Starting phenix.real_space_refine
on Tue Jan 13 15:12:15 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tzg_41758/01_2026/8tzg_41758.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tzg_41758/01_2026/8tzg_41758.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8tzg_41758/01_2026/8tzg_41758.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tzg_41758/01_2026/8tzg_41758.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tzg_41758/01_2026/8tzg_41758.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tzg_41758/01_2026/8tzg_41758.cif"
  }
  resolution = 2.7
  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=   0.029
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: 6
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     Mg      1      5.21       5
     S      48      5.16       5
     C    4573      2.51       5
     N    1188      2.21       5
     O    1262      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7074
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 7016
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 906, 7006
          Classifications: {'peptide': 906}
          Incomplete info: {'truncation_to_alanine': 57}
          Link IDs: {'PTRANS': 41, 'TRANS': 864}
          Chain breaks: 29
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 255
          Unresolved non-hydrogen angles: 310
          Unresolved non-hydrogen dihedrals: 218
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'ASN:plan1': 6, 'ARG:plan': 9, 'GLU:plan': 10, 'TYR:plan': 3, 'HIS:plan': 3, 'PHE:plan': 2, 'ASP:plan': 2, 'GLN:plan1': 2}
          Unresolved non-hydrogen planarities: 165
      Conformer: "B"
        Number of residues, atoms: 906, 7006
          Classifications: {'peptide': 906}
          Incomplete info: {'truncation_to_alanine': 57}
          Link IDs: {'PTRANS': 41, 'TRANS': 864}
          Chain breaks: 29
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 255
          Unresolved non-hydrogen angles: 310
          Unresolved non-hydrogen dihedrals: 218
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'ASN:plan1': 6, 'ARG:plan': 9, 'GLU:plan': 10, 'TYR:plan': 3, 'HIS:plan': 3, 'PHE:plan': 2, 'ASP:plan': 2, 'GLN:plan1': 2}
          Unresolved non-hydrogen planarities: 165
          bond proxies already assigned to first conformer: 7115
    Chain: "A"
      Number of atoms: 58
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 58
          Unusual residues: {' MG': 1, 'A1N': 1, 'GDP': 1}
          Classifications: {'undetermined': 3, 'water': 1}
          Link IDs: {None: 3}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AHIS A1998 " occ=0.48
      ... (18 atoms not shown)
      pdb=" NE2BHIS A1998 " occ=0.52
  Time building chain proxies: 3.05, per 1000 atoms: 0.43
  Number of scatterers: 7074
  At special positions: 0
  Unit cell: (100.045, 119.68, 85.085, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      48     16.00
     P       2     15.00
     Mg      1     11.99
     O    1262      8.00
     N    1188      7.00
     C    4573      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: 0.52
  Conformation dependent library (CDL) restraints added in 484.7 milliseconds
  

  1698 Ramachandran restraints generated.
    849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1716

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 16 sheets defined
      35.8% alpha, 18.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1346 through 1352
    Processing helix  chain 'A' and resid 1432 through 1442
    Processing helix  chain 'A' and resid 1498 through 1515
      removed outlier: 3.669A  pdb=" N   ILE A1513 " --> pdb=" O   LEU A1509 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1530 through 1540
      removed outlier: 4.130A  pdb=" N   ILE A1534 " --> pdb=" O   LEU A1530 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1552 through 1558
      removed outlier: 3.899A  pdb=" N   ARG A1558 " --> pdb=" O   LEU A1554 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1568 through 1578
      removed outlier: 3.806A  pdb=" N   HIS A1574 " --> pdb=" O   PRO A1570 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   PHE A1575 " --> pdb=" O   HIS A1571 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1587 through 1591
      removed outlier: 3.669A  pdb=" N   GLN A1591 " --> pdb=" O   PRO A1588 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1601 through 1605
    Processing helix  chain 'A' and resid 1627 through 1633
    Processing helix  chain 'A' and resid 1647 through 1656
      removed outlier: 3.536A  pdb=" N   LYS A1651 " --> pdb=" O   SER A1647 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   PHE A1656 " --> pdb=" O   LEU A1652 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1669 through 1673
    Processing helix  chain 'A' and resid 1686 through 1688
      No H-bonds generated for 'chain 'A' and resid 1686 through 1688'
    Processing helix  chain 'A' and resid 1703 through 1716
      removed outlier: 3.652A  pdb=" N   ILE A1715 " --> pdb=" O   ARG A1711 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1717 through 1719
      No H-bonds generated for 'chain 'A' and resid 1717 through 1719'
    Processing helix  chain 'A' and resid 1770 through 1792
    Processing helix  chain 'A' and resid 1827 through 1835
    Processing helix  chain 'A' and resid 1851 through 1856
      removed outlier: 3.674A  pdb=" N   ILE A1855 " --> pdb=" O   PRO A1851 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1865 through 1869
      removed outlier: 3.592A  pdb=" N   ILE A1868 " --> pdb=" O   PRO A1865 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   MET A1869 " --> pdb=" O   ARG A1866 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1865 through 1869'
    Processing helix  chain 'A' and resid 1871 through 1873
      No H-bonds generated for 'chain 'A' and resid 1871 through 1873'
    Processing helix  chain 'A' and resid 1880 through 1882
      No H-bonds generated for 'chain 'A' and resid 1880 through 1882'
    Processing helix  chain 'A' and resid 1913 through 1927
      removed outlier: 4.165A  pdb=" N   LEU A1917 " --> pdb=" O   SER A1913 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   HIS A1926 " --> pdb=" O   VAL A1922 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   LEU A1927 " --> pdb=" O   VAL A1923 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1954 through 1961
      removed outlier: 3.557A  pdb=" N   LEU A1958 " --> pdb=" O   SER A1954 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1967 through 1988
      removed outlier: 3.555A  pdb=" N   ARG A1973 " --> pdb=" O   THR A1969 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2040 through 2045
      removed outlier: 3.563A  pdb=" N   ARG A2045 " --> pdb=" O   PRO A2041 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2052 through 2069
      removed outlier: 3.659A  pdb=" N   VAL A2056 " --> pdb=" O   GLN A2052 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2071 through 2077
    Processing helix  chain 'A' and resid 2082 through 2087
    Processing helix  chain 'A' and resid 2094 through 2100
      removed outlier: 3.543A  pdb=" N   TYR A2099 " --> pdb=" O   PRO A2095 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2107 through 2115
    Processing helix  chain 'A' and resid 2124 through 2133
    Processing helix  chain 'A' and resid 2134 through 2140
      removed outlier: 3.758A  pdb=" N   VAL A2138 " --> pdb=" O   SER A2134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2339 through 2343
      removed outlier: 4.015A  pdb=" N   LEU A2343 " --> pdb=" O   THR A2340 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2346 through 2351
    Processing helix  chain 'A' and resid 2389 through 2396
    Processing helix  chain 'A' and resid 2499 through 2522
      removed outlier: 3.529A  pdb=" N   LEU A2517 " --> pdb=" O   VAL A2513 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   ALA A2518 " --> pdb=" O   ARG A2514 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   LYS A2520 " --> pdb=" O   GLU A2516 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   ARG A2522 " --> pdb=" O   ALA A2518 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 1372 through 1376
      removed outlier: 6.489A  pdb=" N   MET A1335 " --> pdb=" O   ASN A1391 " (cutoff:3.500A)
      removed outlier: 7.603A  pdb=" N   TRP A1393 " --> pdb=" O   MET A1335 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   LEU A1337 " --> pdb=" O   TRP A1393 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 1447 through 1450
      removed outlier: 6.519A  pdb=" N   VAL A1447 " --> pdb=" O   ASP A1484 " (cutoff:3.500A)
      removed outlier: 7.827A  pdb=" N   HIS A1486 " --> pdb=" O   VAL A1447 " (cutoff:3.500A)
      removed outlier: 6.056A  pdb=" N   LEU A1449 " --> pdb=" O   HIS A1486 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1582 through 1583
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1661 through 1663
      removed outlier: 4.061A  pdb=" N   GLY A1663 " --> pdb=" O   TYR A1666 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1730 through 1733
      removed outlier: 7.098A  pdb=" N   TYR A1747 " --> pdb=" O   PRO A1768 " (cutoff:3.500A)
      removed outlier: 4.840A  pdb=" N   ILE A1692 " --> pdb=" O   LEU A1813 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1875 through 1876
      removed outlier: 6.764A  pdb=" N   VAL A1893 " --> pdb=" O   LEU A1885 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1875 through 1876
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1990 through 1991
    Processing sheet with id=AA9, first strand: chain 'A' and resid 2000 through 2002
    Processing sheet with id=AB1, first strand: chain 'A' and resid 2155 through 2156
    Processing sheet with id=AB2, first strand: chain 'A' and resid 2202 through 2203
      removed outlier: 3.633A  pdb=" N   VAL A2216 " --> pdb=" O   ALA A2203 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 2247 through 2249
    Processing sheet with id=AB4, first strand: chain 'A' and resid 2300 through 2304
    Processing sheet with id=AB5, first strand: chain 'A' and resid 2354 through 2359
      removed outlier: 7.141A  pdb=" N   ALA A2366 " --> pdb=" O   ILE A2355 " (cutoff:3.500A)
      removed outlier: 4.583A  pdb=" N   VAL A2357 " --> pdb=" O   TYR A2364 " (cutoff:3.500A)
      removed outlier: 6.830A  pdb=" N   TYR A2364 " --> pdb=" O   VAL A2357 " (cutoff:3.500A)
      removed outlier: 5.187A  pdb=" N   VAL A2359 " --> pdb=" O   ALA A2362 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   ALA A2362 " --> pdb=" O   VAL A2359 " (cutoff:3.500A)
      removed outlier: 5.063A  pdb=" N   LYS A2367 " --> pdb=" O   VAL A2372 " (cutoff:3.500A)
      removed outlier: 6.994A  pdb=" N   VAL A2372 " --> pdb=" O   LYS A2367 " (cutoff:3.500A)
      removed outlier: 6.593A  pdb=" N   VAL A2373 " --> pdb=" O   LEU A2386 " (cutoff:3.500A)
      removed outlier: 4.759A  pdb=" N   LEU A2386 " --> pdb=" O   VAL A2373 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   VAL A2375 " --> pdb=" O   CYS A2384 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   LYS A2382 " --> pdb=" O   ASP A2377 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 2414 through 2420
      removed outlier: 6.603A  pdb=" N   GLY A2428 " --> pdb=" O   LYS A2415 " (cutoff:3.500A)
      removed outlier: 4.420A  pdb=" N   LEU A2417 " --> pdb=" O   TRP A2426 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   TRP A2426 " --> pdb=" O   LEU A2417 " (cutoff:3.500A)
      removed outlier: 4.926A  pdb=" N   LEU A2419 " --> pdb=" O   ALA A2424 " (cutoff:3.500A)
      removed outlier: 6.966A  pdb=" N   ALA A2424 " --> pdb=" O   LEU A2419 " (cutoff:3.500A)
      removed outlier: 6.219A  pdb=" N   ILE A2434 " --> pdb=" O   VAL A2447 " (cutoff:3.500A)
      removed outlier: 4.334A  pdb=" N   VAL A2447 " --> pdb=" O   ILE A2434 " (cutoff:3.500A)
      removed outlier: 6.942A  pdb=" N   LEU A2436 " --> pdb=" O   ILE A2445 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 2454 through 2461
      removed outlier: 5.642A  pdb=" N   VAL A2455 " --> pdb=" O   TYR A2475 " (cutoff:3.500A)
      removed outlier: 6.244A  pdb=" N   TYR A2475 " --> pdb=" O   VAL A2455 " (cutoff:3.500A)

    274 hydrogen bonds defined for protein.
    744 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: 1.39

  Time building geometry restraints manager: 0.67 seconds

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

  Histogram of bond lengths:
        1.14 -     1.27: 1136
        1.27 -     1.41: 1696
        1.41 -     1.54: 4244
        1.54 -     1.68: 52
        1.68 -     1.81: 73
  Bond restraints: 7201
  Sorted by residual:
  bond pdb=" C11 A1N A2601 "
       pdb=" N4  A1N A2601 "
    ideal  model  delta    sigma   weight residual
    1.319  1.140  0.179 2.00e-02 2.50e+03 8.04e+01
  bond pdb=" C11 A1N A2601 "
       pdb=" C21 A1N A2601 "
    ideal  model  delta    sigma   weight residual
    1.428  1.311  0.117 2.00e-02 2.50e+03 3.41e+01
  bond pdb=" C20 A1N A2601 "
       pdb=" C21 A1N A2601 "
    ideal  model  delta    sigma   weight residual
    1.405  1.291  0.114 2.00e-02 2.50e+03 3.26e+01
  bond pdb=" C7  A1N A2601 "
       pdb=" N3  A1N A2601 "
    ideal  model  delta    sigma   weight residual
    1.342  1.231  0.111 2.00e-02 2.50e+03 3.10e+01
  bond pdb=" C7  A1N A2601 "
       pdb=" C8  A1N A2601 "
    ideal  model  delta    sigma   weight residual
    1.409  1.298  0.111 2.00e-02 2.50e+03 3.07e+01
  ... (remaining 7196 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.53: 9688
        3.53 -     7.06: 60
        7.06 -    10.60: 5
       10.60 -    14.13: 6
       14.13 -    17.66: 1
  Bond angle restraints: 9760
  Sorted by residual:
  angle pdb=" N   LYS A1910 "
        pdb=" CA  LYS A1910 "
        pdb=" C   LYS A1910 "
      ideal   model   delta    sigma   weight residual
     110.80  128.46  -17.66 2.13e+00 2.20e-01 6.87e+01
  angle pdb=" N   ASN A1909 "
        pdb=" CA  ASN A1909 "
        pdb=" C   ASN A1909 "
      ideal   model   delta    sigma   weight residual
     109.25  119.33  -10.08 1.53e+00 4.27e-01 4.34e+01
  angle pdb=" C   LYS A1910 "
        pdb=" CA  LYS A1910 "
        pdb=" CB  LYS A1910 "
      ideal   model   delta    sigma   weight residual
     110.42   97.69   12.73 1.99e+00 2.53e-01 4.09e+01
  angle pdb=" C   PRO A2080 "
        pdb=" N   ASN A2081 "
        pdb=" CA  ASN A2081 "
      ideal   model   delta    sigma   weight residual
     121.54  132.23  -10.69 1.91e+00 2.74e-01 3.13e+01
  angle pdb=" C   THR A1410 "
        pdb=" CA  THR A1410 "
        pdb=" CB  THR A1410 "
      ideal   model   delta    sigma   weight residual
     115.79  109.89    5.90 1.19e+00 7.06e-01 2.46e+01
  ... (remaining 9755 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.85: 4226
       32.85 -    65.70: 67
       65.70 -    98.55: 10
       98.55 -   131.40: 4
      131.40 -   164.24: 1
  Dihedral angle restraints: 4308
    sinusoidal: 1687
      harmonic: 2621
  Sorted by residual:
  dihedral pdb=" CA  PHE A1545 "
           pdb=" C   PHE A1545 "
           pdb=" N   PRO A1546 "
           pdb=" CA  PRO A1546 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.80  -23.20     0      5.00e+00 4.00e-02 2.15e+01
  dihedral pdb=" C19 A1N A2601 "
           pdb=" C16 A1N A2601 "
           pdb=" C18 A1N A2601 "
           pdb=" O2  A1N A2601 "
      ideal   model   delta sinusoidal    sigma   weight residual
     251.11   86.87  164.24     1      3.00e+01 1.11e-03 2.09e+01
  dihedral pdb=" CA  HIS A1405 "
           pdb=" C   HIS A1405 "
           pdb=" N   PRO A1406 "
           pdb=" CA  PRO A1406 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.08   21.92     0      5.00e+00 4.00e-02 1.92e+01
  ... (remaining 4305 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.095: 1095
       0.095 -    0.190: 60
       0.190 -    0.286: 2
       0.286 -    0.381: 0
       0.381 -    0.476: 1
  Chirality restraints: 1158
  Sorted by residual:
  chirality pdb=" CA  ASN A1909 "
            pdb=" N   ASN A1909 "
            pdb=" C   ASN A1909 "
            pdb=" CB  ASN A1909 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.03    0.48 2.00e-01 2.50e+01 5.66e+00
  chirality pdb=" CA  THR A1343 "
            pdb=" N   THR A1343 "
            pdb=" C   THR A1343 "
            pdb=" CB  THR A1343 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.25    0.28 2.00e-01 2.50e+01 1.91e+00
  chirality pdb=" CA  LYS A1910 "
            pdb=" N   LYS A1910 "
            pdb=" C   LYS A1910 "
            pdb=" CB  LYS A1910 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.88e+00
  ... (remaining 1155 not shown)

  Planarity restraints: 1198
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A1941 "   -0.049 5.00e-02 4.00e+02   7.42e-02 8.81e+00
        pdb=" N   PRO A1942 "    0.128 5.00e-02 4.00e+02
        pdb=" CA  PRO A1942 "   -0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO A1942 "   -0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A1716 "    0.043 5.00e-02 4.00e+02   6.55e-02 6.86e+00
        pdb=" N   PRO A1717 "   -0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO A1717 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A1717 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP A1994 "    0.011 2.00e-02 2.50e+03   2.17e-02 4.69e+00
        pdb=" CG  ASP A1994 "   -0.037 2.00e-02 2.50e+03
        pdb=" OD1 ASP A1994 "    0.014 2.00e-02 2.50e+03
        pdb=" OD2 ASP A1994 "    0.013 2.00e-02 2.50e+03
  ... (remaining 1195 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 114
        2.67 -     3.23: 6284
        3.23 -     3.78: 10344
        3.78 -     4.34: 14555
        4.34 -     4.90: 24254
  Nonbonded interactions: 55551
  Sorted by model distance:
  nonbonded pdb=" O1B GDP A2602 "
            pdb="MG    MG A2603 "
     model   vdw
     2.111 2.170
  nonbonded pdb=" OH  TYR A1992 "
            pdb=" O   ALA A2016 "
     model   vdw
     2.197 3.040
  nonbonded pdb=" NZ  LYS A1996 "
            pdb=" OG1 THR A2035 "
     model   vdw
     2.274 3.120
  nonbonded pdb=" O   GLY A1344 "
            pdb=" N   GLY A1346 "
     model   vdw
     2.287 3.120
  nonbonded pdb=" OG1 THR A1348 "
            pdb="MG    MG A2603 "
     model   vdw
     2.288 2.170
  ... (remaining 55546 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.48 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             4.600
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.780
  Find NCS groups from input model:        0.040
  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:8.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.400
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7295
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      :  0.005   0.179   7201  Z= 0.285
  Angle     :  0.837  17.661   9760  Z= 0.449
  Chirality :  0.047   0.476   1158
  Planarity :  0.005   0.074   1198
  Dihedral  : 14.330 164.244   2592
  Min Nonbonded Distance : 2.111

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  5.67 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  0.53 %
    Favored  : 99.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.30 (0.29), residues: 849
  helix:  0.15 (0.32), residues: 279
  sheet: -0.41 (0.43), residues: 175
  loop : -1.82 (0.29), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A2143 
 TYR   0.017   0.001   TYR A2023 
 PHE   0.016   0.001   PHE A2083 
 TRP   0.010   0.001   TRP A1742 
 HIS   0.005   0.001   HIS A1405 

Details of bonding type rmsd
  covalent geometry    : bond        0.00543 ( 7201)
  covalent geometry    : angle       0.83688 ( 9760)
  hydrogen bonds       : bond        0.20686 (  272)
  hydrogen bonds       : angle       7.94466 (  744)

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

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

  1698 Ramachandran restraints generated.
    849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1698 Ramachandran restraints generated.
    849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 113
  time to evaluate  : 0.309 
Fit side-chains
TARDY: cannot create tardy model for: "ARG A2143 " (corrupted residue). Skipping it.
  outliers start: 1
  outliers final: 0
  residues processed: 113
  average time/residue: 0.5130
  time to fit residues: 61.4903
Evaluate side-chains
  86 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    4.9990
   chunk 45 optimal weight:    0.5980
   chunk 74 optimal weight:    7.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A1783 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4277 r_free = 0.4277 target = 0.196913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.139447 restraints weight = 11229.037|
|-----------------------------------------------------------------------------|
r_work (start): 0.3636 rms_B_bonded: 2.60
r_work: 0.3494 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3380 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3404
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3404 r_free = 0.3404    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3404 r_free = 0.3404    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3404
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7552
moved from start:          0.1465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   7201  Z= 0.166
  Angle     :  0.703  11.499   9760  Z= 0.342
  Chirality :  0.047   0.211   1158
  Planarity :  0.005   0.067   1198
  Dihedral  :  7.932 144.298    969
  Min Nonbonded Distance : 1.915

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.50 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  :  8.92 %
    Favored  : 89.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.29 (0.28), residues: 849
  helix:  0.15 (0.31), residues: 288
  sheet: -0.46 (0.43), residues: 172
  loop : -1.81 (0.28), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A1707 
 TYR   0.016   0.002   TYR A1649 
 PHE   0.026   0.002   PHE A2083 
 TRP   0.012   0.002   TRP A2426 
 HIS   0.005   0.001   HIS A1405 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 7201)
  covalent geometry    : angle       0.70289 ( 9760)
  hydrogen bonds       : bond        0.04478 (  272)
  hydrogen bonds       : angle       5.81643 (  744)

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

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

  1698 Ramachandran restraints generated.
    849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1698 Ramachandran restraints generated.
    849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 96
  time to evaluate  : 0.248 
Fit side-chains
TARDY: cannot create tardy model for: "ARG A2143 " (corrupted residue). Skipping it.
REVERT: A 1338 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7507 (mmm)
REVERT: A 1408 PHE cc_start: 0.7423 (m-10) cc_final: 0.7175 (m-10)
REVERT: A 1607 MET cc_start: 0.7692 (ttp) cc_final: 0.7375 (ttp)
REVERT: A 1654 GLU cc_start: 0.7508 (pt0) cc_final: 0.6123 (tm-30)
REVERT: A 1728 ARG cc_start: 0.8192 (mtp180) cc_final: 0.7305 (ttp80)
REVERT: A 1878 GLU cc_start: 0.7564 (tp30) cc_final: 0.7060 (tp30)
REVERT: A 2301 MET cc_start: 0.6686 (OUTLIER) cc_final: 0.6275 (ttm)
  outliers start: 10
  outliers final: 5
  residues processed: 100
  average time/residue: 0.5149
  time to fit residues: 54.7097
Evaluate side-chains
  89 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 82
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1338 MET
Chi-restraints excluded: chain A residue 1674 SER
Chi-restraints excluded: chain A residue 1839 LEU
Chi-restraints excluded: chain A residue 1909 ASN
Chi-restraints excluded: chain A residue 1951 SER
Chi-restraints excluded: chain A residue 2301 MET
Chi-restraints excluded: chain A residue 2365 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 13 optimal weight:    0.7980
   chunk 77 optimal weight:    3.9990
   chunk 70 optimal weight:   10.0000
   chunk 79 optimal weight:    9.9990
   chunk 5 optimal weight:    0.5980
   chunk 46 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 45 optimal weight:    0.7980
   chunk 59 optimal weight:    0.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A1577 ASN
A1586 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4274 r_free = 0.4274 target = 0.196561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.139584 restraints weight = 10021.467|
|-----------------------------------------------------------------------------|
r_work (start): 0.3633 rms_B_bonded: 2.44
r_work: 0.3489 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3375 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3395
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3395 r_free = 0.3395    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3395 r_free = 0.3395    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3395
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7504
moved from start:          0.1752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7201  Z= 0.170
  Angle     :  0.681   8.422   9760  Z= 0.333
  Chirality :  0.047   0.216   1158
  Planarity :  0.005   0.060   1198
  Dihedral  :  7.422 143.974    969
  Min Nonbonded Distance : 1.945

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.15 %
    Favored  : 93.85 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 10.12 %
    Favored  : 88.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.22 (0.28), residues: 849
  helix:  0.21 (0.32), residues: 289
  sheet: -0.47 (0.42), residues: 172
  loop : -1.76 (0.28), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A1707 
 TYR   0.013   0.002   TYR A1695 
 PHE   0.025   0.002   PHE A2083 
 TRP   0.011   0.001   TRP A1705 
 HIS   0.006   0.001   HIS A1405 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 ( 7201)
  covalent geometry    : angle       0.68117 ( 9760)
  hydrogen bonds       : bond        0.04389 (  272)
  hydrogen bonds       : angle       5.51212 (  744)

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

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

  1698 Ramachandran restraints generated.
    849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1698 Ramachandran restraints generated.
    849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 86
  time to evaluate  : 0.216 
Fit side-chains
TARDY: cannot create tardy model for: "ARG A2143 " (corrupted residue). Skipping it.
REVERT: A 1338 MET cc_start: 0.8102 (OUTLIER) cc_final: 0.7406 (mmm)
REVERT: A 1408 PHE cc_start: 0.7556 (m-10) cc_final: 0.7316 (m-10)
REVERT: A 1597 PHE cc_start: 0.8188 (m-80) cc_final: 0.7954 (m-80)
REVERT: A 1607 MET cc_start: 0.7719 (ttp) cc_final: 0.7384 (ttp)
REVERT: A 1654 GLU cc_start: 0.7465 (pt0) cc_final: 0.6258 (tm-30)
REVERT: A 1728 ARG cc_start: 0.8188 (mtp180) cc_final: 0.7217 (ttp80)
REVERT: A 1878 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.6973 (tp30)
REVERT: A 2153 GLU cc_start: 0.6930 (tt0) cc_final: 0.6678 (tm-30)
REVERT: A 2301 MET cc_start: 0.6712 (OUTLIER) cc_final: 0.6341 (ttm)
REVERT: A 2381 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.7014 (mm-30)
  outliers start: 13
  outliers final: 4
  residues processed: 93
  average time/residue: 0.5490
  time to fit residues: 54.0370
Evaluate side-chains
  91 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 83
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1338 MET
Chi-restraints excluded: chain A residue 1674 SER
Chi-restraints excluded: chain A residue 1839 LEU
Chi-restraints excluded: chain A residue 1878 GLU
Chi-restraints excluded: chain A residue 1951 SER
Chi-restraints excluded: chain A residue 2301 MET
Chi-restraints excluded: chain A residue 2365 ILE
Chi-restraints excluded: chain A residue 2381 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 60 optimal weight:    0.7980
   chunk 20 optimal weight:    4.9990
   chunk 31 optimal weight:    0.0070
   chunk 68 optimal weight:    0.9980
   chunk 30 optimal weight:    0.7980
   chunk 57 optimal weight:    0.0060
   chunk 77 optimal weight:    0.5980
   chunk 50 optimal weight:    0.5980
   chunk 16 optimal weight:    0.6980
   chunk 88 optimal weight:    0.8980
   chunk 52 optimal weight:    0.4980
   overall best weight:    0.3414

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

Flipped N/Q/H residues before XYZ refinement:
A1586 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4304 r_free = 0.4304 target = 0.199730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.141416 restraints weight = 14535.644|
|-----------------------------------------------------------------------------|
r_work (start): 0.3653 rms_B_bonded: 3.01
r_work: 0.3511 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3395 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3395
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3424
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3424 r_free = 0.3424    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3424 r_free = 0.3424    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3424
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7524
moved from start:          0.1847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7201  Z= 0.115
  Angle     :  0.597   8.061   9760  Z= 0.293
  Chirality :  0.044   0.151   1158
  Planarity :  0.005   0.053   1198
  Dihedral  :  7.027 143.638    969
  Min Nonbonded Distance : 1.999

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.26 %
    Favored  : 93.74 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 11.32 %
    Favored  : 87.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.90 (0.29), residues: 849
  helix:  0.56 (0.33), residues: 289
  sheet: -0.49 (0.42), residues: 174
  loop : -1.53 (0.29), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A2143 
 TYR   0.014   0.001   TYR A2475 
 PHE   0.017   0.001   PHE A2083 
 TRP   0.010   0.001   TRP A2426 
 HIS   0.005   0.001   HIS A2510 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 7201)
  covalent geometry    : angle       0.59690 ( 9760)
  hydrogen bonds       : bond        0.03430 (  272)
  hydrogen bonds       : angle       5.14641 (  744)

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

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

  1698 Ramachandran restraints generated.
    849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1698 Ramachandran restraints generated.
    849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 97
  time to evaluate  : 0.286 
Fit side-chains
TARDY: cannot create tardy model for: "ARG A2143 " (corrupted residue). Skipping it.
REVERT: A 1338 MET cc_start: 0.8135 (OUTLIER) cc_final: 0.7459 (mmm)
REVERT: A 1374 LYS cc_start: 0.6665 (mtpt) cc_final: 0.5997 (mtmm)
REVERT: A 1607 MET cc_start: 0.7665 (ttp) cc_final: 0.7266 (ttp)
REVERT: A 1654 GLU cc_start: 0.7496 (pt0) cc_final: 0.6332 (tm-30)
REVERT: A 1728 ARG cc_start: 0.8193 (mtp180) cc_final: 0.7232 (ttp80)
REVERT: A 1753 GLU cc_start: 0.7653 (pt0) cc_final: 0.7392 (pt0)
REVERT: A 1878 GLU cc_start: 0.7471 (tp30) cc_final: 0.6999 (tp30)
REVERT: A 2301 MET cc_start: 0.6660 (OUTLIER) cc_final: 0.6409 (ttm)
  outliers start: 9
  outliers final: 5
  residues processed: 100
  average time/residue: 0.5397
  time to fit residues: 57.0942
Evaluate side-chains
  91 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 84
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1338 MET
Chi-restraints excluded: chain A residue 1403 SER
Chi-restraints excluded: chain A residue 1674 SER
Chi-restraints excluded: chain A residue 1909 ASN
Chi-restraints excluded: chain A residue 1951 SER
Chi-restraints excluded: chain A residue 2301 MET
Chi-restraints excluded: chain A residue 2365 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 46 optimal weight:    0.0030
   chunk 73 optimal weight:    9.9990
   chunk 72 optimal weight:    5.9990
   chunk 42 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9980
   chunk 32 optimal weight:    0.5980
   chunk 26 optimal weight:    2.9990
   chunk 43 optimal weight:    0.7980
   chunk 49 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   overall best weight:    0.8792

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

Flipped N/Q/H residues before XYZ refinement:
A1577 ASN
A1586 GLN
A1609 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.195634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.133689 restraints weight = 20091.676|
|-----------------------------------------------------------------------------|
r_work (start): 0.3576 rms_B_bonded: 3.59
r_work: 0.3420 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3420
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3440
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3440 r_free = 0.3440    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3440 r_free = 0.3440    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3440
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7429
moved from start:          0.2063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   7201  Z= 0.172
  Angle     :  0.656   8.544   9760  Z= 0.321
  Chirality :  0.047   0.191   1158
  Planarity :  0.005   0.062   1198
  Dihedral  :  7.230 143.901    969
  Min Nonbonded Distance : 1.950

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.15 %
    Favored  : 93.85 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 11.32 %
    Favored  : 86.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.94 (0.29), residues: 849
  helix:  0.47 (0.32), residues: 290
  sheet: -0.43 (0.42), residues: 171
  loop : -1.54 (0.29), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A2122 
 TYR   0.013   0.002   TYR A1695 
 PHE   0.025   0.002   PHE A2083 
 TRP   0.011   0.001   TRP A1376 
 HIS   0.006   0.001   HIS A1405 

Details of bonding type rmsd
  covalent geometry    : bond        0.00424 ( 7201)
  covalent geometry    : angle       0.65640 ( 9760)
  hydrogen bonds       : bond        0.04184 (  272)
  hydrogen bonds       : angle       5.23783 (  744)

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

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

  1698 Ramachandran restraints generated.
    849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1698 Ramachandran restraints generated.
    849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 86
  time to evaluate  : 0.295 
Fit side-chains
TARDY: cannot create tardy model for: "ARG A2143 " (corrupted residue). Skipping it.
REVERT: A 1338 MET cc_start: 0.8032 (OUTLIER) cc_final: 0.7321 (mmm)
REVERT: A 1374 LYS cc_start: 0.6731 (mtpt) cc_final: 0.6018 (mtmm)
REVERT: A 1412 ARG cc_start: 0.8615 (ttp80) cc_final: 0.8276 (ttp80)
REVERT: A 1654 GLU cc_start: 0.7394 (pt0) cc_final: 0.6291 (tm-30)
REVERT: A 1728 ARG cc_start: 0.8164 (mtp180) cc_final: 0.7182 (ttp80)
REVERT: A 1878 GLU cc_start: 0.7370 (tp30) cc_final: 0.6820 (tp30)
REVERT: A 1909 ASN cc_start: 0.7697 (OUTLIER) cc_final: 0.6511 (m110)
REVERT: A 2153 GLU cc_start: 0.7154 (tt0) cc_final: 0.6832 (tt0)
  outliers start: 13
  outliers final: 7
  residues processed: 95
  average time/residue: 0.6197
  time to fit residues: 62.1302
Evaluate side-chains
  89 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 80
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1338 MET
Chi-restraints excluded: chain A residue 1389 VAL
Chi-restraints excluded: chain A residue 1403 SER
Chi-restraints excluded: chain A residue 1652 LEU
Chi-restraints excluded: chain A residue 1674 SER
Chi-restraints excluded: chain A residue 1839 LEU
Chi-restraints excluded: chain A residue 1909 ASN
Chi-restraints excluded: chain A residue 1951 SER
Chi-restraints excluded: chain A residue 2365 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 53 optimal weight:    0.9980
   chunk 37 optimal weight:    3.9990
   chunk 14 optimal weight:    5.9990
   chunk 77 optimal weight:    0.6980
   chunk 32 optimal weight:    0.5980
   chunk 18 optimal weight:    0.9980
   chunk 76 optimal weight:    0.1980
   chunk 26 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9990
   chunk 65 optimal weight:    0.6980
   chunk 89 optimal weight:    0.8980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A1586 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.197267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.135842 restraints weight = 20368.380|
|-----------------------------------------------------------------------------|
r_work (start): 0.3594 rms_B_bonded: 3.61
r_work: 0.3442 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3457
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3457 r_free = 0.3457    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3457 r_free = 0.3457    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3457
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7415
moved from start:          0.2127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7201  Z= 0.139
  Angle     :  0.626  10.723   9760  Z= 0.303
  Chirality :  0.045   0.167   1158
  Planarity :  0.005   0.054   1198
  Dihedral  :  7.099 143.785    969
  Min Nonbonded Distance : 1.974

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.03 %
    Favored  : 93.97 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 12.38 %
    Favored  : 86.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.80 (0.29), residues: 849
  helix:  0.64 (0.33), residues: 289
  sheet: -0.44 (0.42), residues: 168
  loop : -1.46 (0.29), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A1707 
 TYR   0.014   0.001   TYR A2475 
 PHE   0.021   0.001   PHE A2083 
 TRP   0.010   0.001   TRP A2426 
 HIS   0.005   0.001   HIS A1405 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 7201)
  covalent geometry    : angle       0.62594 ( 9760)
  hydrogen bonds       : bond        0.03754 (  272)
  hydrogen bonds       : angle       5.07711 (  744)

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

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

  1698 Ramachandran restraints generated.
    849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1698 Ramachandran restraints generated.
    849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 84
  time to evaluate  : 0.285 
Fit side-chains
TARDY: cannot create tardy model for: "ARG A2143 " (corrupted residue). Skipping it.
REVERT: A 1338 MET cc_start: 0.8004 (OUTLIER) cc_final: 0.7276 (mmm)
REVERT: A 1654 GLU cc_start: 0.7340 (pt0) cc_final: 0.6221 (tm-30)
REVERT: A 1728 ARG cc_start: 0.8124 (mtp180) cc_final: 0.7279 (ttp80)
REVERT: A 1878 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.6809 (tp30)
REVERT: A 1909 ASN cc_start: 0.7602 (OUTLIER) cc_final: 0.6418 (m110)
REVERT: A 2153 GLU cc_start: 0.7218 (tt0) cc_final: 0.6888 (tt0)
  outliers start: 12
  outliers final: 7
  residues processed: 93
  average time/residue: 0.5721
  time to fit residues: 56.2540
Evaluate side-chains
  93 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 83
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1338 MET
Chi-restraints excluded: chain A residue 1389 VAL
Chi-restraints excluded: chain A residue 1403 SER
Chi-restraints excluded: chain A residue 1652 LEU
Chi-restraints excluded: chain A residue 1674 SER
Chi-restraints excluded: chain A residue 1839 LEU
Chi-restraints excluded: chain A residue 1878 GLU
Chi-restraints excluded: chain A residue 1909 ASN
Chi-restraints excluded: chain A residue 1951 SER
Chi-restraints excluded: chain A residue 2365 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 42 optimal weight:    2.9990
   chunk 52 optimal weight:    0.7980
   chunk 84 optimal weight:    0.9980
   chunk 0 optimal weight:    6.9990
   chunk 1 optimal weight:    1.9990
   chunk 82 optimal weight:    2.9990
   chunk 60 optimal weight:    0.5980
   chunk 47 optimal weight:    1.9990
   chunk 74 optimal weight:    5.9990
   chunk 14 optimal weight:    0.0170
   chunk 53 optimal weight:    0.6980
   overall best weight:    0.6218

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

Flipped N/Q/H residues before XYZ refinement:
A1586 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.196852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.137962 restraints weight = 13059.816|
|-----------------------------------------------------------------------------|
r_work (start): 0.3618 rms_B_bonded: 2.83
r_work: 0.3475 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3360 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3360
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3372
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3372 r_free = 0.3372    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3372 r_free = 0.3372    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3372
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7494
moved from start:          0.2258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7201  Z= 0.140
  Angle     :  0.627   9.722   9760  Z= 0.303
  Chirality :  0.045   0.168   1158
  Planarity :  0.005   0.064   1198
  Dihedral  :  7.080 143.817    969
  Min Nonbonded Distance : 1.970

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.03 %
    Favored  : 93.97 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 13.05 %
    Favored  : 85.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.69 (0.29), residues: 849
  helix:  0.74 (0.33), residues: 289
  sheet: -0.25 (0.42), residues: 167
  loop : -1.45 (0.29), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A2122 
 TYR   0.011   0.001   TYR A1695 
 PHE   0.021   0.002   PHE A2083 
 TRP   0.010   0.001   TRP A2426 
 HIS   0.005   0.001   HIS A1405 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 7201)
  covalent geometry    : angle       0.62665 ( 9760)
  hydrogen bonds       : bond        0.03762 (  272)
  hydrogen bonds       : angle       5.01261 (  744)

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

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

  1698 Ramachandran restraints generated.
    849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1698 Ramachandran restraints generated.
    849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 88
  time to evaluate  : 0.211 
Fit side-chains
TARDY: cannot create tardy model for: "ARG A2143 " (corrupted residue). Skipping it.
REVERT: A 1338 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.7427 (mmm)
REVERT: A 1374 LYS cc_start: 0.6770 (mtpt) cc_final: 0.6045 (mtmm)
REVERT: A 1654 GLU cc_start: 0.7398 (pt0) cc_final: 0.6250 (tm-30)
REVERT: A 1728 ARG cc_start: 0.8212 (mtp180) cc_final: 0.7279 (ttp80)
REVERT: A 1878 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.6865 (tp30)
REVERT: A 1907 ILE cc_start: 0.8521 (OUTLIER) cc_final: 0.8145 (pp)
REVERT: A 1909 ASN cc_start: 0.7674 (OUTLIER) cc_final: 0.6356 (m110)
REVERT: A 2092 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7862 (pp)
REVERT: A 2153 GLU cc_start: 0.7298 (tt0) cc_final: 0.6955 (tt0)
REVERT: A 2433 HIS cc_start: 0.6950 (m170) cc_final: 0.6722 (m-70)
  outliers start: 14
  outliers final: 8
  residues processed: 97
  average time/residue: 0.5918
  time to fit residues: 60.5398
Evaluate side-chains
  95 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 82
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1338 MET
Chi-restraints excluded: chain A residue 1389 VAL
Chi-restraints excluded: chain A residue 1403 SER
Chi-restraints excluded: chain A residue 1652 LEU
Chi-restraints excluded: chain A residue 1674 SER
Chi-restraints excluded: chain A residue 1839 LEU
Chi-restraints excluded: chain A residue 1878 GLU
Chi-restraints excluded: chain A residue 1907 ILE
Chi-restraints excluded: chain A residue 1909 ASN
Chi-restraints excluded: chain A residue 1951 SER
Chi-restraints excluded: chain A residue 2092 LEU
Chi-restraints excluded: chain A residue 2167 ILE
Chi-restraints excluded: chain A residue 2365 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 65 optimal weight:    0.5980
   chunk 17 optimal weight:    0.0010
   chunk 76 optimal weight:    0.9990
   chunk 72 optimal weight:    6.9990
   chunk 37 optimal weight:    3.9990
   chunk 47 optimal weight:    0.7980
   chunk 84 optimal weight:    0.9990
   chunk 0 optimal weight:    7.9990
   chunk 48 optimal weight:    0.0870
   chunk 38 optimal weight:    0.7980
   chunk 54 optimal weight:    0.7980
   overall best weight:    0.4564

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

Flipped N/Q/H residues before XYZ refinement:
A1577 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4287 r_free = 0.4287 target = 0.198155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.139391 restraints weight = 14244.855|
|-----------------------------------------------------------------------------|
r_work (start): 0.3629 rms_B_bonded: 2.95
r_work: 0.3485 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3370 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3370
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3380
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3380 r_free = 0.3380    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3380 r_free = 0.3380    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3380
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7470
moved from start:          0.2291

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7201  Z= 0.121
  Angle     :  0.602   9.257   9760  Z= 0.291
  Chirality :  0.044   0.155   1158
  Planarity :  0.005   0.055   1198
  Dihedral  :  6.964 143.793    969
  Min Nonbonded Distance : 1.994

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.15 %
    Favored  : 93.85 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 13.45 %
    Favored  : 84.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.59 (0.29), residues: 849
  helix:  0.85 (0.33), residues: 289
  sheet: -0.27 (0.42), residues: 169
  loop : -1.39 (0.29), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A2122 
 TYR   0.016   0.001   TYR A2475 
 PHE   0.018   0.001   PHE A2083 
 TRP   0.010   0.001   TRP A2426 
 HIS   0.004   0.001   HIS A1405 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 7201)
  covalent geometry    : angle       0.60151 ( 9760)
  hydrogen bonds       : bond        0.03453 (  272)
  hydrogen bonds       : angle       4.89991 (  744)

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

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

  1698 Ramachandran restraints generated.
    849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1698 Ramachandran restraints generated.
    849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 90
  time to evaluate  : 0.278 
Fit side-chains
TARDY: cannot create tardy model for: "ARG A2143 " (corrupted residue). Skipping it.
REVERT: A 1374 LYS cc_start: 0.6769 (mtpt) cc_final: 0.6050 (mtmm)
REVERT: A 1654 GLU cc_start: 0.7371 (pt0) cc_final: 0.6215 (tm-30)
REVERT: A 1728 ARG cc_start: 0.8156 (mtp180) cc_final: 0.7204 (ttp80)
REVERT: A 1735 ARG cc_start: 0.7515 (ttt180) cc_final: 0.6860 (ttp-110)
REVERT: A 1878 GLU cc_start: 0.7477 (tp30) cc_final: 0.6893 (tp30)
REVERT: A 1907 ILE cc_start: 0.8526 (OUTLIER) cc_final: 0.8161 (pp)
REVERT: A 1909 ASN cc_start: 0.7619 (OUTLIER) cc_final: 0.6347 (m110)
REVERT: A 2153 GLU cc_start: 0.7338 (tt0) cc_final: 0.6993 (tt0)
REVERT: A 2433 HIS cc_start: 0.6933 (m170) cc_final: 0.6708 (m-70)
REVERT: A 2499 ASN cc_start: 0.8059 (m-40) cc_final: 0.7856 (m110)
  outliers start: 13
  outliers final: 6
  residues processed: 99
  average time/residue: 0.5438
  time to fit residues: 56.8993
Evaluate side-chains
  95 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 87
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1389 VAL
Chi-restraints excluded: chain A residue 1403 SER
Chi-restraints excluded: chain A residue 1652 LEU
Chi-restraints excluded: chain A residue 1907 ILE
Chi-restraints excluded: chain A residue 1909 ASN
Chi-restraints excluded: chain A residue 1951 SER
Chi-restraints excluded: chain A residue 2167 ILE
Chi-restraints excluded: chain A residue 2365 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 27 optimal weight:    0.0010
   chunk 84 optimal weight:    0.9980
   chunk 25 optimal weight:    0.8980
   chunk 74 optimal weight:    0.9980
   chunk 64 optimal weight:    0.5980
   chunk 86 optimal weight:    1.9990
   chunk 3 optimal weight:    4.9990
   chunk 83 optimal weight:    0.7980
   chunk 26 optimal weight:    0.3980
   chunk 73 optimal weight:   10.0000
   chunk 63 optimal weight:    0.3980
   overall best weight:    0.4386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4290 r_free = 0.4290 target = 0.198590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.137277 restraints weight = 20311.135|
|-----------------------------------------------------------------------------|
r_work (start): 0.3611 rms_B_bonded: 3.64
r_work: 0.3457 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3457
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3469
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3469 r_free = 0.3469    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3469 r_free = 0.3469    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3469
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7380
moved from start:          0.2362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7201  Z= 0.120
  Angle     :  0.592   8.693   9760  Z= 0.288
  Chirality :  0.044   0.154   1158
  Planarity :  0.005   0.058   1198
  Dihedral  :  6.922 143.696    969
  Min Nonbonded Distance : 1.993

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.38 %
    Favored  : 93.62 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 13.45 %
    Favored  : 85.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.49 (0.29), residues: 849
  helix:  0.92 (0.33), residues: 289
  sheet: -0.23 (0.42), residues: 171
  loop : -1.32 (0.29), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A2122 
 TYR   0.010   0.001   TYR A1649 
 PHE   0.018   0.001   PHE A2083 
 TRP   0.010   0.001   TRP A2426 
 HIS   0.004   0.001   HIS A2510 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 7201)
  covalent geometry    : angle       0.59226 ( 9760)
  hydrogen bonds       : bond        0.03424 (  272)
  hydrogen bonds       : angle       4.83486 (  744)

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

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

  1698 Ramachandran restraints generated.
    849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1698 Ramachandran restraints generated.
    849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 86
  time to evaluate  : 0.271 
Fit side-chains
TARDY: cannot create tardy model for: "ARG A2143 " (corrupted residue). Skipping it.
REVERT: A 1374 LYS cc_start: 0.6784 (mtpt) cc_final: 0.6130 (mtmm)
REVERT: A 1597 PHE cc_start: 0.8088 (m-80) cc_final: 0.7877 (m-80)
REVERT: A 1654 GLU cc_start: 0.7346 (pt0) cc_final: 0.6197 (tm-30)
REVERT: A 1735 ARG cc_start: 0.7407 (ttt180) cc_final: 0.6792 (ttp-110)
REVERT: A 1878 GLU cc_start: 0.7369 (tp30) cc_final: 0.6790 (tp30)
REVERT: A 1907 ILE cc_start: 0.8458 (OUTLIER) cc_final: 0.8093 (pp)
REVERT: A 1909 ASN cc_start: 0.7581 (OUTLIER) cc_final: 0.6316 (m110)
REVERT: A 2153 GLU cc_start: 0.7286 (tt0) cc_final: 0.6963 (tt0)
REVERT: A 2433 HIS cc_start: 0.6877 (m170) cc_final: 0.6674 (m-70)
REVERT: A 2499 ASN cc_start: 0.7942 (m-40) cc_final: 0.7720 (m110)
  outliers start: 11
  outliers final: 8
  residues processed: 95
  average time/residue: 0.5463
  time to fit residues: 54.9831
Evaluate side-chains
  93 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 83
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1389 VAL
Chi-restraints excluded: chain A residue 1403 SER
Chi-restraints excluded: chain A residue 1652 LEU
Chi-restraints excluded: chain A residue 1674 SER
Chi-restraints excluded: chain A residue 1839 LEU
Chi-restraints excluded: chain A residue 1907 ILE
Chi-restraints excluded: chain A residue 1909 ASN
Chi-restraints excluded: chain A residue 1951 SER
Chi-restraints excluded: chain A residue 2167 ILE
Chi-restraints excluded: chain A residue 2319 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 28 optimal weight:    0.9980
   chunk 9 optimal weight:    7.9990
   chunk 6 optimal weight:    5.9990
   chunk 5 optimal weight:    0.4980
   chunk 89 optimal weight:    0.9990
   chunk 54 optimal weight:    0.0670
   chunk 56 optimal weight:    0.8980
   chunk 10 optimal weight:    5.9990
   chunk 41 optimal weight:    0.0570
   chunk 59 optimal weight:    1.9990
   chunk 50 optimal weight:    0.5980
   overall best weight:    0.4236

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.198756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.137077 restraints weight = 20250.541|
|-----------------------------------------------------------------------------|
r_work (start): 0.3608 rms_B_bonded: 3.67
r_work: 0.3453 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3469
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3469 r_free = 0.3469    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3469 r_free = 0.3469    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3469
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7356
moved from start:          0.2429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7201  Z= 0.121
  Angle     :  0.604   8.678   9760  Z= 0.295
  Chirality :  0.044   0.154   1158
  Planarity :  0.005   0.056   1198
  Dihedral  :  6.923 143.689    969
  Min Nonbonded Distance : 1.998

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.26 %
    Favored  : 93.74 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 13.58 %
    Favored  : 84.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.43 (0.29), residues: 849
  helix:  1.00 (0.33), residues: 289
  sheet: -0.12 (0.42), residues: 167
  loop : -1.34 (0.29), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1412 
 TYR   0.021   0.001   TYR A2475 
 PHE   0.018   0.001   PHE A2083 
 TRP   0.010   0.001   TRP A2426 
 HIS   0.004   0.001   HIS A1405 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 7201)
  covalent geometry    : angle       0.60401 ( 9760)
  hydrogen bonds       : bond        0.03382 (  272)
  hydrogen bonds       : angle       4.82008 (  744)

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

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

  1698 Ramachandran restraints generated.
    849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1698 Ramachandran restraints generated.
    849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 87
  time to evaluate  : 0.268 
Fit side-chains
TARDY: cannot create tardy model for: "ARG A2143 " (corrupted residue). Skipping it.
REVERT: A 1654 GLU cc_start: 0.7346 (pt0) cc_final: 0.6185 (tm-30)
REVERT: A 1735 ARG cc_start: 0.7412 (ttt180) cc_final: 0.6780 (ttp-110)
REVERT: A 1788 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.8304 (mmt)
REVERT: A 1878 GLU cc_start: 0.7364 (tp30) cc_final: 0.6787 (tp30)
REVERT: A 1907 ILE cc_start: 0.8439 (OUTLIER) cc_final: 0.8076 (pp)
REVERT: A 1909 ASN cc_start: 0.7564 (OUTLIER) cc_final: 0.6283 (m110)
REVERT: A 1960 GLN cc_start: 0.7145 (pt0) cc_final: 0.6743 (mm-40)
REVERT: A 2153 GLU cc_start: 0.7284 (tt0) cc_final: 0.6953 (tt0)
REVERT: A 2301 MET cc_start: 0.7044 (ttp) cc_final: 0.6737 (ptm)
REVERT: A 2499 ASN cc_start: 0.7925 (m-40) cc_final: 0.7677 (m110)
  outliers start: 11
  outliers final: 7
  residues processed: 95
  average time/residue: 0.5316
  time to fit residues: 53.6127
Evaluate side-chains
  95 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 85
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1389 VAL
Chi-restraints excluded: chain A residue 1403 SER
Chi-restraints excluded: chain A residue 1652 LEU
Chi-restraints excluded: chain A residue 1674 SER
Chi-restraints excluded: chain A residue 1788 MET
Chi-restraints excluded: chain A residue 1839 LEU
Chi-restraints excluded: chain A residue 1907 ILE
Chi-restraints excluded: chain A residue 1909 ASN
Chi-restraints excluded: chain A residue 1951 SER
Chi-restraints excluded: chain A residue 2167 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 21 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9990
   chunk 39 optimal weight:    1.9990
   chunk 11 optimal weight:    7.9990
   chunk 32 optimal weight:    0.5980
   chunk 87 optimal weight:    0.4980
   chunk 60 optimal weight:    1.9990
   chunk 61 optimal weight:    0.6980
   chunk 9 optimal weight:   20.0000
   chunk 37 optimal weight:    3.9990
   chunk 2 optimal weight:   10.0000
   overall best weight:    0.6782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4272 r_free = 0.4272 target = 0.196875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.136715 restraints weight = 17565.963|
|-----------------------------------------------------------------------------|
r_work (start): 0.3652 rms_B_bonded: 3.50
r_work: 0.3454 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3454
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3464
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3464 r_free = 0.3464    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3464 r_free = 0.3464    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3464
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7368
moved from start:          0.2512

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7201  Z= 0.147
  Angle     :  0.627   9.381   9760  Z= 0.307
  Chirality :  0.045   0.169   1158
  Planarity :  0.005   0.059   1198
  Dihedral  :  7.037 143.784    969
  Min Nonbonded Distance : 1.967

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.15 %
    Favored  : 93.85 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 13.72 %
    Favored  : 84.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.49 (0.29), residues: 849
  helix:  0.93 (0.33), residues: 289
  sheet: -0.22 (0.42), residues: 171
  loop : -1.33 (0.30), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A2122 
 TYR   0.011   0.001   TYR A1695 
 PHE   0.022   0.002   PHE A2083 
 TRP   0.010   0.001   TRP A2426 
 HIS   0.004   0.001   HIS A1405 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 7201)
  covalent geometry    : angle       0.62726 ( 9760)
  hydrogen bonds       : bond        0.03738 (  272)
  hydrogen bonds       : angle       4.93566 (  744)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3372.54 seconds
wall clock time: 58 minutes 4.70 seconds (3484.70 seconds total)