Starting phenix.real_space_refine
on Fri Sep 11 12:41:39 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9yqk_73338/09_2026/9yqk_73338.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9yqk_73338/09_2026/9yqk_73338.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9yqk_73338/09_2026/9yqk_73338.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9yqk_73338/09_2026/9yqk_73338.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9yqk_73338/09_2026/9yqk_73338.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9yqk_73338/09_2026/9yqk_73338.map"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.930
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      51      5.16       5
     C    5721      2.51       5
     N    1523      2.21       5
     O    1630      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 8925
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 8174
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1023, 8174
          Classifications: {'peptide': 1023}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 43, 'TRANS': 979}
          Chain breaks: 17
          Unresolved non-hydrogen bonds: 29
          Unresolved non-hydrogen angles: 38
          Unresolved non-hydrogen dihedrals: 22
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 1, 'ARG:plan': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 18
    Chain: "B"
      Number of atoms: 751
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 100, 751
          Classifications: {'peptide': 100}
          Link IDs: {'PTRANS': 2, 'TRANS': 97}
  Time building chain proxies: 2.21, per 1000 atoms: 0.25
  Number of scatterers: 8925
  At special positions: 0
  Unit cell: (87, 95.12, 146.16, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      51     16.00
     O    1630      8.00
     N    1523      7.00
     C    5721      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.86
  Conformation dependent library (CDL) restraints added in 376.3 milliseconds
  

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2126

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 11 sheets defined
      32.9% alpha, 17.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1346 through 1355
      removed outlier: 3.762A  pdb=" N   MET A1355 " --> pdb=" O   LEU A1351 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1400 through 1404
      removed outlier: 3.969A  pdb=" N   THR A1404 " --> pdb=" O   PHE A1401 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1424 through 1429
      removed outlier: 3.557A  pdb=" N   VAL A1428 " --> pdb=" O   GLY A1424 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ASP A1429 " --> pdb=" O   GLN A1425 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1424 through 1429'
    Processing helix  chain 'A' and resid 1431 through 1442
    Processing helix  chain 'A' and resid 1458 through 1474
      removed outlier: 3.827A  pdb=" N   ARG A1462 " --> pdb=" O   ASP A1458 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1494 through 1511
    Processing helix  chain 'A' and resid 1529 through 1531
      No H-bonds generated for 'chain 'A' and resid 1529 through 1531'
    Processing helix  chain 'A' and resid 1532 through 1539
      removed outlier: 3.945A  pdb=" N   SER A1536 " --> pdb=" O   LYS A1532 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   LYS A1539 " --> pdb=" O   LEU A1535 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1552 through 1558
      removed outlier: 4.122A  pdb=" N   ARG A1558 " --> pdb=" O   LEU A1554 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1567 through 1580
      removed outlier: 4.231A  pdb=" N   HIS A1571 " --> pdb=" O   ASN A1567 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   HIS A1574 " --> pdb=" O   PRO A1570 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1599 through 1613
      removed outlier: 3.826A  pdb=" N   LEU A1603 " --> pdb=" O   GLU A1599 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   ILE A1610 " --> pdb=" O   ILE A1606 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   LEU A1611 " --> pdb=" O   MET A1607 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1628 through 1635
    Processing helix  chain 'A' and resid 1642 through 1644
      No H-bonds generated for 'chain 'A' and resid 1642 through 1644'
    Processing helix  chain 'A' and resid 1645 through 1656
    Processing helix  chain 'A' and resid 1703 through 1712
    Processing helix  chain 'A' and resid 1770 through 1792
    Processing helix  chain 'A' and resid 1793 through 1796
    Processing helix  chain 'A' and resid 1827 through 1835
    Processing helix  chain 'A' and resid 1851 through 1856
    Processing helix  chain 'A' and resid 1865 through 1869
    Processing helix  chain 'A' and resid 1913 through 1925
      removed outlier: 3.749A  pdb=" N   LEU A1917 " --> pdb=" O   SER A1913 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1954 through 1961
      removed outlier: 3.624A  pdb=" N   GLN A1961 " --> pdb=" O   ARG A1957 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1967 through 1986
      removed outlier: 3.736A  pdb=" N   HIS A1972 " --> pdb=" O   ARG A1968 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1996 through 1998
      No H-bonds generated for 'chain 'A' and resid 1996 through 1998'
    Processing helix  chain 'A' and resid 2055 through 2068
    Processing helix  chain 'A' and resid 2094 through 2100
      removed outlier: 3.725A  pdb=" N   GLU A2098 " --> pdb=" O   ASP A2094 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2107 through 2115
    Processing helix  chain 'A' and resid 2124 through 2133
      removed outlier: 3.530A  pdb=" N   PHE A2129 " --> pdb=" O   SER A2125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2134 through 2139
      removed outlier: 3.512A  pdb=" N   VAL A2138 " --> pdb=" O   SER A2134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2339 through 2343
      removed outlier: 3.756A  pdb=" N   GLN A2342 " --> pdb=" O   ARG A2339 " (cutoff:3.500A)
      removed outlier: 4.290A  pdb=" N   LEU A2343 " --> pdb=" O   THR A2340 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 2339 through 2343'
    Processing helix  chain 'A' and resid 2408 through 2412
    Processing helix  chain 'A' and resid 2499 through 2520
      removed outlier: 3.930A  pdb=" N   GLN A2505 " --> pdb=" O   PRO A2501 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 16 through 26
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'B' and resid 51 through 57
    Processing helix  chain 'B' and resid 61 through 71
      removed outlier: 3.548A  pdb=" N   VAL B  65 " --> pdb=" O   HIS B  61 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   VAL B  67 " --> pdb=" O   GLU B  63 " (cutoff:3.500A)
      removed outlier: 4.122A  pdb=" N   THR B  71 " --> pdb=" O   VAL B  67 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 86 through 92
    Processing helix  chain 'B' and resid 97 through 102
    Processing helix  chain 'B' and resid 103 through 105
      No H-bonds generated for 'chain 'B' and resid 103 through 105'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 1372 through 1376
      removed outlier: 3.974A  pdb=" N   LYS A1374 " --> pdb=" O   VAL A1392 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   VAL A1392 " --> pdb=" O   LYS A1374 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   MET A1335 " --> pdb=" O   VAL A1389 " (cutoff:3.500A)
      removed outlier: 8.829A  pdb=" N   ILE A1448 " --> pdb=" O   ALA A1413 " (cutoff:3.500A)
      removed outlier: 7.029A  pdb=" N   TYR A1415 " --> pdb=" O   ILE A1448 " (cutoff:3.500A)
      removed outlier: 8.086A  pdb=" N   VAL A1450 " --> pdb=" O   TYR A1415 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   ALA A1417 " --> pdb=" O   VAL A1450 " (cutoff:3.500A)
      removed outlier: 7.589A  pdb=" N   THR A1452 " --> pdb=" O   ALA A1417 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   TYR A1419 " --> pdb=" O   THR A1452 " (cutoff:3.500A)
      removed outlier: 8.783A  pdb=" N   HIS A1486 " --> pdb=" O   VAL A1447 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   LEU A1449 " --> pdb=" O   HIS A1486 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 1730 through 1733
      removed outlier: 4.347A  pdb=" N   ASN A1730 " --> pdb=" O   ASN A1741 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   ASN A1741 " --> pdb=" O   ASN A1730 " (cutoff:3.500A)
      removed outlier: 5.268A  pdb=" N   TYR A1739 " --> pdb=" O   VAL A1750 " (cutoff:3.500A)
      removed outlier: 7.244A  pdb=" N   VAL A1750 " --> pdb=" O   TYR A1739 " (cutoff:3.500A)
      removed outlier: 5.151A  pdb=" N   ASN A1741 " --> pdb=" O   CYS A1748 " (cutoff:3.500A)
      removed outlier: 7.471A  pdb=" N   CYS A1748 " --> pdb=" O   ASN A1741 " (cutoff:3.500A)
      removed outlier: 7.084A  pdb=" N   TYR A1747 " --> pdb=" O   PRO A1768 " (cutoff:3.500A)
      removed outlier: 4.564A  pdb=" N   ILE A1692 " --> pdb=" O   LEU A1813 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1892 through 1898
      removed outlier: 3.714A  pdb=" N   ALA A1937 " --> pdb=" O   VAL A1946 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 2000 through 2002
    Processing sheet with id=AA5, first strand: chain 'A' and resid 2140 through 2145
      removed outlier: 6.656A  pdb=" N   LEU A2140 " --> pdb=" O   ASP A2497 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   ASP A2497 " --> pdb=" O   LEU A2140 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   VAL A2469 " --> pdb=" O   ALA A2461 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 2152 through 2157
    Processing sheet with id=AA7, first strand: chain 'A' and resid 2199 through 2207
      removed outlier: 4.587A  pdb=" N   CYS A2201 " --> pdb=" O   GLY A2218 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 2245 through 2249
      removed outlier: 4.652A  pdb=" N   LYS A2271 " --> pdb=" O   THR A2267 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 2300 through 2305
    Processing sheet with id=AB1, first strand: chain 'A' and resid 2354 through 2358
      removed outlier: 3.507A  pdb=" N   THR A2356 " --> pdb=" O   ALA A2366 " (cutoff:3.500A)
      removed outlier: 4.879A  pdb=" N   LYS A2367 " --> pdb=" O   VAL A2372 " (cutoff:3.500A)
      removed outlier: 6.634A  pdb=" N   VAL A2372 " --> pdb=" O   LYS A2367 " (cutoff:3.500A)
      removed outlier: 6.623A  pdb=" N   VAL A2373 " --> pdb=" O   LEU A2386 " (cutoff:3.500A)
      removed outlier: 4.606A  pdb=" N   LEU A2386 " --> pdb=" O   VAL A2373 " (cutoff:3.500A)
      removed outlier: 6.540A  pdb=" N   VAL A2375 " --> pdb=" O   CYS A2384 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 2414 through 2420
      removed outlier: 6.761A  pdb=" N   GLY A2428 " --> pdb=" O   LYS A2415 " (cutoff:3.500A)
      removed outlier: 4.610A  pdb=" N   LEU A2417 " --> pdb=" O   TRP A2426 " (cutoff:3.500A)
      removed outlier: 7.100A  pdb=" N   TRP A2426 " --> pdb=" O   LEU A2417 " (cutoff:3.500A)
      removed outlier: 5.746A  pdb=" N   LEU A2419 " --> pdb=" O   ALA A2424 " (cutoff:3.500A)
      removed outlier: 7.604A  pdb=" N   ALA A2424 " --> pdb=" O   LEU A2419 " (cutoff:3.500A)

    320 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: 1.82

  Time building geometry restraints manager: 1.12 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2887
        1.34 -     1.46: 1656
        1.46 -     1.58: 4468
        1.58 -     1.69: 0
        1.69 -     1.81: 79
  Bond restraints: 9090
  Sorted by residual:
  bond pdb=" CA  TYR A2449 "
       pdb=" CB  TYR A2449 "
    ideal  model  delta    sigma   weight residual
    1.530  1.558 -0.028 1.69e-02 3.50e+03 2.69e+00
  bond pdb=" CA  THR A2416 "
       pdb=" CB  THR A2416 "
    ideal  model  delta    sigma   weight residual
    1.535  1.507  0.028 2.02e-02 2.45e+03 1.86e+00
  bond pdb=" N   GLU A1899 "
       pdb=" CA  GLU A1899 "
    ideal  model  delta    sigma   weight residual
    1.457  1.474 -0.016 1.29e-02 6.01e+03 1.60e+00
  bond pdb=" CB  ASP A1429 "
       pdb=" CG  ASP A1429 "
    ideal  model  delta    sigma   weight residual
    1.516  1.547 -0.031 2.50e-02 1.60e+03 1.53e+00
  bond pdb=" CG  ARG A1441 "
       pdb=" CD  ARG A1441 "
    ideal  model  delta    sigma   weight residual
    1.520  1.483  0.037 3.00e-02 1.11e+03 1.51e+00
  ... (remaining 9085 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.60: 12093
        2.60 -     5.21: 171
        5.21 -     7.81: 22
        7.81 -    10.42: 3
       10.42 -    13.02: 1
  Bond angle restraints: 12290
  Sorted by residual:
  angle pdb=" C   HIS A1928 "
        pdb=" N   HIS A1929 "
        pdb=" CA  HIS A1929 "
      ideal   model   delta    sigma   weight residual
     120.26  127.19   -6.93 1.34e+00 5.57e-01 2.67e+01
  angle pdb=" CA  TRP A1791 "
        pdb=" CB  TRP A1791 "
        pdb=" CG  TRP A1791 "
      ideal   model   delta    sigma   weight residual
     113.60  123.01   -9.41 1.90e+00 2.77e-01 2.45e+01
  angle pdb=" N   HIS A1929 "
        pdb=" CA  HIS A1929 "
        pdb=" C   HIS A1929 "
      ideal   model   delta    sigma   weight residual
     112.75  119.36   -6.61 1.36e+00 5.41e-01 2.36e+01
  angle pdb=" CA  LEU A1712 "
        pdb=" CB  LEU A1712 "
        pdb=" CG  LEU A1712 "
      ideal   model   delta    sigma   weight residual
     116.30  129.32  -13.02 3.50e+00 8.16e-02 1.38e+01
  angle pdb=" CA  ARG A1552 "
        pdb=" CB  ARG A1552 "
        pdb=" CG  ARG A1552 "
      ideal   model   delta    sigma   weight residual
     114.10  121.44   -7.34 2.00e+00 2.50e-01 1.35e+01
  ... (remaining 12285 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.98: 4984
       17.98 -    35.96: 420
       35.96 -    53.94: 85
       53.94 -    71.92: 15
       71.92 -    89.90: 5
  Dihedral angle restraints: 5509
    sinusoidal: 2246
      harmonic: 3263
  Sorted by residual:
  dihedral pdb=" CA  HIS A1929 "
           pdb=" C   HIS A1929 "
           pdb=" N   PRO A1930 "
           pdb=" CA  PRO A1930 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -146.68  -33.32     0      5.00e+00 4.00e-02 4.44e+01
  dihedral pdb=" CA  HIS A1928 "
           pdb=" C   HIS A1928 "
           pdb=" N   HIS A1929 "
           pdb=" CA  HIS A1929 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -148.88  -31.12     0      5.00e+00 4.00e-02 3.87e+01
  dihedral pdb=" CA  TYR A1898 "
           pdb=" C   TYR A1898 "
           pdb=" N   GLU A1899 "
           pdb=" CA  GLU A1899 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.75  -23.25     0      5.00e+00 4.00e-02 2.16e+01
  ... (remaining 5506 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 986
       0.044 -    0.088: 322
       0.088 -    0.132: 101
       0.132 -    0.176: 15
       0.176 -    0.220: 1
  Chirality restraints: 1425
  Sorted by residual:
  chirality pdb=" CA  HIS A1405 "
            pdb=" N   HIS A1405 "
            pdb=" C   HIS A1405 "
            pdb=" CB  HIS A1405 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.21e+00
  chirality pdb=" CB  ILE A2434 "
            pdb=" CA  ILE A2434 "
            pdb=" CG1 ILE A2434 "
            pdb=" CG2 ILE A2434 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.81   -0.17 2.00e-01 2.50e+01 7.12e-01
  chirality pdb=" CB  THR A2068 "
            pdb=" CA  THR A2068 "
            pdb=" OG1 THR A2068 "
            pdb=" CG2 THR A2068 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.39    0.16 2.00e-01 2.50e+01 6.64e-01
  ... (remaining 1422 not shown)

  Planarity restraints: 1543
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A1941 "   -0.047 5.00e-02 4.00e+02   7.07e-02 8.00e+00
        pdb=" N   PRO A1942 "    0.122 5.00e-02 4.00e+02
        pdb=" CA  PRO A1942 "   -0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO A1942 "   -0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A1791 "    0.024 2.00e-02 2.50e+03   1.79e-02 7.98e+00
        pdb=" CG  TRP A1791 "   -0.048 2.00e-02 2.50e+03
        pdb=" CD1 TRP A1791 "    0.018 2.00e-02 2.50e+03
        pdb=" CD2 TRP A1791 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A1791 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A1791 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A1791 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A1791 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A1791 "   -0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP A1791 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B  80 "   -0.017 2.00e-02 2.50e+03   1.46e-02 5.36e+00
        pdb=" CG  TRP B  80 "    0.039 2.00e-02 2.50e+03
        pdb=" CD1 TRP B  80 "   -0.018 2.00e-02 2.50e+03
        pdb=" CD2 TRP B  80 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP B  80 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP B  80 "    0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP B  80 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B  80 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B  80 "   -0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP B  80 "   -0.004 2.00e-02 2.50e+03
  ... (remaining 1540 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.68: 186
        2.68 -     3.24: 9014
        3.24 -     3.79: 13320
        3.79 -     4.35: 17645
        4.35 -     4.90: 28736
  Nonbonded interactions: 68901
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS A1468 "
            pdb=" OE1 GLU A1472 "
     model   vdw
     2.129 3.120
  nonbonded pdb=" OE2 GLU A1400 "
            pdb=" NE2 GLN A1657 "
     model   vdw
     2.136 3.120
  nonbonded pdb=" OG  SER A1934 "
            pdb=" OE1 GLU A1948 "
     model   vdw
     2.195 3.040
  nonbonded pdb=" OG1 THR A2246 "
            pdb=" O   LEU A2300 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" OD2 ASP A1863 "
            pdb=" NH2 ARG A1918 "
     model   vdw
     2.210 3.120
  ... (remaining 68896 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:             2.710
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     10.560
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7349
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   0.037   9090  Z= 0.191
  Angle     :  0.799  13.021  12290  Z= 0.423
  Chirality :  0.048   0.220   1425
  Planarity :  0.005   0.071   1543
  Dihedral  : 14.054  89.901   3383
  Min Nonbonded Distance : 2.129

Molprobity Statistics.
  All-atom Clashscore : 15.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.02 %
    Favored  : 91.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.50 %
    Favored  : 99.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.16 (0.26), residues: 1085
  helix:  0.30 (0.30), residues: 316
  sheet: -0.02 (0.34), residues: 245
  loop : -1.84 (0.27), residues: 524

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A1441 
 TYR   0.024   0.002   TYR A1814 
 PHE   0.026   0.002   PHE A1883 
 TRP   0.048   0.003   TRP A1791 
 HIS   0.005   0.001   HIS A2510 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00434 /  0.19 ( 9090)
  covalent geometry    : angle       0.79897 /  0.42 (12290)
  hydrogen bonds       : bond        0.10908 /  7.18 (  320)
  hydrogen bonds       : angle       5.98735 /  4.17 (  897)

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 0.385 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1603 LEU cc_start: 0.8799 (mm) cc_final: 0.7978 (mm)
REVERT: A 1607 MET cc_start: 0.8430 (mpp) cc_final: 0.7473 (mpp)
REVERT: A 2315 MET cc_start: 0.7715 (mmp) cc_final: 0.7279 (mmp)
REVERT: A 2408 MET cc_start: 0.8383 (tpt) cc_final: 0.7997 (tpp)
REVERT: A 2503 GLU cc_start: 0.7343 (tp30) cc_final: 0.6707 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 153
  average time/residue: 0.0809
  time to fit residues: 17.8151
Evaluate side-chains
  119 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 108 optimal weight:    0.7980
   chunk 49 optimal weight:    0.9990
   chunk 97 optimal weight:    0.0970
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.0020
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9980
   chunk 100 optimal weight:    0.6980
   chunk 106 optimal weight:    3.9990
   overall best weight:    0.4586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A1561 GLN
A1687 ASN
A1741 ASN
** A2342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2490 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 = 0.4265 r_free = 0.4265 target = 0.181946 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.136910 restraints weight = 13142.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.138830 restraints weight = 9691.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.140682 restraints weight = 7646.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.141461 restraints weight = 6371.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.141881 restraints weight = 5649.753|
|-----------------------------------------------------------------------------|
r_work (final): 0.3823
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7298
moved from start:          0.1199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9090  Z= 0.137
  Angle     :  0.653   8.413  12290  Z= 0.334
  Chirality :  0.045   0.199   1425
  Planarity :  0.004   0.053   1543
  Dihedral  :  4.898  36.145   1189
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 11.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.65 %
    Favored  : 92.35 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  :  8.88 %
    Favored  : 89.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.95 (0.26), residues: 1085
  helix:  0.64 (0.31), residues: 314
  sheet:  0.17 (0.35), residues: 230
  loop : -1.81 (0.27), residues: 541

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A1441 
 TYR   0.026   0.001   TYR A2449 
 PHE   0.020   0.001   PHE A1575 
 TRP   0.037   0.002   TRP A1791 
 HIS   0.006   0.001   HIS A2391 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00317 /  0.14 ( 9090)
  covalent geometry    : angle       0.65272 /  0.33 (12290)
  hydrogen bonds       : bond        0.03670 /  2.32 (  320)
  hydrogen bonds       : angle       5.16426 /  3.59 (  897)

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 144
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1353 GLN cc_start: 0.8312 (tp40) cc_final: 0.8083 (tp40)
REVERT: A 1603 LEU cc_start: 0.8733 (mm) cc_final: 0.8355 (mm)
REVERT: A 2061 LEU cc_start: 0.8534 (mm) cc_final: 0.8285 (mm)
REVERT: A 2207 LEU cc_start: 0.7722 (mm) cc_final: 0.7495 (mp)
REVERT: A 2408 MET cc_start: 0.8327 (tpt) cc_final: 0.7900 (tpp)
REVERT: A 2421 LYS cc_start: 0.8539 (tppt) cc_final: 0.8127 (tptm)
REVERT: B   29 ASP cc_start: 0.7398 (t70) cc_final: 0.7100 (t70)
REVERT: B  109 ASN cc_start: 0.7358 (t0) cc_final: 0.7071 (t0)
  outliers start: 13
  outliers final: 8
  residues processed: 148
  average time/residue: 0.0781
  time to fit residues: 16.6140
Evaluate side-chains
  133 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 125
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1574 HIS
Chi-restraints excluded: chain A residue 1611 LEU
Chi-restraints excluded: chain A residue 1669 VAL
Chi-restraints excluded: chain A residue 2152 VAL
Chi-restraints excluded: chain A residue 2372 VAL
Chi-restraints excluded: chain A residue 2440 SER
Chi-restraints excluded: chain A residue 2516 GLU
Chi-restraints excluded: chain B residue  101 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 39 optimal weight:    0.8980
   chunk 53 optimal weight:    0.7980
   chunk 101 optimal weight:    1.9990
   chunk 95 optimal weight:    0.6980
   chunk 46 optimal weight:    2.9990
   chunk 74 optimal weight:    0.8980
   chunk 69 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 11 optimal weight:    7.9990
   chunk 99 optimal weight:    0.1980
   chunk 15 optimal weight:    0.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A1560 ASN
** A2342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4240 r_free = 0.4240 target = 0.179460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.133494 restraints weight = 13095.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.134427 restraints weight = 7909.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.136288 restraints weight = 6872.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.137390 restraints weight = 6076.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.137568 restraints weight = 5445.734|
|-----------------------------------------------------------------------------|
r_work (final): 0.3769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7360
moved from start:          0.1559

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   9090  Z= 0.152
  Angle     :  0.628  10.544  12290  Z= 0.320
  Chirality :  0.045   0.195   1425
  Planarity :  0.004   0.055   1543
  Dihedral  :  4.804  35.642   1189
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 11.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.74 %
    Favored  : 92.26 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 12.11 %
    Favored  : 86.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.88 (0.26), residues: 1085
  helix:  0.75 (0.31), residues: 315
  sheet: -0.09 (0.33), residues: 246
  loop : -1.70 (0.28), residues: 524

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A1441 
 TYR   0.015   0.001   TYR A1984 
 PHE   0.013   0.001   PHE A1883 
 TRP   0.032   0.002   TRP A1791 
 HIS   0.004   0.001   HIS A2391 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00362 /  0.15 ( 9090)
  covalent geometry    : angle       0.62808 /  0.32 (12290)
  hydrogen bonds       : bond        0.03570 /  2.26 (  320)
  hydrogen bonds       : angle       5.02197 /  3.49 (  897)

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 132
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1335 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.8254 (ttm)
REVERT: A 1353 GLN cc_start: 0.8200 (tp40) cc_final: 0.7956 (tp40)
REVERT: A 1603 LEU cc_start: 0.8797 (mm) cc_final: 0.8543 (mm)
REVERT: A 1638 LYS cc_start: 0.7185 (mmtp) cc_final: 0.6907 (mmtm)
REVERT: A 1712 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7646 (tt)
REVERT: A 2130 ASP cc_start: 0.8073 (m-30) cc_final: 0.7822 (m-30)
REVERT: A 2408 MET cc_start: 0.8350 (tpt) cc_final: 0.7884 (tpp)
REVERT: A 2421 LYS cc_start: 0.8552 (tppt) cc_final: 0.8146 (tptm)
  outliers start: 18
  outliers final: 11
  residues processed: 140
  average time/residue: 0.0897
  time to fit residues: 18.1525
Evaluate side-chains
  133 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 120
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1335 MET
Chi-restraints excluded: chain A residue 1410 THR
Chi-restraints excluded: chain A residue 1611 LEU
Chi-restraints excluded: chain A residue 1669 VAL
Chi-restraints excluded: chain A residue 1712 LEU
Chi-restraints excluded: chain A residue 1780 VAL
Chi-restraints excluded: chain A residue 2152 VAL
Chi-restraints excluded: chain A residue 2372 VAL
Chi-restraints excluded: chain A residue 2427 ILE
Chi-restraints excluded: chain A residue 2440 SER
Chi-restraints excluded: chain A residue 2511 ILE
Chi-restraints excluded: chain A residue 2516 GLU
Chi-restraints excluded: chain B residue  101 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 44 optimal weight:    0.9990
   chunk 28 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   chunk 15 optimal weight:    0.6980
   chunk 73 optimal weight:    3.9990
   chunk 3 optimal weight:    3.9990
   chunk 19 optimal weight:    7.9990
   chunk 46 optimal weight:    0.8980
   chunk 68 optimal weight:    0.9980
   chunk 93 optimal weight:    0.4980
   chunk 70 optimal weight:    1.9990
   overall best weight:    0.8182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A1854 GLN
** A2342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.177361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.137765 restraints weight = 13309.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.143601 restraints weight = 14287.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.143464 restraints weight = 10972.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.145128 restraints weight = 7023.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.146614 restraints weight = 6032.684|
|-----------------------------------------------------------------------------|
r_work (final): 0.3863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7216
moved from start:          0.1933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9090  Z= 0.165
  Angle     :  0.628  11.032  12290  Z= 0.318
  Chirality :  0.044   0.188   1425
  Planarity :  0.004   0.054   1543
  Dihedral  :  4.841  36.294   1189
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 11.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.65 %
    Favored  : 92.35 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 14.43 %
    Favored  : 82.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.92 (0.26), residues: 1085
  helix:  0.77 (0.30), residues: 317
  sheet: -0.21 (0.33), residues: 239
  loop : -1.70 (0.27), residues: 529

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  33 
 TYR   0.012   0.001   TYR A1814 
 PHE   0.020   0.001   PHE A1575 
 TRP   0.031   0.002   TRP A1791 
 HIS   0.005   0.001   HIS A2391 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00397 /  0.17 ( 9090)
  covalent geometry    : angle       0.62754 /  0.32 (12290)
  hydrogen bonds       : bond        0.03512 /  2.24 (  320)
  hydrogen bonds       : angle       4.99111 /  3.47 (  897)

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 135
  time to evaluate  : 0.355 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1335 MET cc_start: 0.8390 (OUTLIER) cc_final: 0.8002 (ttm)
REVERT: A 1353 GLN cc_start: 0.8111 (tp40) cc_final: 0.7869 (tp40)
REVERT: A 1603 LEU cc_start: 0.8577 (mm) cc_final: 0.8366 (mm)
REVERT: A 1629 ARG cc_start: 0.8380 (mmp80) cc_final: 0.8096 (mmp80)
REVERT: A 1712 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7738 (tt)
REVERT: A 2130 ASP cc_start: 0.8084 (m-30) cc_final: 0.7789 (m-30)
REVERT: A 2408 MET cc_start: 0.8399 (tpt) cc_final: 0.7888 (tpp)
REVERT: A 2421 LYS cc_start: 0.8577 (tppt) cc_final: 0.8117 (tptm)
REVERT: A 2503 GLU cc_start: 0.7080 (tp30) cc_final: 0.6413 (mt-10)
  outliers start: 26
  outliers final: 16
  residues processed: 149
  average time/residue: 0.0873
  time to fit residues: 18.9036
Evaluate side-chains
  142 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 124
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1335 MET
Chi-restraints excluded: chain A residue 1410 THR
Chi-restraints excluded: chain A residue 1611 LEU
Chi-restraints excluded: chain A residue 1650 PHE
Chi-restraints excluded: chain A residue 1669 VAL
Chi-restraints excluded: chain A residue 1712 LEU
Chi-restraints excluded: chain A residue 1780 VAL
Chi-restraints excluded: chain A residue 2152 VAL
Chi-restraints excluded: chain A residue 2301 MET
Chi-restraints excluded: chain A residue 2363 LEU
Chi-restraints excluded: chain A residue 2372 VAL
Chi-restraints excluded: chain A residue 2373 VAL
Chi-restraints excluded: chain A residue 2427 ILE
Chi-restraints excluded: chain A residue 2440 SER
Chi-restraints excluded: chain A residue 2511 ILE
Chi-restraints excluded: chain A residue 2516 GLU
Chi-restraints excluded: chain B residue   84 THR
Chi-restraints excluded: chain B residue  101 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 2 optimal weight:    0.9990
   chunk 51 optimal weight:    2.9990
   chunk 71 optimal weight:    5.9990
   chunk 85 optimal weight:    3.9990
   chunk 83 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9980
   chunk 74 optimal weight:    4.9990
   chunk 67 optimal weight:    0.5980
   chunk 22 optimal weight:    4.9990
   chunk 88 optimal weight:    0.6980
   chunk 73 optimal weight:    0.9980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A1560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.176624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.131868 restraints weight = 13266.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.130456 restraints weight = 10214.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.132075 restraints weight = 9740.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.133849 restraints weight = 7570.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.134313 restraints weight = 6504.569|
|-----------------------------------------------------------------------------|
r_work (final): 0.3733
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7426
moved from start:          0.2178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   9090  Z= 0.161
  Angle     :  0.631  10.164  12290  Z= 0.319
  Chirality :  0.045   0.213   1425
  Planarity :  0.004   0.055   1543
  Dihedral  :  4.835  36.245   1189
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 11.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.20 %
    Favored  : 91.80 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 15.64 %
    Favored  : 81.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.92 (0.26), residues: 1085
  helix:  0.87 (0.30), residues: 318
  sheet: -0.30 (0.33), residues: 246
  loop : -1.73 (0.28), residues: 521

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B  33 
 TYR   0.012   0.001   TYR A1814 
 PHE   0.009   0.001   PHE A2059 
 TRP   0.030   0.002   TRP A1791 
 HIS   0.004   0.001   HIS A2391 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00386 /  0.16 ( 9090)
  covalent geometry    : angle       0.63081 /  0.32 (12290)
  hydrogen bonds       : bond        0.03405 /  2.18 (  320)
  hydrogen bonds       : angle       4.96340 /  3.45 (  897)

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 132
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1335 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.8162 (ttm)
REVERT: A 1353 GLN cc_start: 0.8155 (tp40) cc_final: 0.7877 (tp40)
REVERT: A 1638 LYS cc_start: 0.7181 (mmtp) cc_final: 0.6906 (mmtm)
REVERT: A 1712 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7692 (tt)
REVERT: A 1734 TRP cc_start: 0.8065 (p90) cc_final: 0.7823 (p90)
REVERT: A 1791 TRP cc_start: 0.6340 (t60) cc_final: 0.6128 (t60)
REVERT: A 1944 MET cc_start: 0.6981 (ptt) cc_final: 0.6689 (ptt)
REVERT: A 2130 ASP cc_start: 0.8107 (m-30) cc_final: 0.7766 (m-30)
REVERT: A 2408 MET cc_start: 0.8377 (tpt) cc_final: 0.8015 (tpp)
REVERT: A 2421 LYS cc_start: 0.8511 (tppt) cc_final: 0.8132 (tptm)
REVERT: A 2503 GLU cc_start: 0.7044 (tp30) cc_final: 0.6494 (mt-10)
  outliers start: 26
  outliers final: 21
  residues processed: 146
  average time/residue: 0.0830
  time to fit residues: 17.8212
Evaluate side-chains
  143 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 120
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1335 MET
Chi-restraints excluded: chain A residue 1410 THR
Chi-restraints excluded: chain A residue 1484 ASP
Chi-restraints excluded: chain A residue 1611 LEU
Chi-restraints excluded: chain A residue 1669 VAL
Chi-restraints excluded: chain A residue 1702 MET
Chi-restraints excluded: chain A residue 1712 LEU
Chi-restraints excluded: chain A residue 1780 VAL
Chi-restraints excluded: chain A residue 1954 SER
Chi-restraints excluded: chain A residue 2068 THR
Chi-restraints excluded: chain A residue 2152 VAL
Chi-restraints excluded: chain A residue 2190 THR
Chi-restraints excluded: chain A residue 2216 VAL
Chi-restraints excluded: chain A residue 2301 MET
Chi-restraints excluded: chain A residue 2363 LEU
Chi-restraints excluded: chain A residue 2372 VAL
Chi-restraints excluded: chain A residue 2373 VAL
Chi-restraints excluded: chain A residue 2427 ILE
Chi-restraints excluded: chain A residue 2440 SER
Chi-restraints excluded: chain A residue 2511 ILE
Chi-restraints excluded: chain A residue 2516 GLU
Chi-restraints excluded: chain B residue   84 THR
Chi-restraints excluded: chain B residue  101 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 57 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9990
   chunk 97 optimal weight:    0.8980
   chunk 18 optimal weight:    6.9990
   chunk 95 optimal weight:    0.5980
   chunk 46 optimal weight:    0.7980
   chunk 56 optimal weight:    0.1980
   chunk 102 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 61 optimal weight:    0.0970
   chunk 19 optimal weight:    0.8980
   overall best weight:    0.5178

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A1560 ASN
A2342 GLN
** A2420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2490 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 = 0.4233 r_free = 0.4233 target = 0.178868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.133789 restraints weight = 13299.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.133484 restraints weight = 9896.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.135262 restraints weight = 8773.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.137054 restraints weight = 6872.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.137491 restraints weight = 5996.403|
|-----------------------------------------------------------------------------|
r_work (final): 0.3764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7379
moved from start:          0.2361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9090  Z= 0.132
  Angle     :  0.610   9.587  12290  Z= 0.307
  Chirality :  0.044   0.186   1425
  Planarity :  0.004   0.053   1543
  Dihedral  :  4.707  35.405   1189
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 10.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.56 %
    Favored  : 92.44 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 16.45 %
    Favored  : 80.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.90 (0.26), residues: 1085
  helix:  0.90 (0.30), residues: 324
  sheet: -0.31 (0.32), residues: 248
  loop : -1.75 (0.28), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B  33 
 TYR   0.010   0.001   TYR A1992 
 PHE   0.021   0.001   PHE A1575 
 TRP   0.021   0.002   TRP A1791 
 HIS   0.004   0.001   HIS A2391 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00311 /  0.13 ( 9090)
  covalent geometry    : angle       0.61029 /  0.31 (12290)
  hydrogen bonds       : bond        0.03171 /  2.04 (  320)
  hydrogen bonds       : angle       4.84131 /  3.36 (  897)

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 126
  time to evaluate  : 0.345 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1353 GLN cc_start: 0.8116 (tp40) cc_final: 0.7824 (tp40)
REVERT: A 1638 LYS cc_start: 0.7107 (mmtp) cc_final: 0.6836 (mmtm)
REVERT: A 1712 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7734 (tt)
REVERT: A 1734 TRP cc_start: 0.8042 (p90) cc_final: 0.7769 (p90)
REVERT: A 1738 ILE cc_start: 0.8364 (pt) cc_final: 0.8070 (pt)
REVERT: A 1791 TRP cc_start: 0.6252 (t60) cc_final: 0.5962 (t60)
REVERT: A 1944 MET cc_start: 0.7030 (ptt) cc_final: 0.6718 (ptt)
REVERT: A 2130 ASP cc_start: 0.8097 (m-30) cc_final: 0.7742 (m-30)
REVERT: A 2408 MET cc_start: 0.8314 (tpt) cc_final: 0.8022 (tpp)
REVERT: A 2421 LYS cc_start: 0.8477 (tppt) cc_final: 0.8060 (tptm)
REVERT: B   55 LEU cc_start: 0.8641 (mp) cc_final: 0.8311 (mp)
  outliers start: 28
  outliers final: 18
  residues processed: 142
  average time/residue: 0.0811
  time to fit residues: 16.9792
Evaluate side-chains
  137 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 118
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1611 LEU
Chi-restraints excluded: chain A residue 1650 PHE
Chi-restraints excluded: chain A residue 1669 VAL
Chi-restraints excluded: chain A residue 1702 MET
Chi-restraints excluded: chain A residue 1712 LEU
Chi-restraints excluded: chain A residue 1954 SER
Chi-restraints excluded: chain A residue 2068 THR
Chi-restraints excluded: chain A residue 2152 VAL
Chi-restraints excluded: chain A residue 2190 THR
Chi-restraints excluded: chain A residue 2216 VAL
Chi-restraints excluded: chain A residue 2372 VAL
Chi-restraints excluded: chain A residue 2427 ILE
Chi-restraints excluded: chain A residue 2440 SER
Chi-restraints excluded: chain A residue 2511 ILE
Chi-restraints excluded: chain A residue 2516 GLU
Chi-restraints excluded: chain B residue   53 LEU
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue   84 THR
Chi-restraints excluded: chain B residue  101 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 43 optimal weight:    0.0970
   chunk 50 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9980
   chunk 24 optimal weight:    5.9990
   chunk 93 optimal weight:    1.9990
   chunk 19 optimal weight:    0.0870
   chunk 66 optimal weight:    0.5980
   chunk 20 optimal weight:    6.9990
   chunk 45 optimal weight:    0.6980
   chunk 23 optimal weight:    1.9990
   overall best weight:    0.4956

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A2420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.178324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.139791 restraints weight = 13251.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.142147 restraints weight = 14265.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.143538 restraints weight = 12023.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.145213 restraints weight = 7419.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.146968 restraints weight = 6440.606|
|-----------------------------------------------------------------------------|
r_work (final): 0.3874
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7209
moved from start:          0.2476

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9090  Z= 0.128
  Angle     :  0.621   9.448  12290  Z= 0.308
  Chirality :  0.044   0.176   1425
  Planarity :  0.004   0.053   1543
  Dihedral  :  4.657  35.123   1189
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 10.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.93 %
    Favored  : 92.07 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 17.36 %
    Favored  : 79.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.87 (0.26), residues: 1085
  helix:  0.86 (0.30), residues: 329
  sheet: -0.21 (0.33), residues: 242
  loop : -1.76 (0.28), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B  33 
 TYR   0.013   0.001   TYR A1992 
 PHE   0.017   0.001   PHE A1575 
 TRP   0.020   0.002   TRP A1602 
 HIS   0.003   0.001   HIS A2391 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00302 /  0.13 ( 9090)
  covalent geometry    : angle       0.62072 /  0.31 (12290)
  hydrogen bonds       : bond        0.03108 /  2.01 (  320)
  hydrogen bonds       : angle       4.84032 /  3.36 (  897)

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 126
  time to evaluate  : 0.418 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1353 GLN cc_start: 0.8105 (tp40) cc_final: 0.7816 (tp40)
REVERT: A 1638 LYS cc_start: 0.7010 (mmtp) cc_final: 0.6752 (mmtm)
REVERT: A 1712 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7783 (tt)
REVERT: A 1734 TRP cc_start: 0.8023 (p90) cc_final: 0.7782 (p90)
REVERT: A 1738 ILE cc_start: 0.8454 (pt) cc_final: 0.8132 (pt)
REVERT: A 1944 MET cc_start: 0.7108 (ptt) cc_final: 0.6827 (ptt)
REVERT: A 2130 ASP cc_start: 0.8055 (m-30) cc_final: 0.7667 (m-30)
REVERT: A 2149 ASN cc_start: 0.7596 (t0) cc_final: 0.7369 (t0)
REVERT: A 2408 MET cc_start: 0.8320 (tpt) cc_final: 0.8015 (tpp)
REVERT: A 2421 LYS cc_start: 0.8508 (tppt) cc_final: 0.8043 (tptm)
REVERT: B   55 LEU cc_start: 0.8660 (mp) cc_final: 0.8383 (mp)
  outliers start: 27
  outliers final: 22
  residues processed: 142
  average time/residue: 0.0867
  time to fit residues: 17.9272
Evaluate side-chains
  138 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 115
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1410 THR
Chi-restraints excluded: chain A residue 1569 LEU
Chi-restraints excluded: chain A residue 1611 LEU
Chi-restraints excluded: chain A residue 1650 PHE
Chi-restraints excluded: chain A residue 1669 VAL
Chi-restraints excluded: chain A residue 1702 MET
Chi-restraints excluded: chain A residue 1712 LEU
Chi-restraints excluded: chain A residue 1954 SER
Chi-restraints excluded: chain A residue 2068 THR
Chi-restraints excluded: chain A residue 2132 LEU
Chi-restraints excluded: chain A residue 2152 VAL
Chi-restraints excluded: chain A residue 2190 THR
Chi-restraints excluded: chain A residue 2216 VAL
Chi-restraints excluded: chain A residue 2372 VAL
Chi-restraints excluded: chain A residue 2373 VAL
Chi-restraints excluded: chain A residue 2427 ILE
Chi-restraints excluded: chain A residue 2440 SER
Chi-restraints excluded: chain A residue 2511 ILE
Chi-restraints excluded: chain A residue 2516 GLU
Chi-restraints excluded: chain B residue   53 LEU
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue   84 THR
Chi-restraints excluded: chain B residue  101 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 80 optimal weight:    5.9990
   chunk 85 optimal weight:    0.6980
   chunk 2 optimal weight:    0.5980
   chunk 71 optimal weight:    7.9990
   chunk 61 optimal weight:    0.5980
   chunk 89 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9980
   chunk 11 optimal weight:    7.9990
   chunk 12 optimal weight:    1.9990
   chunk 28 optimal weight:    0.1980
   chunk 8 optimal weight:    0.8980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A1563 GLN
** A2420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.177515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.129183 restraints weight = 13298.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.128642 restraints weight = 11912.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.130480 restraints weight = 8952.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.132542 restraints weight = 7409.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.132968 restraints weight = 6806.115|
|-----------------------------------------------------------------------------|
r_work (final): 0.3717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7453
moved from start:          0.2601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9090  Z= 0.139
  Angle     :  0.631   9.494  12290  Z= 0.313
  Chirality :  0.044   0.172   1425
  Planarity :  0.004   0.054   1543
  Dihedral  :  4.687  35.322   1189
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 10.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.74 %
    Favored  : 92.26 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 17.15 %
    Favored  : 80.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.84 (0.26), residues: 1085
  helix:  0.91 (0.30), residues: 328
  sheet: -0.21 (0.33), residues: 247
  loop : -1.76 (0.28), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  33 
 TYR   0.012   0.001   TYR A1814 
 PHE   0.017   0.001   PHE A1575 
 TRP   0.025   0.002   TRP A1791 
 HIS   0.003   0.001   HIS A2391 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00330 /  0.14 ( 9090)
  covalent geometry    : angle       0.63083 /  0.31 (12290)
  hydrogen bonds       : bond        0.03168 /  2.04 (  320)
  hydrogen bonds       : angle       4.84137 /  3.36 (  897)

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 123
  time to evaluate  : 0.347 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1353 GLN cc_start: 0.8110 (tp40) cc_final: 0.7779 (tp40)
REVERT: A 1429 ASP cc_start: 0.8080 (t0) cc_final: 0.7848 (t0)
REVERT: A 1638 LYS cc_start: 0.7221 (mmtp) cc_final: 0.6967 (mmtm)
REVERT: A 1712 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7684 (tt)
REVERT: A 1734 TRP cc_start: 0.8018 (p90) cc_final: 0.7743 (p90)
REVERT: A 1738 ILE cc_start: 0.8399 (pt) cc_final: 0.8065 (pt)
REVERT: A 1791 TRP cc_start: 0.6142 (t60) cc_final: 0.5842 (t60)
REVERT: A 1944 MET cc_start: 0.7099 (ptt) cc_final: 0.6811 (ptt)
REVERT: A 2130 ASP cc_start: 0.8102 (m-30) cc_final: 0.7733 (m-30)
REVERT: A 2408 MET cc_start: 0.8282 (tpt) cc_final: 0.7955 (tpp)
REVERT: A 2421 LYS cc_start: 0.8472 (tppt) cc_final: 0.8048 (tptm)
REVERT: B   33 ARG cc_start: 0.7014 (ttp80) cc_final: 0.6427 (ttp80)
  outliers start: 25
  outliers final: 23
  residues processed: 139
  average time/residue: 0.0864
  time to fit residues: 17.4846
Evaluate side-chains
  139 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 115
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1410 THR
Chi-restraints excluded: chain A residue 1569 LEU
Chi-restraints excluded: chain A residue 1574 HIS
Chi-restraints excluded: chain A residue 1650 PHE
Chi-restraints excluded: chain A residue 1669 VAL
Chi-restraints excluded: chain A residue 1702 MET
Chi-restraints excluded: chain A residue 1712 LEU
Chi-restraints excluded: chain A residue 1841 VAL
Chi-restraints excluded: chain A residue 1954 SER
Chi-restraints excluded: chain A residue 2068 THR
Chi-restraints excluded: chain A residue 2132 LEU
Chi-restraints excluded: chain A residue 2152 VAL
Chi-restraints excluded: chain A residue 2190 THR
Chi-restraints excluded: chain A residue 2216 VAL
Chi-restraints excluded: chain A residue 2372 VAL
Chi-restraints excluded: chain A residue 2373 VAL
Chi-restraints excluded: chain A residue 2427 ILE
Chi-restraints excluded: chain A residue 2440 SER
Chi-restraints excluded: chain A residue 2511 ILE
Chi-restraints excluded: chain A residue 2516 GLU
Chi-restraints excluded: chain B residue   53 LEU
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue   84 THR
Chi-restraints excluded: chain B residue  101 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 103 optimal weight:    2.9990
   chunk 13 optimal weight:    6.9990
   chunk 62 optimal weight:    0.7980
   chunk 0 optimal weight:    4.9990
   chunk 53 optimal weight:    1.9990
   chunk 78 optimal weight:    0.9990
   chunk 56 optimal weight:    0.0970
   chunk 28 optimal weight:    4.9990
   chunk 20 optimal weight:    7.9990
   chunk 23 optimal weight:    0.6980
   chunk 85 optimal weight:    2.9990
   overall best weight:    0.9182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A1919 GLN
** A2420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  38 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.174968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.129118 restraints weight = 13239.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.128101 restraints weight = 9864.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.129996 restraints weight = 9071.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.131740 restraints weight = 6936.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.131763 restraints weight = 6232.776|
|-----------------------------------------------------------------------------|
r_work (final): 0.3704
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7460
moved from start:          0.2729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9090  Z= 0.179
  Angle     :  0.675  10.006  12290  Z= 0.334
  Chirality :  0.045   0.172   1425
  Planarity :  0.004   0.064   1543
  Dihedral  :  4.866  35.935   1189
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 11.73
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  8.39 %
    Favored  : 91.52 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 17.66 %
    Favored  : 80.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.92 (0.26), residues: 1085
  helix:  0.86 (0.30), residues: 328
  sheet: -0.31 (0.33), residues: 245
  loop : -1.78 (0.28), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  33 
 TYR   0.020   0.001   TYR A1814 
 PHE   0.009   0.001   PHE A1908 
 TRP   0.027   0.002   TRP A1791 
 HIS   0.004   0.001   HIS A2510 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00433 /  0.18 ( 9090)
  covalent geometry    : angle       0.67487 /  0.33 (12290)
  hydrogen bonds       : bond        0.03386 /  2.18 (  320)
  hydrogen bonds       : angle       4.95023 /  3.44 (  897)

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 120
  time to evaluate  : 0.355 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1353 GLN cc_start: 0.8157 (tp40) cc_final: 0.7783 (tp40)
REVERT: A 1429 ASP cc_start: 0.8083 (t0) cc_final: 0.7847 (t0)
REVERT: A 1638 LYS cc_start: 0.7109 (mmtp) cc_final: 0.6878 (mmtm)
REVERT: A 1712 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7816 (tt)
REVERT: A 1734 TRP cc_start: 0.8136 (p90) cc_final: 0.7808 (p90)
REVERT: A 1738 ILE cc_start: 0.8433 (pt) cc_final: 0.8072 (pt)
REVERT: A 1791 TRP cc_start: 0.6506 (t60) cc_final: 0.6136 (t60)
REVERT: A 1944 MET cc_start: 0.7007 (ptt) cc_final: 0.6765 (ptt)
REVERT: A 2130 ASP cc_start: 0.8196 (m-30) cc_final: 0.7788 (m-30)
REVERT: A 2408 MET cc_start: 0.8280 (tpt) cc_final: 0.7967 (tpp)
REVERT: A 2421 LYS cc_start: 0.8537 (tppt) cc_final: 0.8063 (tptm)
REVERT: B   29 ASP cc_start: 0.7240 (t70) cc_final: 0.6764 (t70)
REVERT: B   33 ARG cc_start: 0.7063 (ttp80) cc_final: 0.6426 (ttp80)
  outliers start: 23
  outliers final: 20
  residues processed: 137
  average time/residue: 0.0881
  time to fit residues: 17.5133
Evaluate side-chains
  137 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 116
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1569 LEU
Chi-restraints excluded: chain A residue 1650 PHE
Chi-restraints excluded: chain A residue 1669 VAL
Chi-restraints excluded: chain A residue 1702 MET
Chi-restraints excluded: chain A residue 1712 LEU
Chi-restraints excluded: chain A residue 1841 VAL
Chi-restraints excluded: chain A residue 1954 SER
Chi-restraints excluded: chain A residue 2068 THR
Chi-restraints excluded: chain A residue 2132 LEU
Chi-restraints excluded: chain A residue 2152 VAL
Chi-restraints excluded: chain A residue 2190 THR
Chi-restraints excluded: chain A residue 2216 VAL
Chi-restraints excluded: chain A residue 2372 VAL
Chi-restraints excluded: chain A residue 2373 VAL
Chi-restraints excluded: chain A residue 2427 ILE
Chi-restraints excluded: chain A residue 2511 ILE
Chi-restraints excluded: chain A residue 2516 GLU
Chi-restraints excluded: chain B residue   53 LEU
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue   84 THR
Chi-restraints excluded: chain B residue  101 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 16 optimal weight:    4.9990
   chunk 58 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9990
   chunk 25 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 104 optimal weight:    0.9990
   chunk 95 optimal weight:    1.9990
   chunk 69 optimal weight:    2.9990
   chunk 100 optimal weight:    0.5980
   chunk 24 optimal weight:    7.9990
   chunk 59 optimal weight:    0.0470
   overall best weight:    0.6682

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A2420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.176095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.126986 restraints weight = 12865.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.130662 restraints weight = 8965.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.133300 restraints weight = 7011.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.134871 restraints weight = 5916.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.136312 restraints weight = 5267.962|
|-----------------------------------------------------------------------------|
r_work (final): 0.3766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7417
moved from start:          0.2805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   9090  Z= 0.148
  Angle     :  0.661  10.363  12290  Z= 0.326
  Chirality :  0.044   0.182   1425
  Planarity :  0.004   0.055   1543
  Dihedral  :  4.801  35.891   1189
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 11.51
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  7.56 %
    Favored  : 92.35 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 17.56 %
    Favored  : 80.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.86 (0.26), residues: 1085
  helix:  0.97 (0.30), residues: 328
  sheet: -0.35 (0.33), residues: 247
  loop : -1.76 (0.28), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1629 
 TYR   0.020   0.001   TYR A2018 
 PHE   0.009   0.001   PHE A1908 
 TRP   0.025   0.002   TRP A1791 
 HIS   0.004   0.001   HIS A2391 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00357 /  0.15 ( 9090)
  covalent geometry    : angle       0.66131 /  0.33 (12290)
  hydrogen bonds       : bond        0.03229 /  2.09 (  320)
  hydrogen bonds       : angle       4.87427 /  3.38 (  897)

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 123
  time to evaluate  : 0.214 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1353 GLN cc_start: 0.8153 (tp40) cc_final: 0.7734 (tp40)
REVERT: A 1412 ARG cc_start: 0.6127 (ttm170) cc_final: 0.5409 (tpt170)
REVERT: A 1429 ASP cc_start: 0.7978 (t0) cc_final: 0.7737 (t0)
REVERT: A 1638 LYS cc_start: 0.7103 (mmtp) cc_final: 0.6875 (mmtm)
REVERT: A 1712 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7699 (tt)
REVERT: A 1734 TRP cc_start: 0.8081 (p90) cc_final: 0.7770 (p90)
REVERT: A 1738 ILE cc_start: 0.8401 (pt) cc_final: 0.8017 (pt)
REVERT: A 1791 TRP cc_start: 0.6523 (t60) cc_final: 0.6076 (t60)
REVERT: A 1944 MET cc_start: 0.6995 (ptt) cc_final: 0.6771 (ptt)
REVERT: A 2130 ASP cc_start: 0.8046 (m-30) cc_final: 0.7689 (m-30)
REVERT: A 2421 LYS cc_start: 0.8527 (tppt) cc_final: 0.8096 (tptm)
REVERT: B   33 ARG cc_start: 0.7219 (ttp80) cc_final: 0.6927 (ttp80)
  outliers start: 23
  outliers final: 21
  residues processed: 140
  average time/residue: 0.0861
  time to fit residues: 17.5004
Evaluate side-chains
  141 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 119
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1569 LEU
Chi-restraints excluded: chain A residue 1650 PHE
Chi-restraints excluded: chain A residue 1669 VAL
Chi-restraints excluded: chain A residue 1702 MET
Chi-restraints excluded: chain A residue 1712 LEU
Chi-restraints excluded: chain A residue 1841 VAL
Chi-restraints excluded: chain A residue 1954 SER
Chi-restraints excluded: chain A residue 2068 THR
Chi-restraints excluded: chain A residue 2132 LEU
Chi-restraints excluded: chain A residue 2152 VAL
Chi-restraints excluded: chain A residue 2190 THR
Chi-restraints excluded: chain A residue 2216 VAL
Chi-restraints excluded: chain A residue 2363 LEU
Chi-restraints excluded: chain A residue 2372 VAL
Chi-restraints excluded: chain A residue 2373 VAL
Chi-restraints excluded: chain A residue 2427 ILE
Chi-restraints excluded: chain A residue 2511 ILE
Chi-restraints excluded: chain A residue 2516 GLU
Chi-restraints excluded: chain B residue   53 LEU
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue   84 THR
Chi-restraints excluded: chain B residue  101 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 37 optimal weight:    0.5980
   chunk 3 optimal weight:    0.8980
   chunk 43 optimal weight:    4.9990
   chunk 42 optimal weight:    0.5980
   chunk 107 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9980
   chunk 76 optimal weight:    5.9990
   chunk 25 optimal weight:    0.8980
   chunk 101 optimal weight:    0.5980
   chunk 41 optimal weight:    0.7980
   chunk 16 optimal weight:    4.9990
   overall best weight:    0.6580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A1710 ASN
** A2420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4205 r_free = 0.4205 target = 0.176202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.130148 restraints weight = 13144.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.130333 restraints weight = 9566.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.132554 restraints weight = 7775.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.134334 restraints weight = 6236.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.134408 restraints weight = 5431.574|
|-----------------------------------------------------------------------------|
r_work (final): 0.3737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7413
moved from start:          0.2873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9090  Z= 0.148
  Angle     :  0.669  11.642  12290  Z= 0.328
  Chirality :  0.044   0.177   1425
  Planarity :  0.004   0.055   1543
  Dihedral  :  4.778  35.667   1189
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 11.51
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  7.74 %
    Favored  : 92.17 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 17.66 %
    Favored  : 80.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.88 (0.26), residues: 1085
  helix:  0.95 (0.30), residues: 328
  sheet: -0.37 (0.33), residues: 247
  loop : -1.75 (0.28), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1629 
 TYR   0.020   0.001   TYR A2018 
 PHE   0.009   0.001   PHE A1908 
 TRP   0.029   0.002   TRP A1602 
 HIS   0.003   0.001   HIS A2391 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00356 /  0.15 ( 9090)
  covalent geometry    : angle       0.66948 /  0.33 (12290)
  hydrogen bonds       : bond        0.03219 /  2.08 (  320)
  hydrogen bonds       : angle       4.87937 /  3.38 (  897)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1553.35 seconds
wall clock time: 27 minutes 42.41 seconds (1662.41 seconds total)