outlier: 5.656A  pdb=" N   LYS D  11 " --> pdb=" O   THR D   7 " (cutoff:3.500A)
      removed outlier: 4.663A  pdb=" N   THR D   7 " --> pdb=" O   LYS D  11 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   MET D   1 " --> pdb=" O   VAL D  17 " (cutoff:3.500A)
      removed outlier: 5.405A  pdb=" N   PHE D   4 " --> pdb=" O   GLU D  64 " (cutoff:3.500A)
      removed outlier: 4.045A  pdb=" N   THR D  66 " --> pdb=" O   PHE D   4 " (cutoff:3.500A)
      removed outlier: 6.105A  pdb=" N   LYS D   6 " --> pdb=" O   THR D  66 " (cutoff:3.500A)
      removed outlier: 4.360A  pdb=" N   HIS D  68 " --> pdb=" O   LYS D   6 " (cutoff:3.500A)
      removed outlier: 7.293A  pdb=" N   HIS D  68 " --> pdb=" O   PHE D  45 " (cutoff:3.500A)
      removed outlier: 4.982A  pdb=" N   PHE D  45 " --> pdb=" O   HIS D  68 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   VAL D  70 " --> pdb=" O   LEU D  43 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   LEU D  43 " --> pdb=" O   VAL D  70 " (cutoff:3.500A)
      removed outlier: 5.401A  pdb=" N   ARG D  72 " --> pdb=" O   GLN D  41 " (cutoff:3.500A)
      removed outlier: 5.290A  pdb=" N   GLN D  41 " --> pdb=" O   ARG D  72 " (cutoff:3.500A)
      removed outlier: 5.742A  pdb=" N   LEU D  43 " --> pdb=" O   LEU D  50 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1334 through 1337
      removed outlier: 4.706A  pdb=" N   HIS A1442 " --> pdb=" O   LYS A1315 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   ILE A1444 " --> pdb=" O   GLN A1317 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   GLN A1319 " --> pdb=" O   ILE A1444 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   TYR A1446 " --> pdb=" O   GLN A1319 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   ILE A1396 " --> pdb=" O   HIS A1399 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1636 through 1641
      removed outlier: 6.062A  pdb=" N   LYS A1637 " --> pdb=" O   GLU A1665 " (cutoff:3.500A)
      removed outlier: 7.550A  pdb=" N   GLN A1667 " --> pdb=" O   LYS A1637 " (cutoff:3.500A)
      removed outlier: 6.392A  pdb=" N   ARG A1639 " --> pdb=" O   GLN A1667 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1701 through 1704
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1842 through 1844
      removed outlier: 8.839A  pdb=" N   PHE A1842 " --> pdb=" O   LEU A1852 " (cutoff:3.500A)
      removed outlier: 5.973A  pdb=" N   ILE A1850 " --> pdb=" O   LEU A1844 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1933 through 1935
      removed outlier: 4.373A  pdb=" N   ARG A1988 " --> pdb=" O   ASP A1934 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   THR A1985 " --> pdb=" O   ASN A2009 " (cutoff:3.500A)

    500 hydrogen bonds defined for protein.
    1461 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.00

  Time building geometry restraints manager: 1.34 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2376
        1.33 -     1.45: 2381
        1.45 -     1.57: 6580
        1.57 -     1.69: 0
        1.69 -     1.81: 105
  Bond restraints: 11442
  Sorted by residual:
  bond pdb=" N   SY8 B2101 "
       pdb=" C4  SY8 B2101 "
    ideal  model  delta    sigma   weight residual
    1.456  1.486 -0.030 2.00e-02 2.50e+03 2.28e+00
  bond pdb=" C   PRO B  37 "
       pdb=" N   PRO B  38 "
    ideal  model  delta    sigma   weight residual
    1.334  1.367 -0.033 2.34e-02 1.83e+03 1.95e+00
  bond pdb=" N   ASN C  60 "
       pdb=" CA  ASN C  60 "
    ideal  model  delta    sigma   weight residual
    1.457  1.473 -0.016 1.29e-02 6.01e+03 1.46e+00
  bond pdb=" CB  ASN C  60 "
       pdb=" CG  ASN C  60 "
    ideal  model  delta    sigma   weight residual
    1.516  1.538 -0.022 2.50e-02 1.60e+03 7.98e-01
  bond pdb=" CB  CYS A1273 "
       pdb=" SG  CYS A1273 "
    ideal  model  delta    sigma   weight residual
    1.808  1.781  0.027 3.30e-02 9.18e+02 6.57e-01
  ... (remaining 11437 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.23: 15067
        1.23 -     2.46: 333
        2.46 -     3.69: 86
        3.69 -     4.92: 16
        4.92 -     6.15: 11
  Bond angle restraints: 15513
  Sorted by residual:
  angle pdb=" N   LYS A 945 "
        pdb=" CA  LYS A 945 "
        pdb=" C   LYS A 945 "
      ideal   model   delta    sigma   weight residual
     114.04  107.89    6.15 1.24e+00 6.50e-01 2.46e+01
  angle pdb=" N   VAL A1672 "
        pdb=" CA  VAL A1672 "
        pdb=" C   VAL A1672 "
      ideal   model   delta    sigma   weight residual
     113.42  108.76    4.66 1.17e+00 7.31e-01 1.59e+01
  angle pdb=" C   ILE A 571 "
        pdb=" CA  ILE A 571 "
        pdb=" CB  ILE A 571 "
      ideal   model   delta    sigma   weight residual
     113.70  110.77    2.93 9.50e-01 1.11e+00 9.53e+00
  angle pdb=" C   ALA A 570 "
        pdb=" N   ILE A 571 "
        pdb=" CA  ILE A 571 "
      ideal   model   delta    sigma   weight residual
     120.43  123.27   -2.84 9.60e-01 1.09e+00 8.75e+00
  angle pdb=" CA  VAL A1672 "
        pdb=" C   VAL A1672 "
        pdb=" N   GLY A1673 "
      ideal   model   delta    sigma   weight residual
     118.90  116.48    2.42 9.40e-01 1.13e+00 6.60e+00
  ... (remaining 15508 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    27.18: 6684
       27.18 -    54.36: 235
       54.36 -    81.54: 25
       81.54 -   108.72: 5
      108.72 -   135.91: 3
  Dihedral angle restraints: 6952
    sinusoidal: 2731
      harmonic: 4221
  Sorted by residual:
  dihedral pdb=" C   SY8 B2101 "
           pdb=" C1  SY8 B2101 "
           pdb=" C2  SY8 B2101 "
           pdb=" C3  SY8 B2101 "
      ideal   model   delta sinusoidal    sigma   weight residual
      62.79 -161.30 -135.91     1      3.00e+01 1.11e-03 1.83e+01
  dihedral pdb=" O   SY8 B2101 "
           pdb=" C1  SY8 B2101 "
           pdb=" C2  SY8 B2101 "
           pdb=" C3  SY8 B2101 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -116.28   18.85 -135.13     1      3.00e+01 1.11e-03 1.82e+01
  dihedral pdb=" N   SY8 B2101 "
           pdb=" C3  SY8 B2101 "
           pdb=" C4  SY8 B2101 "
           pdb=" C2  SY8 B2101 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -59.10   63.17 -122.27     1      3.00e+01 1.11e-03 1.64e+01
  ... (remaining 6949 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 1188
       0.030 -    0.061: 432
       0.061 -    0.091: 128
       0.091 -    0.121: 60
       0.121 -    0.151: 10
  Chirality restraints: 1818
  Sorted by residual:
  chirality pdb=" CA  ASN A 741 "
            pdb=" N   ASN A 741 "
            pdb=" C   ASN A 741 "
            pdb=" CB  ASN A 741 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.72e-01
  chirality pdb=" CA  ASN C  60 "
            pdb=" N   ASN C  60 "
            pdb=" C   ASN C  60 "
            pdb=" CB  ASN C  60 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.50e-01
  chirality pdb=" CA  LEU A 886 "
            pdb=" N   LEU A 886 "
            pdb=" C   LEU A 886 "
            pdb=" CB  LEU A 886 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.78e-01
  ... (remaining 1815 not shown)

  Planarity restraints: 1985
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A1847 "   -0.032 5.00e-02 4.00e+02   4.92e-02 3.87e+00
        pdb=" N   PRO A1848 "    0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO A1848 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A1848 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A1956 "   -0.009 2.00e-02 2.50e+03   1.86e-02 3.48e+00
        pdb=" C   ASN A1956 "    0.032 2.00e-02 2.50e+03
        pdb=" O   ASN A1956 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   GLU A1957 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A1677 "    0.027 5.00e-02 4.00e+02   4.15e-02 2.75e+00
        pdb=" N   PRO A1678 "   -0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO A1678 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A1678 "    0.023 5.00e-02 4.00e+02
  ... (remaining 1982 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 1319
        2.75 -     3.29: 10606
        3.29 -     3.83: 17551
        3.83 -     4.36: 18860
        4.36 -     4.90: 34058
  Nonbonded interactions: 82394
  Sorted by model distance:
  nonbonded pdb=" O   THR A1938 "
            pdb=" OG  SER A1941 "
     model   vdw
     2.216 3.040
  nonbonded pdb=" OG1 THR A1862 "
            pdb=" OD1 ASN A1865 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" OG1 THR B  22 "
            pdb=" OE1 GLU B  24 "
     model   vdw
     2.270 3.040
  nonbonded pdb=" O   GLN D  62 "
            pdb=" OG  SER D  65 "
     model   vdw
     2.285 3.040
  nonbonded pdb=" O   ARG A1795 "
            pdb=" ND1 HIS A1799 "
     model   vdw
     2.317 3.120
  ... (remaining 82389 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'B' and (resid 1 through 28 or resid 30 through 47 or resid 49 through 71 \ 
 or (resid 72 and (name N or name CA or name C or name O or name CB )) or resid  \ 
73))
  selection = (chain 'C' and (resid 1 or (resid 2 and (name N or name CA or name C or name O o \ 
r name CB )) or resid 3 through 10 or (resid 11 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 12 through 28 or resid 30 through 32 or (resid \ 
 33 through 34 and (name N or name CA or name C or name O or name CB )) or resid \ 
 35 through 47 or resid 49 through 62 or (resid 63 through 64 and (name N or nam \ 
e CA or name C or name O or name CB )) or resid 65 through 71 or (resid 72 and ( \ 
name N or name CA or name C or name O or name CB )) or resid 73))
  selection = (chain 'D' and (resid 1 or (resid 2 and (name N or name CA or name C or name O o \ 
r name CB )) or resid 3 through 10 or (resid 11 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 12 through 28 or resid 30 through 32 or (resid \ 
 33 through 34 and (name N or name CA or name C or name O or name CB )) or resid \ 
 35 through 47 or resid 49 through 62 or (resid 63 through 64 and (name N or nam \ 
e CA or name C or name O or name CB )) or resid 65 through 73))
}

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:             1.970
  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:          0.220
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     11.880
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.590
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6938
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      :  0.003   0.103  11446  Z= 0.165
  Angle     :  0.499   6.154  15515  Z= 0.266
  Chirality :  0.038   0.151   1818
  Planarity :  0.004   0.049   1984
  Dihedral  : 13.897 135.905   4197
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.23 %
    Favored  : 94.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.17 %
    Favored  : 99.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.47 %
    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 aren not related in a simple way.
  whole:  0.90 (0.24), residues: 1416
  helix:  1.79 (0.20), residues: 746
  sheet:  0.42 (0.55), residues: 108
  loop : -1.02 (0.27), residues: 562

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1760 
 TYR   0.009   0.001   TYR A1668 
 PHE   0.015   0.001   PHE A 723 
 TRP   0.007   0.001   TRP A1773 
 HIS   0.002   0.000   HIS A 747 

Details of bonding type rmsd
  covalent geometry    : bond        0.00220 (11442)
  covalent geometry    : angle       0.49731 (15513)
  hydrogen bonds       : bond        0.07510 (  500)
  hydrogen bonds       : angle       3.92732 ( 1461)
  Misc. bond           : bond        0.07921 (    3)
  link_TRANS           : bond        0.00614 (    1)
  link_TRANS           : angle       3.86433 (    2)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 225
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    1 MET cc_start: 0.4404 (ttt) cc_final: 0.3520 (ppp)
REVERT: C    6 LYS cc_start: 0.7820 (pttp) cc_final: 0.7501 (ttpp)
REVERT: C   24 GLU cc_start: 0.7779 (tt0) cc_final: 0.7525 (tm-30)
REVERT: A  492 GLN cc_start: 0.7969 (mp10) cc_final: 0.7715 (mp10)
REVERT: A  504 GLN cc_start: 0.8260 (mm-40) cc_final: 0.7912 (mm-40)
REVERT: A  521 LEU cc_start: 0.7986 (mt) cc_final: 0.7712 (mt)
REVERT: A  556 MET cc_start: 0.7812 (tpp) cc_final: 0.7589 (ttm)
REVERT: A  597 LEU cc_start: 0.8491 (mt) cc_final: 0.8256 (mt)
REVERT: A  622 SER cc_start: 0.8455 (t) cc_final: 0.8066 (p)
REVERT: A  678 VAL cc_start: 0.7977 (t) cc_final: 0.7772 (p)
REVERT: A  679 ASP cc_start: 0.7544 (t70) cc_final: 0.7070 (t0)
REVERT: A  872 MET cc_start: 0.2686 (ttm) cc_final: 0.1819 (ttm)
REVERT: A  889 VAL cc_start: 0.8213 (t) cc_final: 0.8008 (p)
REVERT: A 1153 PHE cc_start: 0.6433 (m-80) cc_final: 0.6076 (m-80)
REVERT: A 1200 ASP cc_start: 0.6433 (p0) cc_final: 0.6214 (p0)
REVERT: A 1254 ARG cc_start: 0.6914 (ttp-170) cc_final: 0.6389 (ttp-170)
REVERT: A 1539 ASN cc_start: 0.7927 (t0) cc_final: 0.7476 (t0)
REVERT: A 1543 LYS cc_start: 0.7760 (ttpp) cc_final: 0.7341 (ttpp)
REVERT: A 1571 MET cc_start: 0.7001 (mmm) cc_final: 0.6555 (mmm)
REVERT: A 1639 ARG cc_start: 0.7479 (mmt90) cc_final: 0.7210 (mmm-85)
REVERT: A 1698 TRP cc_start: 0.8142 (m100) cc_final: 0.7092 (m100)
REVERT: A 1746 ARG cc_start: 0.7929 (mtp85) cc_final: 0.7588 (mtp85)
REVERT: A 1760 ARG cc_start: 0.8108 (mmt90) cc_final: 0.7878 (mpt-90)
REVERT: A 1789 ILE cc_start: 0.7935 (mm) cc_final: 0.7621 (mt)
REVERT: A 1812 GLN cc_start: 0.8225 (mm110) cc_final: 0.7768 (mm-40)
REVERT: A 1836 GLU cc_start: 0.7793 (tp30) cc_final: 0.7518 (tp30)
REVERT: A 1851 GLU cc_start: 0.6790 (mm-30) cc_final: 0.6461 (mm-30)
REVERT: A 1854 LYS cc_start: 0.7723 (tptm) cc_final: 0.7431 (ttmm)
REVERT: A 1997 PRO cc_start: 0.7213 (Cg_endo) cc_final: 0.6916 (Cg_exo)
REVERT: A 2018 SER cc_start: 0.8713 (t) cc_final: 0.8312 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 225
  average time/residue: 0.1089
  time to fit residues: 34.3534
Evaluate side-chains
  209 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 209
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 98 optimal weight:    0.9990
   chunk 107 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   chunk 130 optimal weight:    1.9990
   chunk 124 optimal weight:    0.4980
   chunk 103 optimal weight:    0.1980
   chunk 77 optimal weight:    0.0010
   chunk 122 optimal weight:    7.9990
   chunk 91 optimal weight:    1.9990
   chunk 55 optimal weight:    0.5980
   overall best weight:    0.4588

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

Flipped N/Q/H residues before XYZ refinement:
A 538 GLN
A 980 HIS
A1146 HIS
A1272 ASN
A2038 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.160711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.124129 restraints weight = 18502.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.127554 restraints weight = 9988.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.129761 restraints weight = 6655.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.131292 restraints weight = 5119.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.131853 restraints weight = 4328.908|
|-----------------------------------------------------------------------------|
r_work (final): 0.3613
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6927
moved from start:          0.0663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  11446  Z= 0.111
  Angle     :  0.487   6.465  15515  Z= 0.247
  Chirality :  0.038   0.151   1818
  Planarity :  0.004   0.054   1984
  Dihedral  :  5.559  99.579   1537
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  :  6.69 %
    Favored  : 92.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.47 %
    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 aren not related in a simple way.
  whole:  0.87 (0.24), residues: 1416
  helix:  1.74 (0.20), residues: 741
  sheet:  0.39 (0.53), residues: 113
  loop : -0.98 (0.27), residues: 562

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1643 
 TYR   0.009   0.001   TYR A1668 
 PHE   0.021   0.001   PHE A1242 
 TRP   0.007   0.001   TRP A1773 
 HIS   0.006   0.001   HIS A 980 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 (11442)
  covalent geometry    : angle       0.48659 (15513)
  hydrogen bonds       : bond        0.03458 (  500)
  hydrogen bonds       : angle       3.89287 ( 1461)
  Misc. bond           : bond        0.00126 (    3)
  link_TRANS           : bond        0.00236 (    1)
  link_TRANS           : angle       0.75503 (    2)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 213
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    1 MET cc_start: 0.4080 (ttt) cc_final: 0.3335 (ppp)
REVERT: C    6 LYS cc_start: 0.7874 (pttp) cc_final: 0.7547 (ttpp)
REVERT: C   24 GLU cc_start: 0.7750 (tt0) cc_final: 0.7521 (tm-30)
REVERT: A  504 GLN cc_start: 0.8178 (mm-40) cc_final: 0.7837 (mm-40)
REVERT: A  521 LEU cc_start: 0.7986 (mt) cc_final: 0.7752 (mt)
REVERT: A  615 LEU cc_start: 0.7668 (mp) cc_final: 0.7311 (mp)
REVERT: A  622 SER cc_start: 0.8417 (t) cc_final: 0.8029 (p)
REVERT: A  679 ASP cc_start: 0.7561 (t70) cc_final: 0.7121 (t0)
REVERT: A  872 MET cc_start: 0.2700 (ttm) cc_final: 0.1776 (ttm)
REVERT: A  889 VAL cc_start: 0.8253 (t) cc_final: 0.8014 (p)
REVERT: A 1153 PHE cc_start: 0.6381 (m-80) cc_final: 0.6089 (m-80)
REVERT: A 1200 ASP cc_start: 0.6384 (p0) cc_final: 0.6156 (p0)
REVERT: A 1254 ARG cc_start: 0.6894 (ttp-170) cc_final: 0.6376 (ttp-170)
REVERT: A 1539 ASN cc_start: 0.7897 (t0) cc_final: 0.7521 (t0)
REVERT: A 1543 LYS cc_start: 0.7818 (ttpp) cc_final: 0.7387 (ttpp)
REVERT: A 1610 MET cc_start: 0.7767 (mtt) cc_final: 0.7567 (mtt)
REVERT: A 1639 ARG cc_start: 0.7479 (mmt90) cc_final: 0.7236 (mmm-85)
REVERT: A 1642 ASN cc_start: 0.7716 (t0) cc_final: 0.7484 (t0)
REVERT: A 1668 TYR cc_start: 0.7400 (m-80) cc_final: 0.6809 (m-10)
REVERT: A 1698 TRP cc_start: 0.8137 (m100) cc_final: 0.7098 (m100)
REVERT: A 1746 ARG cc_start: 0.7864 (mtp85) cc_final: 0.7581 (mtp85)
REVERT: A 1789 ILE cc_start: 0.7911 (mm) cc_final: 0.7553 (mt)
REVERT: A 1836 GLU cc_start: 0.7680 (tp30) cc_final: 0.7408 (tp30)
REVERT: A 1851 GLU cc_start: 0.6279 (mm-30) cc_final: 0.6066 (mm-30)
REVERT: A 1854 LYS cc_start: 0.7750 (tptm) cc_final: 0.7425 (ttmm)
REVERT: A 1997 PRO cc_start: 0.7157 (Cg_endo) cc_final: 0.6841 (Cg_exo)
REVERT: A 2018 SER cc_start: 0.8737 (t) cc_final: 0.8305 (p)
  outliers start: 12
  outliers final: 8
  residues processed: 217
  average time/residue: 0.1051
  time to fit residues: 32.2724
Evaluate side-chains
  214 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 206
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  537 LEU
Chi-restraints excluded: chain A residue  553 LEU
Chi-restraints excluded: chain A residue  683 HIS
Chi-restraints excluded: chain A residue  695 ASP
Chi-restraints excluded: chain A residue 1172 CYS
Chi-restraints excluded: chain A residue 1538 ASP
Chi-restraints excluded: chain A residue 1928 MET
Chi-restraints excluded: chain A residue 2008 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 33 optimal weight:    3.9990
   chunk 125 optimal weight:    3.9990
   chunk 68 optimal weight:    1.9990
   chunk 138 optimal weight:    0.3980
   chunk 11 optimal weight:    2.9990
   chunk 106 optimal weight:    0.0470
   chunk 83 optimal weight:    2.9990
   chunk 48 optimal weight:    0.0030
   chunk 4 optimal weight:    7.9990
   chunk 82 optimal weight:    9.9990
   chunk 45 optimal weight:    0.7980
   overall best weight:    0.6490

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

Flipped N/Q/H residues before XYZ refinement:
A1272 ASN
A1939 HIS
A2038 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.158901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.122931 restraints weight = 18567.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.126194 restraints weight = 10360.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.128023 restraints weight = 6996.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.129507 restraints weight = 5588.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.130109 restraints weight = 4737.218|
|-----------------------------------------------------------------------------|
r_work (final): 0.3588
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6954
moved from start:          0.0937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  11446  Z= 0.130
  Angle     :  0.485   6.918  15515  Z= 0.247
  Chirality :  0.038   0.152   1818
  Planarity :  0.004   0.054   1984
  Dihedral  :  4.879  74.403   1537
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 4.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  :  8.18 %
    Favored  : 90.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.47 %
    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 aren not related in a simple way.
  whole:  0.89 (0.24), residues: 1416
  helix:  1.67 (0.20), residues: 734
  sheet:  0.65 (0.51), residues: 123
  loop : -0.89 (0.27), residues: 559

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1760 
 TYR   0.010   0.001   TYR A1668 
 PHE   0.025   0.002   PHE A1242 
 TRP   0.009   0.001   TRP A1773 
 HIS   0.003   0.000   HIS C  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 (11442)
  covalent geometry    : angle       0.48530 (15513)
  hydrogen bonds       : bond        0.03841 (  500)
  hydrogen bonds       : angle       3.93995 ( 1461)
  Misc. bond           : bond        0.00053 (    3)
  link_TRANS           : bond        0.00032 (    1)
  link_TRANS           : angle       0.41236 (    2)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 204
  time to evaluate  : 0.500 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    1 MET cc_start: 0.4135 (ttt) cc_final: 0.3151 (ptt)
REVERT: C    6 LYS cc_start: 0.7908 (pttp) cc_final: 0.7559 (ttpp)
REVERT: C   24 GLU cc_start: 0.7752 (tt0) cc_final: 0.7503 (tm-30)
REVERT: A  504 GLN cc_start: 0.8194 (mm-40) cc_final: 0.7842 (mm-40)
REVERT: A  521 LEU cc_start: 0.8007 (mt) cc_final: 0.7799 (mt)
REVERT: A  615 LEU cc_start: 0.7718 (mp) cc_final: 0.7378 (mp)
REVERT: A  622 SER cc_start: 0.8428 (t) cc_final: 0.8032 (p)
REVERT: A  679 ASP cc_start: 0.7437 (t70) cc_final: 0.7072 (t0)
REVERT: A  715 MET cc_start: 0.6039 (mmm) cc_final: 0.5411 (mmm)
REVERT: A  783 MET cc_start: 0.7378 (tpp) cc_final: 0.7103 (mmm)
REVERT: A  872 MET cc_start: 0.2606 (ttm) cc_final: 0.1622 (ttm)
REVERT: A  889 VAL cc_start: 0.8222 (t) cc_final: 0.7992 (p)
REVERT: A  958 MET cc_start: 0.7141 (tmm) cc_final: 0.6931 (tmm)
REVERT: A 1153 PHE cc_start: 0.6423 (m-80) cc_final: 0.6132 (m-80)
REVERT: A 1200 ASP cc_start: 0.6448 (p0) cc_final: 0.6222 (p0)
REVERT: A 1254 ARG cc_start: 0.6900 (ttp-170) cc_final: 0.6382 (ttp-170)
REVERT: A 1539 ASN cc_start: 0.7910 (t0) cc_final: 0.7555 (t0)
REVERT: A 1543 LYS cc_start: 0.7829 (ttpp) cc_final: 0.7455 (ttpp)
REVERT: A 1610 MET cc_start: 0.7766 (mtt) cc_final: 0.7517 (mtt)
REVERT: A 1639 ARG cc_start: 0.7504 (mmt90) cc_final: 0.7257 (mmm-85)
REVERT: A 1642 ASN cc_start: 0.7676 (t0) cc_final: 0.7423 (t0)
REVERT: A 1668 TYR cc_start: 0.7477 (m-80) cc_final: 0.7016 (m-80)
REVERT: A 1698 TRP cc_start: 0.8115 (m100) cc_final: 0.7093 (m100)
REVERT: A 1746 ARG cc_start: 0.7870 (mtp85) cc_final: 0.7591 (mtp85)
REVERT: A 1752 MET cc_start: 0.7955 (mtp) cc_final: 0.7746 (mtm)
REVERT: A 1854 LYS cc_start: 0.7768 (tptm) cc_final: 0.7479 (ttmt)
REVERT: A 1997 PRO cc_start: 0.7180 (Cg_endo) cc_final: 0.6876 (Cg_exo)
REVERT: A 2018 SER cc_start: 0.8732 (t) cc_final: 0.8283 (p)
  outliers start: 15
  outliers final: 11
  residues processed: 211
  average time/residue: 0.1092
  time to fit residues: 32.7122
Evaluate side-chains
  212 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 201
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  537 LEU
Chi-restraints excluded: chain A residue  553 LEU
Chi-restraints excluded: chain A residue  583 CYS
Chi-restraints excluded: chain A residue  616 LEU
Chi-restraints excluded: chain A residue  683 HIS
Chi-restraints excluded: chain A residue  695 ASP
Chi-restraints excluded: chain A residue  726 MET
Chi-restraints excluded: chain A residue 1172 CYS
Chi-restraints excluded: chain A residue 1491 CYS
Chi-restraints excluded: chain A residue 1538 ASP
Chi-restraints excluded: chain A residue 1928 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 78 optimal weight:    9.9990
   chunk 105 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9980
   chunk 102 optimal weight:    0.2980
   chunk 15 optimal weight:    8.9990
   chunk 80 optimal weight:    0.0070
   chunk 35 optimal weight:    0.9980
   chunk 12 optimal weight:    5.9990
   chunk 34 optimal weight:    0.0980
   chunk 86 optimal weight:    1.9990
   chunk 90 optimal weight:    0.0870
   overall best weight:    0.2976

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

Flipped N/Q/H residues before XYZ refinement:
A1272 ASN
A2038 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.160662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.124117 restraints weight = 18593.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.127625 restraints weight = 9984.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.129762 restraints weight = 6609.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.131383 restraints weight = 5105.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.131894 restraints weight = 4293.522|
|-----------------------------------------------------------------------------|
r_work (final): 0.3616
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6921
moved from start:          0.1010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  11446  Z= 0.092
  Angle     :  0.455   9.772  15515  Z= 0.230
  Chirality :  0.037   0.149   1818
  Planarity :  0.004   0.058   1984
  Dihedral  :  4.575  79.146   1537
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  :  9.50 %
    Favored  : 88.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.47 %
    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 aren not related in a simple way.
  whole:  1.03 (0.24), residues: 1416
  helix:  1.81 (0.20), residues: 734
  sheet:  0.65 (0.51), residues: 125
  loop : -0.85 (0.28), residues: 557

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1760 
 TYR   0.009   0.001   TYR A1668 
 PHE   0.019   0.001   PHE A1242 
 TRP   0.007   0.001   TRP A1773 
 HIS   0.002   0.000   HIS A 661 

Details of bonding type rmsd
  covalent geometry    : bond        0.00206 (11442)
  covalent geometry    : angle       0.45512 (15513)
  hydrogen bonds       : bond        0.03092 (  500)
  hydrogen bonds       : angle       3.81671 ( 1461)
  Misc. bond           : bond        0.00068 (    3)
  link_TRANS           : bond        0.00069 (    1)
  link_TRANS           : angle       0.29997 (    2)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 204
  time to evaluate  : 0.424 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    1 MET cc_start: 0.3976 (ttt) cc_final: 0.3026 (ptt)
REVERT: C   24 GLU cc_start: 0.7738 (tt0) cc_final: 0.7488 (tm-30)
REVERT: A  504 GLN cc_start: 0.8178 (mm-40) cc_final: 0.7845 (mm-40)
REVERT: A  521 LEU cc_start: 0.8009 (mt) cc_final: 0.7778 (mt)
REVERT: A  615 LEU cc_start: 0.7687 (mp) cc_final: 0.7407 (mp)
REVERT: A  622 SER cc_start: 0.8402 (t) cc_final: 0.7972 (p)
REVERT: A  679 ASP cc_start: 0.7435 (t70) cc_final: 0.7018 (t0)
REVERT: A  872 MET cc_start: 0.2706 (ttm) cc_final: 0.1743 (ttm)
REVERT: A  889 VAL cc_start: 0.8208 (t) cc_final: 0.7972 (p)
REVERT: A  958 MET cc_start: 0.7218 (tmm) cc_final: 0.6866 (tmm)
REVERT: A 1153 PHE cc_start: 0.6379 (m-80) cc_final: 0.6063 (m-80)
REVERT: A 1200 ASP cc_start: 0.6414 (p0) cc_final: 0.6169 (p0)
REVERT: A 1254 ARG cc_start: 0.6883 (ttp-170) cc_final: 0.6418 (ttp-170)
REVERT: A 1539 ASN cc_start: 0.7881 (t0) cc_final: 0.7461 (t0)
REVERT: A 1610 MET cc_start: 0.7711 (OUTLIER) cc_final: 0.7443 (mtt)
REVERT: A 1639 ARG cc_start: 0.7478 (mmt90) cc_final: 0.7238 (mmm-85)
REVERT: A 1698 TRP cc_start: 0.8114 (m100) cc_final: 0.7060 (m100)
REVERT: A 1746 ARG cc_start: 0.7855 (mtp85) cc_final: 0.7595 (mtp85)
REVERT: A 1854 LYS cc_start: 0.7771 (tptm) cc_final: 0.7448 (ttmm)
REVERT: A 1997 PRO cc_start: 0.7176 (Cg_endo) cc_final: 0.6858 (Cg_exo)
REVERT: A 2018 SER cc_start: 0.8654 (t) cc_final: 0.8205 (p)
  outliers start: 21
  outliers final: 10
  residues processed: 210
  average time/residue: 0.1096
  time to fit residues: 32.6855
Evaluate side-chains
  215 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 204
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  553 LEU
Chi-restraints excluded: chain A residue  571 ILE
Chi-restraints excluded: chain A residue  616 LEU
Chi-restraints excluded: chain A residue  683 HIS
Chi-restraints excluded: chain A residue  695 ASP
Chi-restraints excluded: chain A residue 1172 CYS
Chi-restraints excluded: chain A residue 1491 CYS
Chi-restraints excluded: chain A residue 1541 MET
Chi-restraints excluded: chain A residue 1610 MET
Chi-restraints excluded: chain A residue 1928 MET
Chi-restraints excluded: chain A residue 2008 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 57 optimal weight:    0.9990
   chunk 87 optimal weight:    6.9990
   chunk 112 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9980
   chunk 103 optimal weight:    3.9990
   chunk 4 optimal weight:    7.9990
   chunk 108 optimal weight:    1.9990
   chunk 69 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 22 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
A1272 ASN
A2038 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.154632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.118368 restraints weight = 18452.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.121647 restraints weight = 10379.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.121921 restraints weight = 7410.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.123129 restraints weight = 6173.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.123280 restraints weight = 5415.509|
|-----------------------------------------------------------------------------|
r_work (final): 0.3473
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7127
moved from start:          0.1656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.106  11446  Z= 0.300
  Angle     :  0.657  10.099  15515  Z= 0.334
  Chirality :  0.045   0.170   1818
  Planarity :  0.005   0.063   1984
  Dihedral  :  5.153  96.183   1537
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.43 %
    Favored  : 93.57 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 10.90 %
    Favored  : 87.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.47 %
    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 aren not related in a simple way.
  whole:  0.27 (0.23), residues: 1416
  helix:  1.03 (0.19), residues: 736
  sheet:  0.46 (0.51), residues: 126
  loop : -1.01 (0.27), residues: 554

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A1988 
 TYR   0.018   0.002   TYR A1717 
 PHE   0.041   0.003   PHE A1148 
 TRP   0.016   0.002   TRP A1578 
 HIS   0.007   0.001   HIS C  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00717 (11442)
  covalent geometry    : angle       0.65697 (15513)
  hydrogen bonds       : bond        0.06448 (  500)
  hydrogen bonds       : angle       4.54635 ( 1461)
  Misc. bond           : bond        0.00068 (    3)
  link_TRANS           : bond        0.00057 (    1)
  link_TRANS           : angle       0.54734 (    2)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 218
  time to evaluate  : 0.425 
Fit side-chains
   revert: symmetry clash
REVERT: B    1 MET cc_start: 0.4870 (ttt) cc_final: 0.3202 (pmm)
REVERT: C   24 GLU cc_start: 0.7832 (tt0) cc_final: 0.7599 (tm-30)
REVERT: D    1 MET cc_start: 0.0394 (ptm) cc_final: -0.0608 (ptm)
REVERT: A  504 GLN cc_start: 0.8315 (mm-40) cc_final: 0.7939 (mm-40)
REVERT: A  615 LEU cc_start: 0.7967 (mp) cc_final: 0.7610 (mp)
REVERT: A  622 SER cc_start: 0.8543 (t) cc_final: 0.8150 (p)
REVERT: A  723 PHE cc_start: 0.8272 (OUTLIER) cc_final: 0.7837 (m-10)
REVERT: A  872 MET cc_start: 0.2821 (ttm) cc_final: 0.1742 (ttm)
REVERT: A 1153 PHE cc_start: 0.6662 (m-80) cc_final: 0.6456 (m-80)
REVERT: A 1254 ARG cc_start: 0.7069 (ttp-170) cc_final: 0.6580 (ttp-170)
REVERT: A 1272 ASN cc_start: 0.7370 (m-40) cc_final: 0.7126 (m110)
REVERT: A 1282 VAL cc_start: 0.6140 (p) cc_final: 0.4874 (m)
REVERT: A 1539 ASN cc_start: 0.7874 (t0) cc_final: 0.7527 (t0)
REVERT: A 1543 LYS cc_start: 0.7804 (ttpp) cc_final: 0.7394 (ttpp)
REVERT: A 1610 MET cc_start: 0.7721 (OUTLIER) cc_final: 0.7405 (mtt)
REVERT: A 1746 ARG cc_start: 0.7870 (mtp85) cc_final: 0.7617 (mtp85)
REVERT: A 1843 THR cc_start: 0.7839 (p) cc_final: 0.7585 (p)
REVERT: A 1854 LYS cc_start: 0.7777 (tptm) cc_final: 0.7496 (ttmt)
REVERT: A 1997 PRO cc_start: 0.7489 (Cg_endo) cc_final: 0.7187 (Cg_exo)
REVERT: A 2018 SER cc_start: 0.8681 (t) cc_final: 0.8144 (p)
  outliers start: 22
  outliers final: 15
  residues processed: 227
  average time/residue: 0.1031
  time to fit residues: 33.8131
Evaluate side-chains
  233 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 216
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  571 ILE
Chi-restraints excluded: chain A residue  583 CYS
Chi-restraints excluded: chain A residue  586 VAL
Chi-restraints excluded: chain A residue  616 LEU
Chi-restraints excluded: chain A residue  632 ILE
Chi-restraints excluded: chain A residue  695 ASP
Chi-restraints excluded: chain A residue  711 LEU
Chi-restraints excluded: chain A residue  723 PHE
Chi-restraints excluded: chain A residue  726 MET
Chi-restraints excluded: chain A residue 1172 CYS
Chi-restraints excluded: chain A residue 1491 CYS
Chi-restraints excluded: chain A residue 1541 MET
Chi-restraints excluded: chain A residue 1610 MET
Chi-restraints excluded: chain A residue 1704 THR
Chi-restraints excluded: chain A residue 1803 ILE
Chi-restraints excluded: chain A residue 1817 THR
Chi-restraints excluded: chain A residue 1928 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 70 optimal weight:    0.6980
   chunk 17 optimal weight:    0.5980
   chunk 35 optimal weight:    0.6980
   chunk 107 optimal weight:    0.7980
   chunk 67 optimal weight:    3.9990
   chunk 130 optimal weight:    0.7980
   chunk 83 optimal weight:   40.0000
   chunk 14 optimal weight:   20.0000
   chunk 5 optimal weight:    6.9990
   chunk 85 optimal weight:   20.0000
   chunk 15 optimal weight:    6.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A1737 HIS
A2038 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.157984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.121961 restraints weight = 18378.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.125083 restraints weight = 10229.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.127194 restraints weight = 6988.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.128291 restraints weight = 5456.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.129286 restraints weight = 4722.387|
|-----------------------------------------------------------------------------|
r_work (final): 0.3562
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6991
moved from start:          0.1550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  11446  Z= 0.145
  Angle     :  0.517   8.852  15515  Z= 0.265
  Chirality :  0.039   0.159   1818
  Planarity :  0.004   0.064   1984
  Dihedral  :  4.804  97.319   1537
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 5.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 12.47 %
    Favored  : 85.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.47 %
    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 aren not related in a simple way.
  whole:  0.59 (0.24), residues: 1416
  helix:  1.39 (0.20), residues: 736
  sheet:  0.50 (0.52), residues: 124
  loop : -0.99 (0.28), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1639 
 TYR   0.011   0.001   TYR A1668 
 PHE   0.021   0.002   PHE A1148 
 TRP   0.011   0.001   TRP A1773 
 HIS   0.003   0.000   HIS C  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 (11442)
  covalent geometry    : angle       0.51741 (15513)
  hydrogen bonds       : bond        0.04387 (  500)
  hydrogen bonds       : angle       4.17599 ( 1461)
  Misc. bond           : bond        0.00100 (    3)
  link_TRANS           : bond        0.00084 (    1)
  link_TRANS           : angle       0.36997 (    2)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 211
  time to evaluate  : 0.376 
Fit side-chains
   revert: symmetry clash
REVERT: B    1 MET cc_start: 0.4278 (ttt) cc_final: 0.3397 (ptp)
REVERT: C   24 GLU cc_start: 0.7745 (tt0) cc_final: 0.7521 (tm-30)
REVERT: D    1 MET cc_start: 0.0088 (ptm) cc_final: -0.0887 (ptm)
REVERT: A  504 GLN cc_start: 0.8177 (mm-40) cc_final: 0.7827 (mm-40)
REVERT: A  615 LEU cc_start: 0.7848 (mp) cc_final: 0.7518 (mp)
REVERT: A  622 SER cc_start: 0.8531 (t) cc_final: 0.8146 (p)
REVERT: A  679 ASP cc_start: 0.7449 (t70) cc_final: 0.7034 (t0)
REVERT: A  872 MET cc_start: 0.2769 (ttm) cc_final: 0.1696 (ttm)
REVERT: A  889 VAL cc_start: 0.8234 (t) cc_final: 0.7965 (p)
REVERT: A  958 MET cc_start: 0.7280 (tmm) cc_final: 0.6667 (tmm)
REVERT: A 1153 PHE cc_start: 0.6584 (m-80) cc_final: 0.6348 (m-80)
REVERT: A 1200 ASP cc_start: 0.6759 (p0) cc_final: 0.6526 (p0)
REVERT: A 1254 ARG cc_start: 0.6943 (ttp-170) cc_final: 0.6617 (ttp-170)
REVERT: A 1610 MET cc_start: 0.7656 (OUTLIER) cc_final: 0.7422 (mtt)
REVERT: A 1668 TYR cc_start: 0.7617 (m-80) cc_final: 0.7360 (m-80)
REVERT: A 1698 TRP cc_start: 0.8068 (m100) cc_final: 0.7044 (m100)
REVERT: A 1746 ARG cc_start: 0.7844 (mtp85) cc_final: 0.7615 (mtp85)
REVERT: A 1854 LYS cc_start: 0.7791 (tptm) cc_final: 0.7490 (ttmt)
REVERT: A 1997 PRO cc_start: 0.7367 (Cg_endo) cc_final: 0.7082 (Cg_exo)
REVERT: A 2018 SER cc_start: 0.8703 (t) cc_final: 0.8241 (p)
  outliers start: 21
  outliers final: 13
  residues processed: 218
  average time/residue: 0.0987
  time to fit residues: 31.0919
Evaluate side-chains
  220 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 206
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  553 LEU
Chi-restraints excluded: chain A residue  571 ILE
Chi-restraints excluded: chain A residue  616 LEU
Chi-restraints excluded: chain A residue  632 ILE
Chi-restraints excluded: chain A residue  688 LEU
Chi-restraints excluded: chain A residue  695 ASP
Chi-restraints excluded: chain A residue 1172 CYS
Chi-restraints excluded: chain A residue 1491 CYS
Chi-restraints excluded: chain A residue 1541 MET
Chi-restraints excluded: chain A residue 1610 MET
Chi-restraints excluded: chain A residue 1672 VAL
Chi-restraints excluded: chain A residue 1704 THR
Chi-restraints excluded: chain A residue 1803 ILE
Chi-restraints excluded: chain A residue 1928 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 66 optimal weight:    1.9990
   chunk 15 optimal weight:   50.0000
   chunk 20 optimal weight:    2.9990
   chunk 95 optimal weight:    1.9990
   chunk 120 optimal weight:    8.9990
   chunk 60 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 127 optimal weight:    0.9980
   chunk 88 optimal weight:    7.9990
   chunk 53 optimal weight:    0.9990
   chunk 33 optimal weight:    2.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
** B  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1272 ASN
A2038 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.155206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.119248 restraints weight = 18418.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.122376 restraints weight = 10224.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.124170 restraints weight = 6957.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.125590 restraints weight = 5516.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.126098 restraints weight = 4750.250|
|-----------------------------------------------------------------------------|
r_work (final): 0.3526
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7044
moved from start:          0.1796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.067  11446  Z= 0.237
  Angle     :  0.600   9.042  15515  Z= 0.306
  Chirality :  0.043   0.174   1818
  Planarity :  0.005   0.065   1984
  Dihedral  :  4.990 101.603   1537
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.50 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 12.63 %
    Favored  : 85.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.47 %
    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 aren not related in a simple way.
  whole:  0.33 (0.23), residues: 1416
  helix:  1.14 (0.20), residues: 735
  sheet:  0.41 (0.51), residues: 124
  loop : -1.05 (0.27), residues: 557

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 551 
 TYR   0.014   0.002   TYR A1668 
 PHE   0.033   0.003   PHE A1148 
 TRP   0.014   0.002   TRP A1773 
 HIS   0.005   0.001   HIS C  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00567 (11442)
  covalent geometry    : angle       0.60048 (15513)
  hydrogen bonds       : bond        0.05538 (  500)
  hydrogen bonds       : angle       4.39576 ( 1461)
  Misc. bond           : bond        0.00045 (    3)
  link_TRANS           : bond        0.00068 (    1)
  link_TRANS           : angle       0.53122 (    2)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 210
  time to evaluate  : 0.386 
Fit side-chains
   revert: symmetry clash
REVERT: B    1 MET cc_start: 0.4576 (ttt) cc_final: 0.3659 (ptp)
REVERT: C   24 GLU cc_start: 0.7744 (tt0) cc_final: 0.7511 (tm-30)
REVERT: D    1 MET cc_start: 0.0044 (ptm) cc_final: -0.0317 (ptm)
REVERT: A  504 GLN cc_start: 0.8181 (mm-40) cc_final: 0.7823 (mm-40)
REVERT: A  615 LEU cc_start: 0.7956 (mp) cc_final: 0.7607 (mp)
REVERT: A  622 SER cc_start: 0.8545 (t) cc_final: 0.8188 (p)
REVERT: A  723 PHE cc_start: 0.8212 (OUTLIER) cc_final: 0.7851 (m-10)
REVERT: A  872 MET cc_start: 0.2779 (ttm) cc_final: 0.1689 (ttm)
REVERT: A  889 VAL cc_start: 0.8232 (t) cc_final: 0.7965 (p)
REVERT: A  958 MET cc_start: 0.7386 (tmm) cc_final: 0.7045 (tmm)
REVERT: A 1200 ASP cc_start: 0.6858 (p0) cc_final: 0.6631 (p0)
REVERT: A 1254 ARG cc_start: 0.6969 (ttp-170) cc_final: 0.6647 (ttp-170)
REVERT: A 1610 MET cc_start: 0.7703 (OUTLIER) cc_final: 0.7455 (mtt)
REVERT: A 1746 ARG cc_start: 0.7846 (mtp85) cc_final: 0.7635 (mtp85)
REVERT: A 1752 MET cc_start: 0.8084 (mtp) cc_final: 0.7869 (mtm)
REVERT: A 1841 ASP cc_start: 0.7295 (t0) cc_final: 0.7078 (t0)
REVERT: A 1854 LYS cc_start: 0.7765 (tptm) cc_final: 0.7486 (ttmt)
REVERT: A 1997 PRO cc_start: 0.7378 (Cg_endo) cc_final: 0.7061 (Cg_exo)
REVERT: A 2018 SER cc_start: 0.8698 (t) cc_final: 0.8224 (p)
  outliers start: 27
  outliers final: 19
  residues processed: 219
  average time/residue: 0.1078
  time to fit residues: 33.3077
Evaluate side-chains
  230 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 209
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  537 LEU
Chi-restraints excluded: chain A residue  553 LEU
Chi-restraints excluded: chain A residue  571 ILE
Chi-restraints excluded: chain A residue  586 VAL
Chi-restraints excluded: chain A residue  616 LEU
Chi-restraints excluded: chain A residue  632 ILE
Chi-restraints excluded: chain A residue  688 LEU
Chi-restraints excluded: chain A residue  695 ASP
Chi-restraints excluded: chain A residue  723 PHE
Chi-restraints excluded: chain A residue  726 MET
Chi-restraints excluded: chain A residue 1172 CYS
Chi-restraints excluded: chain A residue 1491 CYS
Chi-restraints excluded: chain A residue 1534 TYR
Chi-restraints excluded: chain A residue 1538 ASP
Chi-restraints excluded: chain A residue 1541 MET
Chi-restraints excluded: chain A residue 1610 MET
Chi-restraints excluded: chain A residue 1672 VAL
Chi-restraints excluded: chain A residue 1704 THR
Chi-restraints excluded: chain A residue 1803 ILE
Chi-restraints excluded: chain A residue 1817 THR
Chi-restraints excluded: chain A residue 1928 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 51 optimal weight:    0.9980
   chunk 50 optimal weight:    0.3980
   chunk 64 optimal weight:    1.9990
   chunk 31 optimal weight:    0.5980
   chunk 133 optimal weight:    0.8980
   chunk 58 optimal weight:    0.5980
   chunk 139 optimal weight:    0.7980
   chunk 88 optimal weight:    5.9990
   chunk 76 optimal weight:    0.7980
   chunk 38 optimal weight:    0.7980
   chunk 98 optimal weight:    0.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** B  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1691 GLN
A2038 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.158260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.123585 restraints weight = 18427.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.125498 restraints weight = 10533.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.126367 restraints weight = 8308.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.127559 restraints weight = 6731.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.127739 restraints weight = 5438.817|
|-----------------------------------------------------------------------------|
r_work (final): 0.3530
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7058
moved from start:          0.1719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  11446  Z= 0.133
  Angle     :  0.529   8.823  15515  Z= 0.269
  Chirality :  0.039   0.182   1818
  Planarity :  0.004   0.067   1984
  Dihedral  :  4.778 100.476   1537
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.65 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 13.38 %
    Favored  : 84.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.47 %
    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 aren not related in a simple way.
  whole:  0.62 (0.24), residues: 1416
  helix:  1.43 (0.20), residues: 735
  sheet:  0.40 (0.51), residues: 124
  loop : -0.95 (0.28), residues: 557

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A2023 
 TYR   0.011   0.001   TYR A1668 
 PHE   0.034   0.002   PHE A1242 
 TRP   0.011   0.001   TRP A1773 
 HIS   0.002   0.000   HIS C  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 (11442)
  covalent geometry    : angle       0.52885 (15513)
  hydrogen bonds       : bond        0.04079 (  500)
  hydrogen bonds       : angle       4.14480 ( 1461)
  Misc. bond           : bond        0.00053 (    3)
  link_TRANS           : bond        0.00052 (    1)
  link_TRANS           : angle       0.31125 (    2)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 213
  time to evaluate  : 0.403 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   24 GLU cc_start: 0.7769 (tt0) cc_final: 0.7521 (tm-30)
REVERT: D    1 MET cc_start: 0.0095 (ptm) cc_final: -0.0178 (ptm)
REVERT: A  504 GLN cc_start: 0.8266 (mm-40) cc_final: 0.7880 (mm-40)
REVERT: A  615 LEU cc_start: 0.7871 (mp) cc_final: 0.7540 (mp)
REVERT: A  622 SER cc_start: 0.8482 (t) cc_final: 0.8147 (p)
REVERT: A  679 ASP cc_start: 0.7432 (t70) cc_final: 0.7033 (t0)
REVERT: A  872 MET cc_start: 0.2807 (ttm) cc_final: 0.1745 (ttm)
REVERT: A  889 VAL cc_start: 0.8225 (t) cc_final: 0.7931 (p)
REVERT: A  958 MET cc_start: 0.7387 (tmm) cc_final: 0.7152 (tmm)
REVERT: A 1254 ARG cc_start: 0.7034 (ttp-170) cc_final: 0.6692 (ttp-170)
REVERT: A 1272 ASN cc_start: 0.7521 (m-40) cc_final: 0.7265 (t0)
REVERT: A 1610 MET cc_start: 0.7730 (OUTLIER) cc_final: 0.7493 (mtt)
REVERT: A 1746 ARG cc_start: 0.7834 (mtp85) cc_final: 0.7608 (mtp85)
REVERT: A 1854 LYS cc_start: 0.7803 (tptm) cc_final: 0.7514 (ttmt)
REVERT: A 1997 PRO cc_start: 0.7457 (Cg_endo) cc_final: 0.7138 (Cg_exo)
REVERT: A 2018 SER cc_start: 0.8728 (t) cc_final: 0.8242 (p)
  outliers start: 20
  outliers final: 16
  residues processed: 219
  average time/residue: 0.1059
  time to fit residues: 33.2052
Evaluate side-chains
  225 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 208
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  537 LEU
Chi-restraints excluded: chain A residue  553 LEU
Chi-restraints excluded: chain A residue  571 ILE
Chi-restraints excluded: chain A residue  616 LEU
Chi-restraints excluded: chain A residue  632 ILE
Chi-restraints excluded: chain A residue  688 LEU
Chi-restraints excluded: chain A residue  695 ASP
Chi-restraints excluded: chain A residue 1172 CYS
Chi-restraints excluded: chain A residue 1491 CYS
Chi-restraints excluded: chain A residue 1534 TYR
Chi-restraints excluded: chain A residue 1541 MET
Chi-restraints excluded: chain A residue 1610 MET
Chi-restraints excluded: chain A residue 1672 VAL
Chi-restraints excluded: chain A residue 1704 THR
Chi-restraints excluded: chain A residue 1803 ILE
Chi-restraints excluded: chain A residue 1817 THR
Chi-restraints excluded: chain A residue 1928 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 1 optimal weight:   10.0000
   chunk 123 optimal weight:    1.9990
   chunk 35 optimal weight:    0.5980
   chunk 81 optimal weight:    8.9990
   chunk 89 optimal weight:    0.6980
   chunk 36 optimal weight:    0.6980
   chunk 104 optimal weight:    3.9990
   chunk 17 optimal weight:    0.6980
   chunk 120 optimal weight:   10.0000
   chunk 53 optimal weight:    0.8980
   chunk 117 optimal weight:    0.7980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** B  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2038 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.157955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.122180 restraints weight = 18304.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.125334 restraints weight = 10178.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.127461 restraints weight = 6923.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.128366 restraints weight = 5403.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.129535 restraints weight = 4732.750|
|-----------------------------------------------------------------------------|
r_work (final): 0.3566
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6985
moved from start:          0.1773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058  11446  Z= 0.145
  Angle     :  0.552   8.722  15515  Z= 0.281
  Chirality :  0.040   0.176   1818
  Planarity :  0.005   0.067   1984
  Dihedral  :  4.746 100.823   1537
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.50 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 14.12 %
    Favored  : 84.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.47 %
    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 aren not related in a simple way.
  whole:  0.63 (0.24), residues: 1416
  helix:  1.46 (0.20), residues: 732
  sheet:  0.39 (0.50), residues: 124
  loop : -0.96 (0.28), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1639 
 TYR   0.015   0.001   TYR A1668 
 PHE   0.036   0.002   PHE A1242 
 TRP   0.010   0.001   TRP A1773 
 HIS   0.002   0.000   HIS C  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 (11442)
  covalent geometry    : angle       0.55199 (15513)
  hydrogen bonds       : bond        0.04289 (  500)
  hydrogen bonds       : angle       4.18441 ( 1461)
  Misc. bond           : bond        0.00049 (    3)
  link_TRANS           : bond        0.00086 (    1)
  link_TRANS           : angle       0.34477 (    2)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 207
  time to evaluate  : 0.421 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   24 GLU cc_start: 0.7717 (tt0) cc_final: 0.7486 (tm-30)
REVERT: D    1 MET cc_start: -0.0092 (ptm) cc_final: -0.0394 (ptm)
REVERT: A  504 GLN cc_start: 0.8100 (mm-40) cc_final: 0.7776 (mm-40)
REVERT: A  615 LEU cc_start: 0.7909 (mp) cc_final: 0.7568 (mp)
REVERT: A  622 SER cc_start: 0.8504 (t) cc_final: 0.8131 (p)
REVERT: A  624 ASN cc_start: 0.7910 (t0) cc_final: 0.7305 (t0)
REVERT: A  872 MET cc_start: 0.2696 (ttm) cc_final: 0.1628 (ttm)
REVERT: A  889 VAL cc_start: 0.8205 (t) cc_final: 0.7922 (p)
REVERT: A 1254 ARG cc_start: 0.6946 (ttp-170) cc_final: 0.6635 (ttp-170)
REVERT: A 1272 ASN cc_start: 0.7492 (m-40) cc_final: 0.7266 (t0)
REVERT: A 1610 MET cc_start: 0.7683 (OUTLIER) cc_final: 0.7456 (mtt)
REVERT: A 1668 TYR cc_start: 0.7635 (m-80) cc_final: 0.7362 (m-80)
REVERT: A 1746 ARG cc_start: 0.7831 (mtp85) cc_final: 0.7612 (mtp85)
REVERT: A 1854 LYS cc_start: 0.7811 (tptm) cc_final: 0.7536 (ttmt)
REVERT: A 2018 SER cc_start: 0.8713 (t) cc_final: 0.8260 (p)
  outliers start: 16
  outliers final: 14
  residues processed: 213
  average time/residue: 0.1031
  time to fit residues: 31.3990
Evaluate side-chains
  218 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 203
  time to evaluate  : 0.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  537 LEU
Chi-restraints excluded: chain A residue  553 LEU
Chi-restraints excluded: chain A residue  571 ILE
Chi-restraints excluded: chain A residue  616 LEU
Chi-restraints excluded: chain A residue  632 ILE
Chi-restraints excluded: chain A residue  688 LEU
Chi-restraints excluded: chain A residue  695 ASP
Chi-restraints excluded: chain A residue 1172 CYS
Chi-restraints excluded: chain A residue 1491 CYS
Chi-restraints excluded: chain A residue 1534 TYR
Chi-restraints excluded: chain A residue 1610 MET
Chi-restraints excluded: chain A residue 1672 VAL
Chi-restraints excluded: chain A residue 1803 ILE
Chi-restraints excluded: chain A residue 1817 THR
Chi-restraints excluded: chain A residue 1928 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 122 optimal weight:    9.9990
   chunk 3 optimal weight:    2.9990
   chunk 38 optimal weight:    0.7980
   chunk 79 optimal weight:   20.0000
   chunk 74 optimal weight:    0.7980
   chunk 61 optimal weight:    0.9990
   chunk 106 optimal weight:    0.7980
   chunk 31 optimal weight:    1.9990
   chunk 133 optimal weight:    0.6980
   chunk 42 optimal weight:    0.5980
   chunk 48 optimal weight:    0.6980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** B  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2038 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.157260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.122566 restraints weight = 18429.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.124380 restraints weight = 10603.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.125704 restraints weight = 8358.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.126723 restraints weight = 6258.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.126902 restraints weight = 5543.546|
|-----------------------------------------------------------------------------|
r_work (final): 0.3528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7057
moved from start:          0.1813

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065  11446  Z= 0.144
  Angle     :  0.545   8.406  15515  Z= 0.276
  Chirality :  0.040   0.172   1818
  Planarity :  0.005   0.070   1984
  Dihedral  :  4.743 101.658   1537
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.29 %
    Favored  : 93.71 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 13.79 %
    Favored  : 84.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.47 %
    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 aren not related in a simple way.
  whole:  0.64 (0.24), residues: 1416
  helix:  1.45 (0.20), residues: 733
  sheet:  0.43 (0.50), residues: 124
  loop : -0.94 (0.28), residues: 559

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1639 
 TYR   0.014   0.001   TYR A1668 
 PHE   0.033   0.002   PHE A1242 
 TRP   0.010   0.001   TRP A1773 
 HIS   0.002   0.000   HIS C  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 (11442)
  covalent geometry    : angle       0.54521 (15513)
  hydrogen bonds       : bond        0.04213 (  500)
  hydrogen bonds       : angle       4.15515 ( 1461)
  Misc. bond           : bond        0.00048 (    3)
  link_TRANS           : bond        0.00084 (    1)
  link_TRANS           : angle       0.34002 (    2)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 206
  time to evaluate  : 0.501 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   24 GLU cc_start: 0.7783 (tt0) cc_final: 0.7534 (tm-30)
REVERT: D    1 MET cc_start: 0.0046 (ptm) cc_final: -0.0226 (ptm)
REVERT: A  504 GLN cc_start: 0.8210 (mm-40) cc_final: 0.7831 (mm-40)
REVERT: A  615 LEU cc_start: 0.7887 (mp) cc_final: 0.7552 (mp)
REVERT: A  622 SER cc_start: 0.8498 (t) cc_final: 0.8143 (p)
REVERT: A  624 ASN cc_start: 0.7915 (t0) cc_final: 0.7300 (t0)
REVERT: A  679 ASP cc_start: 0.7430 (t70) cc_final: 0.7042 (t0)
REVERT: A  872 MET cc_start: 0.2771 (ttm) cc_final: 0.1742 (ttm)
REVERT: A  889 VAL cc_start: 0.8209 (t) cc_final: 0.7922 (p)
REVERT: A  958 MET cc_start: 0.7227 (tmm) cc_final: 0.6661 (tmm)
REVERT: A 1254 ARG cc_start: 0.7050 (ttp-170) cc_final: 0.6698 (ttp-170)
REVERT: A 1610 MET cc_start: 0.7685 (OUTLIER) cc_final: 0.7474 (mtt)
REVERT: A 1668 TYR cc_start: 0.7627 (m-80) cc_final: 0.7345 (m-80)
REVERT: A 1746 ARG cc_start: 0.7841 (mtp85) cc_final: 0.7611 (mtp85)
REVERT: A 1854 LYS cc_start: 0.7838 (tptm) cc_final: 0.7538 (ttmt)
REVERT: A 2018 SER cc_start: 0.8710 (t) cc_final: 0.8208 (p)
  outliers start: 20
  outliers final: 17
  residues processed: 214
  average time/residue: 0.1101
  time to fit residues: 33.5960
Evaluate side-chains
  222 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 204
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  537 LEU
Chi-restraints excluded: chain A residue  553 LEU
Chi-restraints excluded: chain A residue  571 ILE
Chi-restraints excluded: chain A residue  586 VAL
Chi-restraints excluded: chain A residue  616 LEU
Chi-restraints excluded: chain A residue  632 ILE
Chi-restraints excluded: chain A residue  688 LEU
Chi-restraints excluded: chain A residue  695 ASP
Chi-restraints excluded: chain A residue 1172 CYS
Chi-restraints excluded: chain A residue 1491 CYS
Chi-restraints excluded: chain A residue 1534 TYR
Chi-restraints excluded: chain A residue 1541 MET
Chi-restraints excluded: chain A residue 1610 MET
Chi-restraints excluded: chain A residue 1672 VAL
Chi-restraints excluded: chain A residue 1704 THR
Chi-restraints excluded: chain A residue 1803 ILE
Chi-restraints excluded: chain A residue 1817 THR
Chi-restraints excluded: chain A residue 1928 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 88 optimal weight:    0.9990
   chunk 34 optimal weight:    0.7980
   chunk 26 optimal weight:    4.9990
   chunk 133 optimal weight:    4.9990
   chunk 134 optimal weight:    2.9990
   chunk 136 optimal weight:    2.9990
   chunk 92 optimal weight:    0.5980
   chunk 105 optimal weight:    3.9990
   chunk 0 optimal weight:    9.9990
   chunk 37 optimal weight:    0.9990
   chunk 139 optimal weight:    2.9990
   overall best weight:    1.2786

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

Flipped N/Q/H residues before XYZ refinement:
** B  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1272 ASN
A2038 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.154833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.119830 restraints weight = 18510.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.121445 restraints weight = 10024.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.123011 restraints weight = 7556.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.123783 restraints weight = 5816.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.123981 restraints weight = 5218.686|
|-----------------------------------------------------------------------------|
r_work (final): 0.3495
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7095
moved from start:          0.2008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.080  11446  Z= 0.223
  Angle     :  0.614   9.647  15515  Z= 0.310
  Chirality :  0.042   0.173   1818
  Planarity :  0.005   0.069   1984
  Dihedral  :  4.992 105.826   1537
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.78 %
    Favored  : 93.22 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 13.87 %
    Favored  : 84.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.47 %
    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 aren not related in a simple way.
  whole:  0.36 (0.23), residues: 1416
  helix:  1.16 (0.20), residues: 735
  sheet:  0.41 (0.50), residues: 124
  loop : -1.03 (0.27), residues: 557

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 551 
 TYR   0.018   0.002   TYR A1668 
 PHE   0.034   0.003   PHE A1242 
 TRP   0.013   0.002   TRP A1773 
 HIS   0.004   0.001   HIS C  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00534 (11442)
  covalent geometry    : angle       0.61409 (15513)
  hydrogen bonds       : bond        0.05358 (  500)
  hydrogen bonds       : angle       4.38727 ( 1461)
  Misc. bond           : bond        0.00046 (    3)
  link_TRANS           : bond        0.00082 (    1)
  link_TRANS           : angle       0.42709 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2019.17 seconds
wall clock time: 35 minutes 33.23 seconds (2133.23 seconds total)