Starting phenix.real_space_refine
on Thu May  1 01:43:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9b13_44064/05_2025/9b13_44064_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9b13_44064/05_2025/9b13_44064.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9b13_44064/05_2025/9b13_44064.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9b13_44064/05_2025/9b13_44064.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9b13_44064/05_2025/9b13_44064_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9b13_44064/05_2025/9b13_44064_neut.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.967
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Ca      1      9.91       5
     S      49      5.16       5
     C    6358      2.51       5
     N    1699      2.21       5
     O    1906      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 10013
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 6745
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 842, 6745
          Classifications: {'peptide': 842}
          Link IDs: {'PTRANS': 44, 'TRANS': 797}
          Chain breaks: 8
    Chain: "H"
      Number of atoms: 1697
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 226, 1697
          Classifications: {'peptide': 226}
          Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 214}
          Chain breaks: 2
    Chain: "L"
      Number of atoms: 1570
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 206, 1570
          Classifications: {'peptide': 206}
          Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 195}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 7.54, per 1000 atoms: 0.75
  Number of scatterers: 10013
  At special positions: 0
  Unit cell: (96.481, 81.928, 170.863, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Ca      1     19.99
     S      49     16.00
     O    1906      8.00
     N    1699      7.00
     C    6358      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  25 " - pdb=" SG  CYS H  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 160 " - pdb=" SG  CYS H 216 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  24 " - pdb=" SG  CYS L  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 135 " - pdb=" SG  CYS L 195 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.55
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2492 Ramachandran restraints generated.
    1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2406

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 18 sheets defined
      27.3% alpha, 24.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 844 through 848
    Processing helix  chain 'A' and resid 851 through 861
    Processing helix  chain 'A' and resid 934 through 936
      No H-bonds generated for 'chain 'A' and resid 934 through 936'
    Processing helix  chain 'A' and resid 949 through 958
    Processing helix  chain 'A' and resid 963 through 966
    Processing helix  chain 'A' and resid 988 through 1010
      removed outlier: 3.927A  pdb=" N   GLU A1001 " --> pdb=" O   SER A 997 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1015 through 1028
    Processing helix  chain 'A' and resid 1038 through 1046
    Processing helix  chain 'A' and resid 1195 through 1208
    Processing helix  chain 'A' and resid 1211 through 1219
    Processing helix  chain 'A' and resid 1250 through 1254
    Processing helix  chain 'A' and resid 1274 through 1288
    Processing helix  chain 'A' and resid 1308 through 1317
    Processing helix  chain 'A' and resid 1323 through 1335
      removed outlier: 3.623A  pdb=" N   LYS A1333 " --> pdb=" O   SER A1329 " (cutoff:3.500A)
      removed outlier: 4.483A  pdb=" N   PHE A1334 " --> pdb=" O   ILE A1330 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   GLU A1335 " --> pdb=" O   ILE A1331 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1337 through 1343
      removed outlier: 3.546A  pdb=" N   CYS A1341 " --> pdb=" O   ASN A1337 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   HIS A1342 " --> pdb=" O   ILE A1338 " (cutoff:3.500A)
      removed outlier: 4.358A  pdb=" N   GLN A1343 " --> pdb=" O   SER A1339 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1337 through 1343'
    Processing helix  chain 'A' and resid 1347 through 1356
    Processing helix  chain 'A' and resid 1404 through 1412
      removed outlier: 3.914A  pdb=" N   GLN A1408 " --> pdb=" O   GLU A1404 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   LEU A1410 " --> pdb=" O   TYR A1406 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1443 through 1453
      removed outlier: 3.781A  pdb=" N   SER A1453 " --> pdb=" O   ALA A1449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1471 through 1486
    Processing helix  chain 'A' and resid 1496 through 1500
    Processing helix  chain 'A' and resid 1509 through 1513
    Processing helix  chain 'A' and resid 1643 through 1648
    Processing helix  chain 'A' and resid 1731 through 1735
    Processing helix  chain 'A' and resid 1741 through 1751
    Processing helix  chain 'A' and resid 1752 through 1759
    Processing helix  chain 'A' and resid 1780 through 1787
      removed outlier: 4.412A  pdb=" N   HIS A1786 " --> pdb=" O   MET A1782 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   GLY A1787 " --> pdb=" O   PHE A1783 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1799 through 1809
      removed outlier: 3.701A  pdb=" N   PHE A1809 " --> pdb=" O   ASN A1805 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1810 through 1815
      removed outlier: 3.790A  pdb=" N   GLY A1813 " --> pdb=" O   GLU A1810 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1821 through 1826
      removed outlier: 4.079A  pdb=" N   TRP A1825 " --> pdb=" O   PRO A1821 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1909 through 1912
      removed outlier: 3.778A  pdb=" N   LEU A1912 " --> pdb=" O   PHE A1909 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1909 through 1912'
    Processing helix  chain 'A' and resid 1936 through 1938
      No H-bonds generated for 'chain 'A' and resid 1936 through 1938'
    Processing helix  chain 'A' and resid 1977 through 1983
      removed outlier: 3.524A  pdb=" N   ASN A1983 " --> pdb=" O   SER A1979 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1984 through 1991
      removed outlier: 4.691A  pdb=" N   LYS A1988 " --> pdb=" O   THR A1984 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2016 through 2026
    Processing helix  chain 'A' and resid 2068 through 2075
      removed outlier: 3.801A  pdb=" N   ILE A2072 " --> pdb=" O   ASP A2068 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 31 through 35
    Processing helix  chain 'H' and resid 90 through 94
    Processing helix  chain 'H' and resid 176 through 178
      No H-bonds generated for 'chain 'H' and resid 176 through 178'
    Processing helix  chain 'H' and resid 207 through 209
      No H-bonds generated for 'chain 'H' and resid 207 through 209'
    Processing helix  chain 'H' and resid 221 through 224
    Processing helix  chain 'L' and resid 80 through 84
      removed outlier: 3.500A  pdb=" N   PHE L  84 " --> pdb=" O   PRO L  81 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 122 through 128
      removed outlier: 3.739A  pdb=" N   SER L 128 " --> pdb=" O   SER L 124 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 184 through 189
    Processing sheet with id=AA1, first strand: chain 'A' and resid 873 through 879
      removed outlier: 3.599A  pdb=" N   ALA A 862 " --> pdb=" O   LEU A 879 " (cutoff:3.500A)
      removed outlier: 4.434A  pdb=" N   HIS A 984 " --> pdb=" O   TYR A 867 " (cutoff:3.500A)
      removed outlier: 4.225A  pdb=" N   ALA A 940 " --> pdb=" O   LEU A 972 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 1223 through 1225
      removed outlier: 3.500A  pdb=" N   CYS A1225 " --> pdb=" O   ILE A1302 " (cutoff:3.500A)
      removed outlier: 4.293A  pdb=" N   ILE A1302 " --> pdb=" O   CYS A1225 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1441 through 1442
      removed outlier: 6.481A  pdb=" N   ILE A1417 " --> pdb=" O   SER A1465 " (cutoff:3.500A)
      removed outlier: 7.782A  pdb=" N   GLU A1467 " --> pdb=" O   ILE A1417 " (cutoff:3.500A)
      removed outlier: 6.167A  pdb=" N   LEU A1419 " --> pdb=" O   GLU A1467 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   HIS A1469 " --> pdb=" O   LEU A1419 " (cutoff:3.500A)
      removed outlier: 6.845A  pdb=" N   CYS A1421 " --> pdb=" O   HIS A1469 " (cutoff:3.500A)
      removed outlier: 6.305A  pdb=" N   ILE A1462 " --> pdb=" O   LEU A1517 " (cutoff:3.500A)
      removed outlier: 7.472A  pdb=" N   LYS A1519 " --> pdb=" O   ILE A1462 " (cutoff:3.500A)
      removed outlier: 6.322A  pdb=" N   ILE A1464 " --> pdb=" O   LYS A1519 " (cutoff:3.500A)
      removed outlier: 4.202A  pdb=" N   CYS A1653 " --> pdb=" O   LEU A1518 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1737 through 1740
      removed outlier: 7.162A  pdb=" N   SER A1737 " --> pdb=" O   ARG A1765 " (cutoff:3.500A)
      removed outlier: 8.738A  pdb=" N   TYR A1767 " --> pdb=" O   SER A1737 " (cutoff:3.500A)
      removed outlier: 7.413A  pdb=" N   LEU A1739 " --> pdb=" O   TYR A1767 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1901 through 1907
      removed outlier: 4.951A  pdb=" N   TYR A1850 " --> pdb=" O   MET A1967 " (cutoff:3.500A)
      removed outlier: 6.669A  pdb=" N   MET A1967 " --> pdb=" O   TYR A1850 " (cutoff:3.500A)
      removed outlier: 5.329A  pdb=" N   LEU A1852 " --> pdb=" O   ARG A1965 " (cutoff:3.500A)
      removed outlier: 7.019A  pdb=" N   ARG A1965 " --> pdb=" O   LEU A1852 " (cutoff:3.500A)
      removed outlier: 5.306A  pdb=" N   ILE A1854 " --> pdb=" O   ASN A1963 " (cutoff:3.500A)
      removed outlier: 6.932A  pdb=" N   ASN A1963 " --> pdb=" O   ILE A1854 " (cutoff:3.500A)
      removed outlier: 7.122A  pdb=" N   SER A1958 " --> pdb=" O   LEU A1947 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   LEU A1947 " --> pdb=" O   SER A1958 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   SER A1964 " --> pdb=" O   GLY A1941 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1869 through 1872
      removed outlier: 3.825A  pdb=" N   ASP A1874 " --> pdb=" O   ARG A1916 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   CYS A1883 " --> pdb=" O   VAL A1875 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1869 through 1872
    Processing sheet with id=AA8, first strand: chain 'A' and resid 2006 through 2011
      removed outlier: 3.716A  pdb=" N   VAL A1997 " --> pdb=" O   ALA A2007 " (cutoff:3.500A)
      removed outlier: 18.326A  pdb=" N   LYS A1994 " --> pdb=" O   TYR A2082 " (cutoff:3.500A)
      removed outlier: 12.575A  pdb=" N   GLY A2084 " --> pdb=" O   LYS A1994 " (cutoff:3.500A)
      removed outlier: 8.388A  pdb=" N   THR A1996 " --> pdb=" O   GLY A2084 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   ILE A2086 " --> pdb=" O   THR A1996 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   LEU A2088 " --> pdb=" O   HIS A1998 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   VAL A2083 " --> pdb=" O   HIS A2045 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   HIS A2045 " --> pdb=" O   VAL A2083 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   VAL A2087 " --> pdb=" O   MET A2041 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 7 through 10
      removed outlier: 3.693A  pdb=" N   CYS H  25 " --> pdb=" O   ALA H  82 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   ALA H  82 " --> pdb=" O   CYS H  25 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'H' and resid 49 through 54
      removed outlier: 6.775A  pdb=" N   TRP H  39 " --> pdb=" O   VAL H  51 " (cutoff:3.500A)
      removed outlier: 4.968A  pdb=" N   SER H  53 " --> pdb=" O   ILE H  37 " (cutoff:3.500A)
      removed outlier: 7.245A  pdb=" N   ILE H  37 " --> pdb=" O   SER H  53 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   SER H  36 " --> pdb=" O   SER H 102 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 49 through 54
      removed outlier: 6.775A  pdb=" N   TRP H  39 " --> pdb=" O   VAL H  51 " (cutoff:3.500A)
      removed outlier: 4.968A  pdb=" N   SER H  53 " --> pdb=" O   ILE H  37 " (cutoff:3.500A)
      removed outlier: 7.245A  pdb=" N   ILE H  37 " --> pdb=" O   SER H  53 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 140 through 144
      removed outlier: 3.613A  pdb=" N   GLY H 159 " --> pdb=" O   LEU H 144 " (cutoff:3.500A)
      removed outlier: 6.234A  pdb=" N   TYR H 196 " --> pdb=" O   ASP H 164 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'H' and resid 171 through 174
      removed outlier: 4.360A  pdb=" N   TYR H 214 " --> pdb=" O   VAL H 231 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'L' and resid 11 through 13
      removed outlier: 3.667A  pdb=" N   ALA L  85 " --> pdb=" O   VAL L 105 " (cutoff:3.500A)
      removed outlier: 6.395A  pdb=" N   TRP L  36 " --> pdb=" O   LEU L  48 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'L' and resid 20 through 25
    Processing sheet with id=AB7, first strand: chain 'L' and resid 90 through 92
      removed outlier: 3.693A  pdb=" N   THR L  98 " --> pdb=" O   GLN L  91 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'L' and resid 115 through 119
      removed outlier: 5.349A  pdb=" N   SER L 132 " --> pdb=" O   LEU L 182 " (cutoff:3.500A)
      removed outlier: 7.631A  pdb=" N   LEU L 182 " --> pdb=" O   SER L 132 " (cutoff:3.500A)
      removed outlier: 5.845A  pdb=" N   VAL L 134 " --> pdb=" O   LEU L 180 " (cutoff:3.500A)
      removed outlier: 7.299A  pdb=" N   LEU L 180 " --> pdb=" O   VAL L 134 " (cutoff:3.500A)
      removed outlier: 5.147A  pdb=" N   LEU L 136 " --> pdb=" O   SER L 178 " (cutoff:3.500A)
      removed outlier: 7.035A  pdb=" N   SER L 178 " --> pdb=" O   LEU L 136 " (cutoff:3.500A)
      removed outlier: 4.898A  pdb=" N   ASN L 138 " --> pdb=" O   LEU L 176 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   LEU L 176 " --> pdb=" O   ASN L 138 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'L' and resid 154 through 156
      removed outlier: 4.266A  pdb=" N   TRP L 149 " --> pdb=" O   GLN L 156 " (cutoff:3.500A)

    349 hydrogen bonds defined for protein.
    897 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.70

  Time building geometry restraints manager: 3.01 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3237
        1.34 -     1.46: 2369
        1.46 -     1.58: 4561
        1.58 -     1.70: 0
        1.70 -     1.81: 70
  Bond restraints: 10237
  Sorted by residual:
  bond pdb=" N   HIS A 838 "
       pdb=" CA  HIS A 838 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 2.93e+00
  bond pdb=" N   GLU H   4 "
       pdb=" CA  GLU H   4 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.88e+00
  bond pdb=" N   ILE L   3 "
       pdb=" CA  ILE L   3 "
    ideal  model  delta    sigma   weight residual
    1.458  1.489 -0.031 1.90e-02 2.77e+03 2.72e+00
  bond pdb=" CA  ILE A1854 "
       pdb=" C   ILE A1854 "
    ideal  model  delta    sigma   weight residual
    1.527  1.515  0.012 9.70e-03 1.06e+04 1.55e+00
  bond pdb=" CB  PRO A2090 "
       pdb=" CG  PRO A2090 "
    ideal  model  delta    sigma   weight residual
    1.492  1.542 -0.050 5.00e-02 4.00e+02 1.01e+00
  ... (remaining 10232 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.14: 13171
        1.14 -     2.28: 584
        2.28 -     3.42: 89
        3.42 -     4.56: 27
        4.56 -     5.70: 3
  Bond angle restraints: 13874
  Sorted by residual:
  angle pdb=" C   SER L  53 "
        pdb=" CA  SER L  53 "
        pdb=" CB  SER L  53 "
      ideal   model   delta    sigma   weight residual
     115.79  110.42    5.37 1.19e+00 7.06e-01 2.04e+01
  angle pdb=" C   SER L  51 "
        pdb=" CA  SER L  51 "
        pdb=" CB  SER L  51 "
      ideal   model   delta    sigma   weight residual
     117.23  111.53    5.70 1.36e+00 5.41e-01 1.76e+01
  angle pdb=" CA  SER L  51 "
        pdb=" C   SER L  51 "
        pdb=" N   ALA L  52 "
      ideal   model   delta    sigma   weight residual
     119.98  117.66    2.32 8.50e-01 1.38e+00 7.42e+00
  angle pdb=" N   GLU A2079 "
        pdb=" CA  GLU A2079 "
        pdb=" C   GLU A2079 "
      ideal   model   delta    sigma   weight residual
     114.56  111.27    3.29 1.27e+00 6.20e-01 6.73e+00
  angle pdb=" CA  TYR A2082 "
        pdb=" CB  TYR A2082 "
        pdb=" CG  TYR A2082 "
      ideal   model   delta    sigma   weight residual
     113.90  118.25   -4.35 1.80e+00 3.09e-01 5.84e+00
  ... (remaining 13869 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.22: 5742
       16.22 -    32.45: 335
       32.45 -    48.67: 65
       48.67 -    64.90: 19
       64.90 -    81.12: 2
  Dihedral angle restraints: 6163
    sinusoidal: 2449
      harmonic: 3714
  Sorted by residual:
  dihedral pdb=" CA  LYS A1333 "
           pdb=" C   LYS A1333 "
           pdb=" N   PHE A1334 "
           pdb=" CA  PHE A1334 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.39  -20.61     0      5.00e+00 4.00e-02 1.70e+01
  dihedral pdb=" CA  PRO A1971 "
           pdb=" C   PRO A1971 "
           pdb=" N   SER A1972 "
           pdb=" CA  SER A1972 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.29  -19.71     0      5.00e+00 4.00e-02 1.55e+01
  dihedral pdb=" CA  LEU A 842 "
           pdb=" C   LEU A 842 "
           pdb=" N   ILE A 843 "
           pdb=" CA  ILE A 843 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.96   19.04     0      5.00e+00 4.00e-02 1.45e+01
  ... (remaining 6160 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 962
       0.031 -    0.062: 422
       0.062 -    0.094: 80
       0.094 -    0.125: 84
       0.125 -    0.156: 8
  Chirality restraints: 1556
  Sorted by residual:
  chirality pdb=" CA  ILE L  49 "
            pdb=" N   ILE L  49 "
            pdb=" C   ILE L  49 "
            pdb=" CB  ILE L  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.08e-01
  chirality pdb=" CA  ILE A1927 "
            pdb=" N   ILE A1927 "
            pdb=" C   ILE A1927 "
            pdb=" CB  ILE A1927 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.91e-01
  chirality pdb=" CA  ILE L   3 "
            pdb=" N   ILE L   3 "
            pdb=" C   ILE L   3 "
            pdb=" CB  ILE L   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.83e-01
  ... (remaining 1553 not shown)

  Planarity restraints: 1774
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A2077 "   -0.032 5.00e-02 4.00e+02   4.81e-02 3.69e+00
        pdb=" N   PRO A2078 "    0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO A2078 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A2078 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A1658 "    0.021 5.00e-02 4.00e+02   3.22e-02 1.66e+00
        pdb=" N   PRO A1659 "   -0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO A1659 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A1659 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A1506 "   -0.021 5.00e-02 4.00e+02   3.16e-02 1.60e+00
        pdb=" N   PRO A1507 "    0.055 5.00e-02 4.00e+02
        pdb=" CA  PRO A1507 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A1507 "   -0.018 5.00e-02 4.00e+02
  ... (remaining 1771 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.63: 218
        2.63 -     3.20: 9671
        3.20 -     3.77: 14485
        3.77 -     4.33: 20637
        4.33 -     4.90: 33476
  Nonbonded interactions: 78487
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 963 "
            pdb=" OG1 THR A 967 "
     model   vdw
     2.068 3.040
  nonbonded pdb=" OD1 ASN A2012 "
            pdb=" OG1 THR A2015 "
     model   vdw
     2.082 3.040
  nonbonded pdb=" O   TYR L 187 "
            pdb=" OH  TYR L 193 "
     model   vdw
     2.096 3.040
  nonbonded pdb=" OD1 ASN A1316 "
            pdb=" N   GLY A2084 "
     model   vdw
     2.101 3.120
  nonbonded pdb=" NZ  LYS H 226 "
            pdb=" OD1 ASP H 228 "
     model   vdw
     2.102 3.120
  ... (remaining 78482 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
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             8.720
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.540
  Check model and map are aligned:         0.080
  Set scattering table:                    0.090
  Process input model:                     27.330
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.050
  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:2.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.710
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7394
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  10241  Z= 0.199
  Angle     :  0.570   5.698  13882  Z= 0.321
  Chirality :  0.041   0.156   1556
  Planarity :  0.004   0.048   1774
  Dihedral  : 11.167  81.123   3745
  Min Nonbonded Distance : 2.068

Molprobity Statistics.
  All-atom Clashscore : 10.01
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  8.43 %
    Favored  : 91.49 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  :  5.49 %
    Favored  : 90.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.29 (0.24), residues: 1246
  helix: -0.05 (0.32), residues: 254
  sheet: -0.73 (0.29), residues: 340
  loop : -1.22 (0.25), residues: 652

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 890 
 HIS   0.003   0.001   HIS A1803 
 PHE   0.012   0.001   PHE A1218 
 TYR   0.015   0.001   TYR H 104 
 ARG   0.004   0.000   ARG A1452 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.22921 (  342)
  hydrogen bonds       : angle       8.85516 (  897)
  SS BOND              : bond        0.00346 (    4)
  SS BOND              : angle       0.50325 (    8)
  covalent geometry    : bond        0.00417 (10237)
  covalent geometry    : angle       0.57049 (13874)

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

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

  2492 Ramachandran restraints generated.
    1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2492 Ramachandran restraints generated.
    1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  293 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 251
  time to evaluate  : 1.147 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  995 LEU cc_start: 0.7663 (mt) cc_final: 0.7265 (tt)
REVERT: A 1754 LYS cc_start: 0.8258 (mttt) cc_final: 0.7976 (tttt)
REVERT: A 1767 TYR cc_start: 0.8354 (OUTLIER) cc_final: 0.7866 (p90)
REVERT: A 1773 ILE cc_start: 0.8290 (pt) cc_final: 0.8013 (mm)
REVERT: A 1826 ASP cc_start: 0.6894 (t0) cc_final: 0.6590 (t0)
REVERT: A 1895 LEU cc_start: 0.8590 (mt) cc_final: 0.8335 (mp)
REVERT: A 1981 MET cc_start: 0.8611 (mmm) cc_final: 0.8406 (mmt)
REVERT: A 2038 TYR cc_start: 0.7857 (m-80) cc_final: 0.7610 (m-80)
REVERT: H   89 LEU cc_start: 0.8742 (mt) cc_final: 0.7874 (mt)
REVERT: L   91 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8150 (pp30)
REVERT: L  140 PHE cc_start: 0.8373 (p90) cc_final: 0.7738 (p90)
REVERT: L  174 TYR cc_start: 0.7439 (m-80) cc_final: 0.7202 (m-80)
  outliers start: 42
  outliers final: 20
  residues processed: 285
  average time/residue: 0.2528
  time to fit residues: 96.7800
Evaluate side-chains
  197 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 175
  time to evaluate  : 1.032 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  884 ASP
Chi-restraints excluded: chain A residue  887 THR
Chi-restraints excluded: chain A residue  936 PHE
Chi-restraints excluded: chain A residue  984 HIS
Chi-restraints excluded: chain A residue 1003 THR
Chi-restraints excluded: chain A residue 1302 ILE
Chi-restraints excluded: chain A residue 1417 ILE
Chi-restraints excluded: chain A residue 1425 ASP
Chi-restraints excluded: chain A residue 1736 ILE
Chi-restraints excluded: chain A residue 1767 TYR
Chi-restraints excluded: chain A residue 1774 ASP
Chi-restraints excluded: chain A residue 1812 ASN
Chi-restraints excluded: chain A residue 1823 VAL
Chi-restraints excluded: chain A residue 1944 HIS
Chi-restraints excluded: chain A residue 2082 TYR
Chi-restraints excluded: chain H residue   37 ILE
Chi-restraints excluded: chain H residue   99 CYS
Chi-restraints excluded: chain H residue  104 TYR
Chi-restraints excluded: chain H residue  130 THR
Chi-restraints excluded: chain L residue   54 SER
Chi-restraints excluded: chain L residue   90 GLN
Chi-restraints excluded: chain L residue   91 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 106 optimal weight:   10.0000
   chunk 95 optimal weight:    1.9990
   chunk 52 optimal weight:    0.2980
   chunk 32 optimal weight:    3.9990
   chunk 64 optimal weight:    0.3980
   chunk 51 optimal weight:    6.9990
   chunk 98 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 73 optimal weight:    5.9990
   chunk 114 optimal weight:    3.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
** A 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 951 HIS
** A1408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1777 ASN
A1902 GLN
** L 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.155409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.120110 restraints weight = 19617.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.119436 restraints weight = 13735.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.120501 restraints weight = 11813.589|
|-----------------------------------------------------------------------------|
r_work (final): 0.3635
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7470
moved from start:          0.2532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  10241  Z= 0.173
  Angle     :  0.661   8.638  13882  Z= 0.343
  Chirality :  0.045   0.222   1556
  Planarity :  0.004   0.047   1774
  Dihedral  :  7.099  57.258   1399
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.62 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 10.36 %
    Favored  : 85.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.88 (0.24), residues: 1246
  helix:  0.65 (0.32), residues: 272
  sheet: -0.61 (0.27), residues: 364
  loop : -1.08 (0.26), residues: 610

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 845 
 HIS   0.006   0.001   HIS A 951 
 PHE   0.018   0.002   PHE A1199 
 TYR   0.020   0.002   TYR H 108 
 ARG   0.004   0.001   ARG A1415 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04278 (  342)
  hydrogen bonds       : angle       6.28548 (  897)
  SS BOND              : bond        0.00457 (    4)
  SS BOND              : angle       1.06906 (    8)
  covalent geometry    : bond        0.00402 (10237)
  covalent geometry    : angle       0.66025 (13874)

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

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

  2492 Ramachandran restraints generated.
    1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2492 Ramachandran restraints generated.
    1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 202
  time to evaluate  : 1.129 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  995 LEU cc_start: 0.7783 (mt) cc_final: 0.7346 (tt)
REVERT: A 1278 GLN cc_start: 0.8721 (mp10) cc_final: 0.8023 (mp10)
REVERT: A 1373 LYS cc_start: 0.9162 (pttt) cc_final: 0.8881 (pttm)
REVERT: A 1773 ILE cc_start: 0.8040 (pt) cc_final: 0.7705 (mm)
REVERT: A 1826 ASP cc_start: 0.7015 (t0) cc_final: 0.6616 (t0)
REVERT: A 2038 TYR cc_start: 0.7745 (m-80) cc_final: 0.7492 (m-10)
REVERT: L   91 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.8121 (pp30)
REVERT: L  140 PHE cc_start: 0.8238 (p90) cc_final: 0.7802 (p90)
REVERT: L  141 TYR cc_start: 0.7453 (t80) cc_final: 0.7194 (t80)
  outliers start: 49
  outliers final: 36
  residues processed: 232
  average time/residue: 0.2439
  time to fit residues: 77.3859
Evaluate side-chains
  210 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 173
  time to evaluate  : 1.007 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  877 CYS
Chi-restraints excluded: chain A residue  884 ASP
Chi-restraints excluded: chain A residue  887 THR
Chi-restraints excluded: chain A residue  936 PHE
Chi-restraints excluded: chain A residue  937 SER
Chi-restraints excluded: chain A residue  984 HIS
Chi-restraints excluded: chain A residue 1003 THR
Chi-restraints excluded: chain A residue 1004 THR
Chi-restraints excluded: chain A residue 1302 ILE
Chi-restraints excluded: chain A residue 1338 ILE
Chi-restraints excluded: chain A residue 1417 ILE
Chi-restraints excluded: chain A residue 1428 MET
Chi-restraints excluded: chain A residue 1450 ILE
Chi-restraints excluded: chain A residue 1462 ILE
Chi-restraints excluded: chain A residue 1524 LYS
Chi-restraints excluded: chain A residue 1736 ILE
Chi-restraints excluded: chain A residue 1751 TYR
Chi-restraints excluded: chain A residue 1771 THR
Chi-restraints excluded: chain A residue 1785 LEU
Chi-restraints excluded: chain A residue 1863 SER
Chi-restraints excluded: chain A residue 1902 GLN
Chi-restraints excluded: chain A residue 1912 LEU
Chi-restraints excluded: chain A residue 1913 VAL
Chi-restraints excluded: chain A residue 1922 ASN
Chi-restraints excluded: chain A residue 1933 ILE
Chi-restraints excluded: chain A residue 1944 HIS
Chi-restraints excluded: chain A residue 2082 TYR
Chi-restraints excluded: chain H residue   37 ILE
Chi-restraints excluded: chain H residue   53 SER
Chi-restraints excluded: chain H residue  104 TYR
Chi-restraints excluded: chain H residue  130 THR
Chi-restraints excluded: chain H residue  142 PHE
Chi-restraints excluded: chain L residue   51 SER
Chi-restraints excluded: chain L residue   90 GLN
Chi-restraints excluded: chain L residue   91 GLN
Chi-restraints excluded: chain L residue  130 THR
Chi-restraints excluded: chain L residue  170 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 109 optimal weight:    5.9990
   chunk 120 optimal weight:    7.9990
   chunk 78 optimal weight:    3.9990
   chunk 85 optimal weight:    6.9990
   chunk 94 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 111 optimal weight:    3.9990
   chunk 91 optimal weight:    3.9990
   chunk 69 optimal weight:    1.9990
   chunk 73 optimal weight:    8.9990
   chunk 96 optimal weight:    3.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 951 HIS
** A1408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1758 HIS
** A1762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1991 GLN
H 175 ASN
** L  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.150975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.116737 restraints weight = 20367.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.114428 restraints weight = 14379.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.115805 restraints weight = 12058.231|
|-----------------------------------------------------------------------------|
r_work (final): 0.3567
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7576
moved from start:          0.3123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.057  10241  Z= 0.286
  Angle     :  0.744   9.898  13882  Z= 0.383
  Chirality :  0.047   0.188   1556
  Planarity :  0.005   0.050   1774
  Dihedral  :  7.370  58.777   1388
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 13.33
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  7.62 %
    Favored  : 92.30 %
  Rotamer:
    Outliers :  5.93 %
    Allowed  : 13.29 %
    Favored  : 80.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.15 (0.24), residues: 1246
  helix:  0.25 (0.31), residues: 271
  sheet: -0.68 (0.28), residues: 361
  loop : -1.22 (0.26), residues: 614

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP H 123 
 HIS   0.006   0.001   HIS A1388 
 PHE   0.020   0.002   PHE A1199 
 TYR   0.029   0.002   TYR H 108 
 ARG   0.008   0.001   ARG A2055 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04382 (  342)
  hydrogen bonds       : angle       6.29305 (  897)
  SS BOND              : bond        0.00476 (    4)
  SS BOND              : angle       0.70393 (    8)
  covalent geometry    : bond        0.00656 (10237)
  covalent geometry    : angle       0.74391 (13874)

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

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

  2492 Ramachandran restraints generated.
    1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2492 Ramachandran restraints generated.
    1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 169
  time to evaluate  : 1.127 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  995 LEU cc_start: 0.7900 (mt) cc_final: 0.7432 (tt)
REVERT: A 1373 LYS cc_start: 0.9206 (pttt) cc_final: 0.8948 (pttm)
REVERT: A 1422 TRP cc_start: 0.8382 (m100) cc_final: 0.8065 (m100)
REVERT: A 1745 LYS cc_start: 0.7424 (OUTLIER) cc_final: 0.7078 (mtpt)
REVERT: A 1773 ILE cc_start: 0.8140 (pt) cc_final: 0.7791 (mm)
REVERT: A 1826 ASP cc_start: 0.7088 (t0) cc_final: 0.6684 (t0)
REVERT: A 1845 MET cc_start: 0.5792 (mtt) cc_final: 0.5525 (mtt)
REVERT: A 2041 MET cc_start: 0.7845 (tmm) cc_final: 0.7209 (tmm)
REVERT: L   91 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.8419 (pp30)
REVERT: L  140 PHE cc_start: 0.8111 (p90) cc_final: 0.7664 (p90)
REVERT: L  141 TYR cc_start: 0.7366 (t80) cc_final: 0.7005 (t80)
REVERT: L  174 TYR cc_start: 0.7349 (m-80) cc_final: 0.7065 (m-80)
  outliers start: 67
  outliers final: 50
  residues processed: 210
  average time/residue: 0.2488
  time to fit residues: 71.0132
Evaluate side-chains
  210 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 158
  time to evaluate  : 1.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  854 VAL
Chi-restraints excluded: chain A residue  877 CYS
Chi-restraints excluded: chain A residue  884 ASP
Chi-restraints excluded: chain A residue  887 THR
Chi-restraints excluded: chain A residue  936 PHE
Chi-restraints excluded: chain A residue  937 SER
Chi-restraints excluded: chain A residue  984 HIS
Chi-restraints excluded: chain A residue 1003 THR
Chi-restraints excluded: chain A residue 1004 THR
Chi-restraints excluded: chain A residue 1225 CYS
Chi-restraints excluded: chain A residue 1290 THR
Chi-restraints excluded: chain A residue 1302 ILE
Chi-restraints excluded: chain A residue 1328 LEU
Chi-restraints excluded: chain A residue 1338 ILE
Chi-restraints excluded: chain A residue 1374 ASP
Chi-restraints excluded: chain A residue 1407 SER
Chi-restraints excluded: chain A residue 1414 CYS
Chi-restraints excluded: chain A residue 1417 ILE
Chi-restraints excluded: chain A residue 1425 ASP
Chi-restraints excluded: chain A residue 1428 MET
Chi-restraints excluded: chain A residue 1450 ILE
Chi-restraints excluded: chain A residue 1462 ILE
Chi-restraints excluded: chain A residue 1490 LEU
Chi-restraints excluded: chain A residue 1736 ILE
Chi-restraints excluded: chain A residue 1745 LYS
Chi-restraints excluded: chain A residue 1771 THR
Chi-restraints excluded: chain A residue 1785 LEU
Chi-restraints excluded: chain A residue 1797 THR
Chi-restraints excluded: chain A residue 1823 VAL
Chi-restraints excluded: chain A residue 1863 SER
Chi-restraints excluded: chain A residue 1883 CYS
Chi-restraints excluded: chain A residue 1902 GLN
Chi-restraints excluded: chain A residue 1912 LEU
Chi-restraints excluded: chain A residue 1913 VAL
Chi-restraints excluded: chain A residue 1922 ASN
Chi-restraints excluded: chain A residue 1933 ILE
Chi-restraints excluded: chain A residue 1944 HIS
Chi-restraints excluded: chain A residue 2057 GLN
Chi-restraints excluded: chain A residue 2082 TYR
Chi-restraints excluded: chain H residue   53 SER
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain H residue  104 TYR
Chi-restraints excluded: chain H residue  130 THR
Chi-restraints excluded: chain H residue  190 LEU
Chi-restraints excluded: chain H residue  197 SER
Chi-restraints excluded: chain L residue   31 SER
Chi-restraints excluded: chain L residue   51 SER
Chi-restraints excluded: chain L residue   90 GLN
Chi-restraints excluded: chain L residue   91 GLN
Chi-restraints excluded: chain L residue   97 ILE
Chi-restraints excluded: chain L residue  130 THR
Chi-restraints excluded: chain L residue  170 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 85 optimal weight:    4.9990
   chunk 43 optimal weight:    2.9990
   chunk 81 optimal weight:    6.9990
   chunk 100 optimal weight:   20.0000
   chunk 33 optimal weight:    2.9990
   chunk 41 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9980
   chunk 31 optimal weight:    0.6980
   chunk 16 optimal weight:    1.9990
   chunk 107 optimal weight:    0.0470
   overall best weight:    0.9280

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

Flipped N/Q/H residues before XYZ refinement:
A 951 HIS
** A 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1408 GLN
** A1762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1902 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.155945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.119999 restraints weight = 19693.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.121970 restraints weight = 12985.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.122865 restraints weight = 8923.435|
|-----------------------------------------------------------------------------|
r_work (final): 0.3686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7396
moved from start:          0.3566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10241  Z= 0.123
  Angle     :  0.611   8.405  13882  Z= 0.311
  Chirality :  0.044   0.236   1556
  Planarity :  0.004   0.046   1774
  Dihedral  :  6.518  58.969   1386
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.65 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 16.12 %
    Favored  : 79.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.78 (0.24), residues: 1246
  helix:  0.70 (0.31), residues: 265
  sheet: -0.45 (0.28), residues: 368
  loop : -1.05 (0.26), residues: 613

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A1019 
 HIS   0.004   0.001   HIS A 951 
 PHE   0.017   0.001   PHE A 857 
 TYR   0.021   0.001   TYR H 108 
 ARG   0.006   0.000   ARG A2055 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03332 (  342)
  hydrogen bonds       : angle       5.49788 (  897)
  SS BOND              : bond        0.00207 (    4)
  SS BOND              : angle       0.55718 (    8)
  covalent geometry    : bond        0.00281 (10237)
  covalent geometry    : angle       0.61140 (13874)

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

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

  2492 Ramachandran restraints generated.
    1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2492 Ramachandran restraints generated.
    1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 175
  time to evaluate  : 1.116 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1373 LYS cc_start: 0.9161 (pttt) cc_final: 0.8917 (pttm)
REVERT: A 1754 LYS cc_start: 0.7479 (tttt) cc_final: 0.7183 (tttt)
REVERT: A 1773 ILE cc_start: 0.8100 (pt) cc_final: 0.7825 (mm)
REVERT: A 1826 ASP cc_start: 0.7037 (t0) cc_final: 0.6641 (t0)
REVERT: A 1933 ILE cc_start: 0.8529 (OUTLIER) cc_final: 0.8282 (pt)
REVERT: A 2041 MET cc_start: 0.7734 (tmm) cc_final: 0.7251 (tmm)
REVERT: H   94 THR cc_start: 0.8244 (m) cc_final: 0.7862 (p)
REVERT: L   91 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.8156 (pp30)
REVERT: L  174 TYR cc_start: 0.7190 (m-80) cc_final: 0.6939 (m-80)
  outliers start: 47
  outliers final: 35
  residues processed: 205
  average time/residue: 0.2688
  time to fit residues: 75.2297
Evaluate side-chains
  188 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 151
  time to evaluate  : 1.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  854 VAL
Chi-restraints excluded: chain A residue  884 ASP
Chi-restraints excluded: chain A residue  891 MET
Chi-restraints excluded: chain A residue  936 PHE
Chi-restraints excluded: chain A residue  937 SER
Chi-restraints excluded: chain A residue  969 VAL
Chi-restraints excluded: chain A residue  986 VAL
Chi-restraints excluded: chain A residue 1004 THR
Chi-restraints excluded: chain A residue 1038 THR
Chi-restraints excluded: chain A residue 1290 THR
Chi-restraints excluded: chain A residue 1302 ILE
Chi-restraints excluded: chain A residue 1338 ILE
Chi-restraints excluded: chain A residue 1407 SER
Chi-restraints excluded: chain A residue 1417 ILE
Chi-restraints excluded: chain A residue 1428 MET
Chi-restraints excluded: chain A residue 1462 ILE
Chi-restraints excluded: chain A residue 1490 LEU
Chi-restraints excluded: chain A residue 1524 LYS
Chi-restraints excluded: chain A residue 1736 ILE
Chi-restraints excluded: chain A residue 1751 TYR
Chi-restraints excluded: chain A residue 1771 THR
Chi-restraints excluded: chain A residue 1791 VAL
Chi-restraints excluded: chain A residue 1823 VAL
Chi-restraints excluded: chain A residue 1863 SER
Chi-restraints excluded: chain A residue 1902 GLN
Chi-restraints excluded: chain A residue 1912 LEU
Chi-restraints excluded: chain A residue 1913 VAL
Chi-restraints excluded: chain A residue 1922 ASN
Chi-restraints excluded: chain A residue 1933 ILE
Chi-restraints excluded: chain A residue 2082 TYR
Chi-restraints excluded: chain H residue   53 SER
Chi-restraints excluded: chain H residue  104 TYR
Chi-restraints excluded: chain H residue  197 SER
Chi-restraints excluded: chain L residue   51 SER
Chi-restraints excluded: chain L residue   90 GLN
Chi-restraints excluded: chain L residue   91 GLN
Chi-restraints excluded: chain L residue  170 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 59 optimal weight:    0.0870
   chunk 78 optimal weight:    9.9990
   chunk 73 optimal weight:    0.7980
   chunk 69 optimal weight:    0.7980
   chunk 4 optimal weight:    6.9990
   chunk 10 optimal weight:    1.9990
   chunk 56 optimal weight:    3.9990
   chunk 44 optimal weight:    5.9990
   chunk 121 optimal weight:   10.0000
   chunk 18 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   overall best weight:    1.3362

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

Flipped N/Q/H residues before XYZ refinement:
** A 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 951 HIS
** A 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  85 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.154939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.120325 restraints weight = 19814.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.118900 restraints weight = 14086.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.120440 restraints weight = 11305.940|
|-----------------------------------------------------------------------------|
r_work (final): 0.3644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7441
moved from start:          0.3808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10241  Z= 0.145
  Angle     :  0.619   9.590  13882  Z= 0.314
  Chirality :  0.044   0.299   1556
  Planarity :  0.004   0.049   1774
  Dihedral  :  6.013  59.191   1379
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 10.11
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  5.22 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  4.78 %
    Allowed  : 16.12 %
    Favored  : 79.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.73 (0.24), residues: 1246
  helix:  0.69 (0.31), residues: 265
  sheet: -0.31 (0.29), residues: 345
  loop : -1.05 (0.26), residues: 636

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 890 
 HIS   0.005   0.001   HIS A1803 
 PHE   0.013   0.001   PHE H  32 
 TYR   0.021   0.001   TYR L 141 
 ARG   0.010   0.001   ARG H  22 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03415 (  342)
  hydrogen bonds       : angle       5.40497 (  897)
  SS BOND              : bond        0.00368 (    4)
  SS BOND              : angle       0.60900 (    8)
  covalent geometry    : bond        0.00336 (10237)
  covalent geometry    : angle       0.61871 (13874)

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

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

  2492 Ramachandran restraints generated.
    1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2492 Ramachandran restraints generated.
    1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 164
  time to evaluate  : 1.535 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  841 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7947 (pt0)
REVERT: A 1315 VAL cc_start: 0.8688 (p) cc_final: 0.8483 (p)
REVERT: A 1370 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7849 (tm-30)
REVERT: A 1373 LYS cc_start: 0.9189 (pttt) cc_final: 0.8954 (pttm)
REVERT: A 1767 TYR cc_start: 0.8423 (OUTLIER) cc_final: 0.7693 (p90)
REVERT: A 1773 ILE cc_start: 0.8116 (pt) cc_final: 0.7822 (mm)
REVERT: A 1826 ASP cc_start: 0.7197 (t0) cc_final: 0.6762 (t0)
REVERT: A 1933 ILE cc_start: 0.8610 (OUTLIER) cc_final: 0.8333 (pt)
REVERT: A 2041 MET cc_start: 0.7763 (tmm) cc_final: 0.7276 (tmm)
REVERT: H   94 THR cc_start: 0.8223 (m) cc_final: 0.7960 (p)
REVERT: L   91 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.8094 (pp30)
REVERT: L  184 LYS cc_start: 0.9340 (tppt) cc_final: 0.9077 (mmmt)
  outliers start: 54
  outliers final: 39
  residues processed: 199
  average time/residue: 0.2488
  time to fit residues: 68.3228
Evaluate side-chains
  196 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 152
  time to evaluate  : 1.054 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  841 GLU
Chi-restraints excluded: chain A residue  854 VAL
Chi-restraints excluded: chain A residue  884 ASP
Chi-restraints excluded: chain A residue  891 MET
Chi-restraints excluded: chain A residue  936 PHE
Chi-restraints excluded: chain A residue  937 SER
Chi-restraints excluded: chain A residue  969 VAL
Chi-restraints excluded: chain A residue  986 VAL
Chi-restraints excluded: chain A residue 1003 THR
Chi-restraints excluded: chain A residue 1004 THR
Chi-restraints excluded: chain A residue 1038 THR
Chi-restraints excluded: chain A residue 1225 CYS
Chi-restraints excluded: chain A residue 1290 THR
Chi-restraints excluded: chain A residue 1302 ILE
Chi-restraints excluded: chain A residue 1338 ILE
Chi-restraints excluded: chain A residue 1370 GLU
Chi-restraints excluded: chain A residue 1407 SER
Chi-restraints excluded: chain A residue 1417 ILE
Chi-restraints excluded: chain A residue 1428 MET
Chi-restraints excluded: chain A residue 1462 ILE
Chi-restraints excluded: chain A residue 1490 LEU
Chi-restraints excluded: chain A residue 1524 LYS
Chi-restraints excluded: chain A residue 1736 ILE
Chi-restraints excluded: chain A residue 1751 TYR
Chi-restraints excluded: chain A residue 1767 TYR
Chi-restraints excluded: chain A residue 1771 THR
Chi-restraints excluded: chain A residue 1791 VAL
Chi-restraints excluded: chain A residue 1823 VAL
Chi-restraints excluded: chain A residue 1902 GLN
Chi-restraints excluded: chain A residue 1907 VAL
Chi-restraints excluded: chain A residue 1912 LEU
Chi-restraints excluded: chain A residue 1913 VAL
Chi-restraints excluded: chain A residue 1922 ASN
Chi-restraints excluded: chain A residue 1933 ILE
Chi-restraints excluded: chain A residue 1944 HIS
Chi-restraints excluded: chain A residue 2057 GLN
Chi-restraints excluded: chain A residue 2082 TYR
Chi-restraints excluded: chain H residue   37 ILE
Chi-restraints excluded: chain H residue   53 SER
Chi-restraints excluded: chain H residue  104 TYR
Chi-restraints excluded: chain H residue  197 SER
Chi-restraints excluded: chain L residue   51 SER
Chi-restraints excluded: chain L residue   90 GLN
Chi-restraints excluded: chain L residue   91 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 10 optimal weight:    7.9990
   chunk 91 optimal weight:    7.9990
   chunk 25 optimal weight:    0.5980
   chunk 6 optimal weight:    5.9990
   chunk 111 optimal weight:    5.9990
   chunk 35 optimal weight:    7.9990
   chunk 120 optimal weight:   30.0000
   chunk 123 optimal weight:   40.0000
   chunk 12 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9980
   chunk 107 optimal weight:    9.9990
   overall best weight:    3.1186

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

Flipped N/Q/H residues before XYZ refinement:
** A 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 951 HIS
** A 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1902 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.150748 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.115706 restraints weight = 20313.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.114472 restraints weight = 14701.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.115503 restraints weight = 12107.680|
|-----------------------------------------------------------------------------|
r_work (final): 0.3557
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7600
moved from start:          0.3897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.060  10241  Z= 0.279
  Angle     :  0.743   8.705  13882  Z= 0.380
  Chirality :  0.047   0.267   1556
  Planarity :  0.005   0.055   1774
  Dihedral  :  6.658  59.321   1379
  Min Nonbonded Distance : 2.309

Molprobity Statistics.
  All-atom Clashscore : 14.18
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  6.82 %
    Favored  : 93.02 %
  Rotamer:
    Outliers :  5.85 %
    Allowed  : 16.65 %
    Favored  : 77.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.26 (0.24), residues: 1246
  helix: -0.10 (0.30), residues: 271
  sheet: -0.56 (0.28), residues: 353
  loop : -1.29 (0.25), residues: 622

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 890 
 HIS   0.007   0.001   HIS A 984 
 PHE   0.019   0.002   PHE H  32 
 TYR   0.028   0.002   TYR H 108 
 ARG   0.006   0.001   ARG L  25 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04205 (  342)
  hydrogen bonds       : angle       6.00634 (  897)
  SS BOND              : bond        0.00506 (    4)
  SS BOND              : angle       0.84565 (    8)
  covalent geometry    : bond        0.00645 (10237)
  covalent geometry    : angle       0.74250 (13874)

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

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

  2492 Ramachandran restraints generated.
    1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2492 Ramachandran restraints generated.
    1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 156
  time to evaluate  : 1.185 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  841 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8012 (pt0)
REVERT: A 1373 LYS cc_start: 0.9209 (pttt) cc_final: 0.8945 (pttm)
REVERT: A 1422 TRP cc_start: 0.8387 (m100) cc_final: 0.8135 (m100)
REVERT: A 1767 TYR cc_start: 0.8464 (OUTLIER) cc_final: 0.7962 (p90)
REVERT: A 1773 ILE cc_start: 0.8151 (pt) cc_final: 0.7851 (mm)
REVERT: A 1826 ASP cc_start: 0.7305 (t0) cc_final: 0.6851 (t0)
REVERT: A 1845 MET cc_start: 0.5600 (mtt) cc_final: 0.5293 (mtt)
REVERT: A 2041 MET cc_start: 0.7923 (tmm) cc_final: 0.7304 (tmm)
REVERT: L   90 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.7852 (pp30)
REVERT: L   91 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.8449 (pp30)
  outliers start: 66
  outliers final: 52
  residues processed: 197
  average time/residue: 0.2441
  time to fit residues: 66.1587
Evaluate side-chains
  200 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 144
  time to evaluate  : 1.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  841 GLU
Chi-restraints excluded: chain A residue  847 VAL
Chi-restraints excluded: chain A residue  854 VAL
Chi-restraints excluded: chain A residue  877 CYS
Chi-restraints excluded: chain A residue  884 ASP
Chi-restraints excluded: chain A residue  891 MET
Chi-restraints excluded: chain A residue  936 PHE
Chi-restraints excluded: chain A residue  937 SER
Chi-restraints excluded: chain A residue  986 VAL
Chi-restraints excluded: chain A residue 1003 THR
Chi-restraints excluded: chain A residue 1004 THR
Chi-restraints excluded: chain A residue 1038 THR
Chi-restraints excluded: chain A residue 1039 LEU
Chi-restraints excluded: chain A residue 1199 PHE
Chi-restraints excluded: chain A residue 1225 CYS
Chi-restraints excluded: chain A residue 1290 THR
Chi-restraints excluded: chain A residue 1302 ILE
Chi-restraints excluded: chain A residue 1338 ILE
Chi-restraints excluded: chain A residue 1407 SER
Chi-restraints excluded: chain A residue 1414 CYS
Chi-restraints excluded: chain A residue 1417 ILE
Chi-restraints excluded: chain A residue 1425 ASP
Chi-restraints excluded: chain A residue 1428 MET
Chi-restraints excluded: chain A residue 1450 ILE
Chi-restraints excluded: chain A residue 1462 ILE
Chi-restraints excluded: chain A residue 1490 LEU
Chi-restraints excluded: chain A residue 1524 LYS
Chi-restraints excluded: chain A residue 1736 ILE
Chi-restraints excluded: chain A residue 1751 TYR
Chi-restraints excluded: chain A residue 1767 TYR
Chi-restraints excluded: chain A residue 1771 THR
Chi-restraints excluded: chain A residue 1785 LEU
Chi-restraints excluded: chain A residue 1791 VAL
Chi-restraints excluded: chain A residue 1823 VAL
Chi-restraints excluded: chain A residue 1863 SER
Chi-restraints excluded: chain A residue 1883 CYS
Chi-restraints excluded: chain A residue 1902 GLN
Chi-restraints excluded: chain A residue 1907 VAL
Chi-restraints excluded: chain A residue 1912 LEU
Chi-restraints excluded: chain A residue 1913 VAL
Chi-restraints excluded: chain A residue 1922 ASN
Chi-restraints excluded: chain A residue 1944 HIS
Chi-restraints excluded: chain A residue 1954 ILE
Chi-restraints excluded: chain A residue 2057 GLN
Chi-restraints excluded: chain A residue 2082 TYR
Chi-restraints excluded: chain H residue   50 TRP
Chi-restraints excluded: chain H residue   53 SER
Chi-restraints excluded: chain H residue  104 TYR
Chi-restraints excluded: chain H residue  164 ASP
Chi-restraints excluded: chain H residue  190 LEU
Chi-restraints excluded: chain H residue  197 SER
Chi-restraints excluded: chain L residue   22 ILE
Chi-restraints excluded: chain L residue   48 LEU
Chi-restraints excluded: chain L residue   51 SER
Chi-restraints excluded: chain L residue   90 GLN
Chi-restraints excluded: chain L residue   91 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 34 optimal weight:    0.0980
   chunk 76 optimal weight:    1.9990
   chunk 6 optimal weight:    0.7980
   chunk 97 optimal weight:    9.9990
   chunk 80 optimal weight:    6.9990
   chunk 120 optimal weight:   40.0000
   chunk 82 optimal weight:    0.9980
   chunk 28 optimal weight:    0.6980
   chunk 3 optimal weight:    4.9990
   chunk 17 optimal weight:    5.9990
   chunk 60 optimal weight:    0.8980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A1762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 161 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.155759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.120838 restraints weight = 20271.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.120434 restraints weight = 14179.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.121385 restraints weight = 12049.392|
|-----------------------------------------------------------------------------|
r_work (final): 0.3657
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7441
moved from start:          0.4254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  10241  Z= 0.121
  Angle     :  0.642  10.287  13882  Z= 0.323
  Chirality :  0.044   0.298   1556
  Planarity :  0.004   0.053   1774
  Dihedral  :  6.057  59.986   1379
  Min Nonbonded Distance : 2.316

Molprobity Statistics.
  All-atom Clashscore : 9.96
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  4.74 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 19.13 %
    Favored  : 77.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.89 (0.24), residues: 1246
  helix:  0.46 (0.31), residues: 265
  sheet: -0.44 (0.28), residues: 347
  loop : -1.09 (0.26), residues: 634

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A1422 
 HIS   0.005   0.001   HIS A1803 
 PHE   0.011   0.001   PHE A 857 
 TYR   0.031   0.001   TYR H 108 
 ARG   0.006   0.001   ARG L  25 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03373 (  342)
  hydrogen bonds       : angle       5.40229 (  897)
  SS BOND              : bond        0.00385 (    4)
  SS BOND              : angle       0.69101 (    8)
  covalent geometry    : bond        0.00281 (10237)
  covalent geometry    : angle       0.64220 (13874)

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

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

  2492 Ramachandran restraints generated.
    1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2492 Ramachandran restraints generated.
    1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 164
  time to evaluate  : 1.259 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1373 LYS cc_start: 0.9186 (pttt) cc_final: 0.8926 (pttm)
REVERT: A 1400 GLU cc_start: 0.8380 (mp0) cc_final: 0.8046 (mp0)
REVERT: A 1407 SER cc_start: 0.8741 (m) cc_final: 0.8392 (t)
REVERT: A 1478 MET cc_start: 0.8300 (tpp) cc_final: 0.7127 (tpp)
REVERT: A 1654 GLN cc_start: 0.8302 (mp10) cc_final: 0.7918 (mp10)
REVERT: A 1773 ILE cc_start: 0.8125 (pt) cc_final: 0.7843 (mm)
REVERT: A 1826 ASP cc_start: 0.7167 (t0) cc_final: 0.6722 (t0)
REVERT: A 1831 MET cc_start: 0.7103 (tpp) cc_final: 0.6856 (tpp)
REVERT: A 1845 MET cc_start: 0.5396 (mtt) cc_final: 0.5031 (mtt)
REVERT: A 2041 MET cc_start: 0.7737 (tmm) cc_final: 0.7248 (tmm)
REVERT: H   94 THR cc_start: 0.8236 (m) cc_final: 0.7938 (p)
REVERT: L   90 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.7940 (pp30)
  outliers start: 39
  outliers final: 31
  residues processed: 190
  average time/residue: 0.2884
  time to fit residues: 77.2617
Evaluate side-chains
  185 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 153
  time to evaluate  : 1.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  854 VAL
Chi-restraints excluded: chain A residue  877 CYS
Chi-restraints excluded: chain A residue  884 ASP
Chi-restraints excluded: chain A residue  891 MET
Chi-restraints excluded: chain A residue  936 PHE
Chi-restraints excluded: chain A residue 1004 THR
Chi-restraints excluded: chain A residue 1038 THR
Chi-restraints excluded: chain A residue 1199 PHE
Chi-restraints excluded: chain A residue 1225 CYS
Chi-restraints excluded: chain A residue 1290 THR
Chi-restraints excluded: chain A residue 1302 ILE
Chi-restraints excluded: chain A residue 1417 ILE
Chi-restraints excluded: chain A residue 1428 MET
Chi-restraints excluded: chain A residue 1446 VAL
Chi-restraints excluded: chain A residue 1462 ILE
Chi-restraints excluded: chain A residue 1490 LEU
Chi-restraints excluded: chain A residue 1524 LYS
Chi-restraints excluded: chain A residue 1736 ILE
Chi-restraints excluded: chain A residue 1751 TYR
Chi-restraints excluded: chain A residue 1771 THR
Chi-restraints excluded: chain A residue 1791 VAL
Chi-restraints excluded: chain A residue 1823 VAL
Chi-restraints excluded: chain A residue 1902 GLN
Chi-restraints excluded: chain A residue 1913 VAL
Chi-restraints excluded: chain A residue 1922 ASN
Chi-restraints excluded: chain A residue 2082 TYR
Chi-restraints excluded: chain H residue   50 TRP
Chi-restraints excluded: chain H residue   53 SER
Chi-restraints excluded: chain H residue  130 THR
Chi-restraints excluded: chain H residue  197 SER
Chi-restraints excluded: chain L residue   51 SER
Chi-restraints excluded: chain L residue   90 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 113 optimal weight:    8.9990
   chunk 29 optimal weight:    0.9990
   chunk 1 optimal weight:    0.8980
   chunk 24 optimal weight:    0.3980
   chunk 83 optimal weight:    3.9990
   chunk 122 optimal weight:    6.9990
   chunk 98 optimal weight:    6.9990
   chunk 88 optimal weight:    5.9990
   chunk 116 optimal weight:   20.0000
   chunk 65 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
A 951 HIS
** A1762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1902 GLN
** L  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.156526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.122167 restraints weight = 20013.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.120653 restraints weight = 13736.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.122452 restraints weight = 11256.287|
|-----------------------------------------------------------------------------|
r_work (final): 0.3671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7428
moved from start:          0.4440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  10241  Z= 0.122
  Angle     :  0.626  11.060  13882  Z= 0.315
  Chirality :  0.044   0.306   1556
  Planarity :  0.004   0.056   1774
  Dihedral  :  5.609  58.970   1374
  Min Nonbonded Distance : 2.365

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  4.90 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 19.31 %
    Favored  : 77.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.67 (0.24), residues: 1246
  helix:  0.60 (0.32), residues: 266
  sheet: -0.31 (0.28), residues: 347
  loop : -0.92 (0.26), residues: 633

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 845 
 HIS   0.005   0.001   HIS A1803 
 PHE   0.011   0.001   PHE L 140 
 TYR   0.033   0.001   TYR H 108 
 ARG   0.005   0.000   ARG L  25 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03165 (  342)
  hydrogen bonds       : angle       5.24707 (  897)
  SS BOND              : bond        0.00409 (    4)
  SS BOND              : angle       0.82057 (    8)
  covalent geometry    : bond        0.00286 (10237)
  covalent geometry    : angle       0.62622 (13874)

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

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

  2492 Ramachandran restraints generated.
    1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2492 Ramachandran restraints generated.
    1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 161
  time to evaluate  : 1.208 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1373 LYS cc_start: 0.9197 (pttt) cc_final: 0.8945 (pttm)
REVERT: A 1400 GLU cc_start: 0.8399 (mp0) cc_final: 0.8035 (mp0)
REVERT: A 1407 SER cc_start: 0.8742 (m) cc_final: 0.8408 (t)
REVERT: A 1478 MET cc_start: 0.8267 (tpp) cc_final: 0.7341 (tpp)
REVERT: A 1654 GLN cc_start: 0.8311 (mp10) cc_final: 0.8010 (mp10)
REVERT: A 1773 ILE cc_start: 0.8133 (pt) cc_final: 0.7860 (mm)
REVERT: A 1826 ASP cc_start: 0.7213 (t0) cc_final: 0.6744 (t0)
REVERT: A 1831 MET cc_start: 0.7101 (tpp) cc_final: 0.6847 (tpp)
REVERT: A 1845 MET cc_start: 0.5435 (mtt) cc_final: 0.5123 (mtt)
REVERT: A 2041 MET cc_start: 0.7697 (tmm) cc_final: 0.7265 (tmm)
REVERT: H   94 THR cc_start: 0.8218 (m) cc_final: 0.7950 (p)
REVERT: L   90 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.7888 (pp30)
  outliers start: 37
  outliers final: 33
  residues processed: 185
  average time/residue: 0.2461
  time to fit residues: 64.1275
Evaluate side-chains
  186 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 152
  time to evaluate  : 1.055 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  854 VAL
Chi-restraints excluded: chain A residue  877 CYS
Chi-restraints excluded: chain A residue  891 MET
Chi-restraints excluded: chain A residue  936 PHE
Chi-restraints excluded: chain A residue  951 HIS
Chi-restraints excluded: chain A residue  986 VAL
Chi-restraints excluded: chain A residue 1004 THR
Chi-restraints excluded: chain A residue 1038 THR
Chi-restraints excluded: chain A residue 1199 PHE
Chi-restraints excluded: chain A residue 1225 CYS
Chi-restraints excluded: chain A residue 1290 THR
Chi-restraints excluded: chain A residue 1302 ILE
Chi-restraints excluded: chain A residue 1338 ILE
Chi-restraints excluded: chain A residue 1417 ILE
Chi-restraints excluded: chain A residue 1428 MET
Chi-restraints excluded: chain A residue 1490 LEU
Chi-restraints excluded: chain A residue 1524 LYS
Chi-restraints excluded: chain A residue 1736 ILE
Chi-restraints excluded: chain A residue 1751 TYR
Chi-restraints excluded: chain A residue 1767 TYR
Chi-restraints excluded: chain A residue 1771 THR
Chi-restraints excluded: chain A residue 1791 VAL
Chi-restraints excluded: chain A residue 1823 VAL
Chi-restraints excluded: chain A residue 1902 GLN
Chi-restraints excluded: chain A residue 1913 VAL
Chi-restraints excluded: chain A residue 1922 ASN
Chi-restraints excluded: chain A residue 2082 TYR
Chi-restraints excluded: chain H residue   50 TRP
Chi-restraints excluded: chain H residue   53 SER
Chi-restraints excluded: chain H residue  130 THR
Chi-restraints excluded: chain H residue  197 SER
Chi-restraints excluded: chain L residue   51 SER
Chi-restraints excluded: chain L residue   90 GLN
Chi-restraints excluded: chain L residue   91 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 21 optimal weight:    4.9990
   chunk 23 optimal weight:    7.9990
   chunk 22 optimal weight:    0.9990
   chunk 92 optimal weight:    0.7980
   chunk 38 optimal weight:    0.0070
   chunk 51 optimal weight:    0.8980
   chunk 7 optimal weight:    0.8980
   chunk 103 optimal weight:   10.0000
   chunk 16 optimal weight:    0.9980
   chunk 120 optimal weight:   40.0000
   chunk 0 optimal weight:    5.9990
   overall best weight:    0.7198

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

Flipped N/Q/H residues before XYZ refinement:
A 951 HIS
** A1762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1902 GLN
H  31 ASN
** L  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.157415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.122837 restraints weight = 19974.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.124124 restraints weight = 12829.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.125184 restraints weight = 10149.904|
|-----------------------------------------------------------------------------|
r_work (final): 0.3722
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7342
moved from start:          0.4599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058  10241  Z= 0.117
  Angle     :  0.624  11.804  13882  Z= 0.312
  Chirality :  0.044   0.324   1556
  Planarity :  0.004   0.056   1774
  Dihedral  :  5.441  58.434   1372
  Min Nonbonded Distance : 2.175

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.57 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 19.75 %
    Favored  : 76.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.55 (0.24), residues: 1246
  helix:  0.72 (0.32), residues: 266
  sheet: -0.17 (0.28), residues: 345
  loop : -0.91 (0.25), residues: 635

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A1422 
 HIS   0.005   0.001   HIS A 951 
 PHE   0.015   0.001   PHE H  32 
 TYR   0.030   0.001   TYR H 108 
 ARG   0.004   0.000   ARG L  25 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03058 (  342)
  hydrogen bonds       : angle       5.13068 (  897)
  SS BOND              : bond        0.00384 (    4)
  SS BOND              : angle       0.85923 (    8)
  covalent geometry    : bond        0.00275 (10237)
  covalent geometry    : angle       0.62362 (13874)

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

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

  2492 Ramachandran restraints generated.
    1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2492 Ramachandran restraints generated.
    1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 158
  time to evaluate  : 1.351 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1373 LYS cc_start: 0.9188 (pttt) cc_final: 0.8939 (pttm)
REVERT: A 1400 GLU cc_start: 0.8391 (mp0) cc_final: 0.8050 (mp0)
REVERT: A 1407 SER cc_start: 0.8759 (m) cc_final: 0.8439 (t)
REVERT: A 1478 MET cc_start: 0.8257 (tpp) cc_final: 0.7260 (tpp)
REVERT: A 1654 GLN cc_start: 0.8391 (mp10) cc_final: 0.8084 (mp10)
REVERT: A 1826 ASP cc_start: 0.7123 (t0) cc_final: 0.6719 (t0)
REVERT: A 2041 MET cc_start: 0.7687 (tmm) cc_final: 0.7279 (tmm)
REVERT: H   94 THR cc_start: 0.8225 (m) cc_final: 0.7961 (p)
REVERT: L   90 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.7947 (pp30)
  outliers start: 37
  outliers final: 28
  residues processed: 181
  average time/residue: 0.3012
  time to fit residues: 76.1922
Evaluate side-chains
  180 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 151
  time to evaluate  : 1.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  854 VAL
Chi-restraints excluded: chain A residue  877 CYS
Chi-restraints excluded: chain A residue  891 MET
Chi-restraints excluded: chain A residue  936 PHE
Chi-restraints excluded: chain A residue  937 SER
Chi-restraints excluded: chain A residue 1004 THR
Chi-restraints excluded: chain A residue 1038 THR
Chi-restraints excluded: chain A residue 1199 PHE
Chi-restraints excluded: chain A residue 1290 THR
Chi-restraints excluded: chain A residue 1302 ILE
Chi-restraints excluded: chain A residue 1338 ILE
Chi-restraints excluded: chain A residue 1417 ILE
Chi-restraints excluded: chain A residue 1428 MET
Chi-restraints excluded: chain A residue 1446 VAL
Chi-restraints excluded: chain A residue 1490 LEU
Chi-restraints excluded: chain A residue 1524 LYS
Chi-restraints excluded: chain A residue 1736 ILE
Chi-restraints excluded: chain A residue 1751 TYR
Chi-restraints excluded: chain A residue 1771 THR
Chi-restraints excluded: chain A residue 1791 VAL
Chi-restraints excluded: chain A residue 1823 VAL
Chi-restraints excluded: chain A residue 1913 VAL
Chi-restraints excluded: chain A residue 1944 HIS
Chi-restraints excluded: chain A residue 2082 TYR
Chi-restraints excluded: chain H residue   53 SER
Chi-restraints excluded: chain H residue  130 THR
Chi-restraints excluded: chain H residue  197 SER
Chi-restraints excluded: chain L residue   51 SER
Chi-restraints excluded: chain L residue   90 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 89 optimal weight:    0.6980
   chunk 49 optimal weight:    5.9990
   chunk 98 optimal weight:   20.0000
   chunk 109 optimal weight:    1.9990
   chunk 100 optimal weight:    2.9990
   chunk 39 optimal weight:    0.7980
   chunk 82 optimal weight:    0.2980
   chunk 90 optimal weight:    1.9990
   chunk 96 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
A 951 HIS
** A1762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1902 GLN
H  31 ASN
** L  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.157013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.122711 restraints weight = 20075.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.121998 restraints weight = 13720.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.123429 restraints weight = 11532.001|
|-----------------------------------------------------------------------------|
r_work (final): 0.3686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7407
moved from start:          0.4702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059  10241  Z= 0.129
  Angle     :  0.654  11.973  13882  Z= 0.327
  Chirality :  0.045   0.342   1556
  Planarity :  0.004   0.056   1774
  Dihedral  :  5.396  57.685   1372
  Min Nonbonded Distance : 2.127

Molprobity Statistics.
  All-atom Clashscore : 9.96
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.06 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 20.28 %
    Favored  : 76.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.49 (0.24), residues: 1246
  helix:  0.76 (0.32), residues: 266
  sheet: -0.11 (0.28), residues: 345
  loop : -0.87 (0.25), residues: 635

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A1422 
 HIS   0.006   0.001   HIS A 951 
 PHE   0.012   0.001   PHE L 140 
 TYR   0.032   0.001   TYR H 108 
 ARG   0.004   0.000   ARG A1415 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03114 (  342)
  hydrogen bonds       : angle       5.13515 (  897)
  SS BOND              : bond        0.00348 (    4)
  SS BOND              : angle       0.79017 (    8)
  covalent geometry    : bond        0.00309 (10237)
  covalent geometry    : angle       0.65425 (13874)

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

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

  2492 Ramachandran restraints generated.
    1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2492 Ramachandran restraints generated.
    1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 158
  time to evaluate  : 1.161 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1373 LYS cc_start: 0.9186 (pttt) cc_final: 0.8945 (pttm)
REVERT: A 1400 GLU cc_start: 0.8383 (mp0) cc_final: 0.8014 (mp0)
REVERT: A 1478 MET cc_start: 0.8327 (tpp) cc_final: 0.7852 (tpp)
REVERT: A 1654 GLN cc_start: 0.8346 (mp10) cc_final: 0.8020 (mp10)
REVERT: A 1826 ASP cc_start: 0.7193 (t0) cc_final: 0.6761 (t0)
REVERT: A 2041 MET cc_start: 0.7703 (tmm) cc_final: 0.7284 (tmm)
REVERT: H   94 THR cc_start: 0.8302 (m) cc_final: 0.8009 (p)
REVERT: L   90 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.7919 (pp30)
  outliers start: 34
  outliers final: 32
  residues processed: 181
  average time/residue: 0.2447
  time to fit residues: 62.3946
Evaluate side-chains
  183 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 150
  time to evaluate  : 1.062 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  854 VAL
Chi-restraints excluded: chain A residue  877 CYS
Chi-restraints excluded: chain A residue  936 PHE
Chi-restraints excluded: chain A residue  937 SER
Chi-restraints excluded: chain A residue  951 HIS
Chi-restraints excluded: chain A residue 1003 THR
Chi-restraints excluded: chain A residue 1004 THR
Chi-restraints excluded: chain A residue 1038 THR
Chi-restraints excluded: chain A residue 1199 PHE
Chi-restraints excluded: chain A residue 1290 THR
Chi-restraints excluded: chain A residue 1302 ILE
Chi-restraints excluded: chain A residue 1338 ILE
Chi-restraints excluded: chain A residue 1417 ILE
Chi-restraints excluded: chain A residue 1428 MET
Chi-restraints excluded: chain A residue 1446 VAL
Chi-restraints excluded: chain A residue 1490 LEU
Chi-restraints excluded: chain A residue 1524 LYS
Chi-restraints excluded: chain A residue 1736 ILE
Chi-restraints excluded: chain A residue 1751 TYR
Chi-restraints excluded: chain A residue 1767 TYR
Chi-restraints excluded: chain A residue 1771 THR
Chi-restraints excluded: chain A residue 1791 VAL
Chi-restraints excluded: chain A residue 1823 VAL
Chi-restraints excluded: chain A residue 1902 GLN
Chi-restraints excluded: chain A residue 1913 VAL
Chi-restraints excluded: chain A residue 1944 HIS
Chi-restraints excluded: chain A residue 2057 GLN
Chi-restraints excluded: chain A residue 2082 TYR
Chi-restraints excluded: chain H residue   53 SER
Chi-restraints excluded: chain H residue  130 THR
Chi-restraints excluded: chain H residue  197 SER
Chi-restraints excluded: chain L residue   51 SER
Chi-restraints excluded: chain L residue   90 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 99 optimal weight:    5.9990
   chunk 78 optimal weight:   20.0000
   chunk 29 optimal weight:    0.9990
   chunk 71 optimal weight:    1.9990
   chunk 119 optimal weight:    9.9990
   chunk 65 optimal weight:    0.9980
   chunk 28 optimal weight:    0.7980
   chunk 31 optimal weight:    3.9990
   chunk 88 optimal weight:    2.9990
   chunk 20 optimal weight:    0.6980
   chunk 19 optimal weight:    0.2980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A 951 HIS
** A 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1762 GLN
H  31 ASN
** L  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.157590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.122538 restraints weight = 20046.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.122289 restraints weight = 12845.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.123626 restraints weight = 10302.598|
|-----------------------------------------------------------------------------|
r_work (final): 0.3688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7392
moved from start:          0.4807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058  10241  Z= 0.122
  Angle     :  0.650  12.040  13882  Z= 0.327
  Chirality :  0.044   0.329   1556
  Planarity :  0.004   0.055   1774
  Dihedral  :  5.323  57.392   1372
  Min Nonbonded Distance : 2.137

Molprobity Statistics.
  All-atom Clashscore : 10.16
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.65 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 20.28 %
    Favored  : 76.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.40 (0.24), residues: 1246
  helix:  0.78 (0.32), residues: 267
  sheet: -0.06 (0.28), residues: 351
  loop : -0.80 (0.25), residues: 628

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A1422 
 HIS   0.005   0.001   HIS A 984 
 PHE   0.012   0.001   PHE L 140 
 TYR   0.030   0.001   TYR H 108 
 ARG   0.003   0.000   ARG L  25 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03096 (  342)
  hydrogen bonds       : angle       5.03679 (  897)
  SS BOND              : bond        0.00327 (    4)
  SS BOND              : angle       0.77335 (    8)
  covalent geometry    : bond        0.00289 (10237)
  covalent geometry    : angle       0.65019 (13874)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6081.23 seconds
wall clock time: 109 minutes 2.55 seconds (6542.55 seconds total)