Starting phenix.real_space_refine
on Tue Jan 13 16:14:35 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8smc_40588/01_2026/8smc_40588.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8smc_40588/01_2026/8smc_40588.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.02
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8smc_40588/01_2026/8smc_40588.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8smc_40588/01_2026/8smc_40588.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8smc_40588/01_2026/8smc_40588.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8smc_40588/01_2026/8smc_40588.map"
  }
  resolution = 4.02
  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=   0.063
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
     S      42      5.16       5
     C    4953      2.51       5
     N    1316      2.21       5
     O    1358      1.98       5
     F       3      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 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: 7674
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "C"
      Number of atoms: 7622
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1084, 7622
          Classifications: {'peptide': 1084}
          Incomplete info: {'truncation_to_alanine': 276}
          Link IDs: {'PTRANS': 48, 'TRANS': 1035}
          Chain breaks: 11
          Unresolved non-hydrogen bonds: 1051
          Unresolved non-hydrogen angles: 1289
          Unresolved non-hydrogen dihedrals: 855
          Unresolved non-hydrogen chiralities: 42
          Planarities with less than four sites: {'ASN:plan1': 27, 'ARG:plan': 26, 'GLN:plan1': 21, 'ASP:plan': 33, 'GLU:plan': 47, 'TYR:plan': 4, 'PHE:plan': 7, 'HIS:plan': 8}
          Unresolved non-hydrogen planarities: 692
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'GDP': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 24
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 24
          Unusual residues: {'TVT': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.89, per 1000 atoms: 0.25
  Number of scatterers: 7674
  At special positions: 0
  Unit cell: (71.496, 98.307, 144.482, 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      42     16.00
     P       2     15.00
     F       3      9.00
     O    1358      8.00
     N    1316      7.00
     C    4953      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: 0.61
  Conformation dependent library (CDL) restraints added in 273.8 milliseconds
  

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2052

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 17 sheets defined
      29.7% alpha, 12.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.37
  Creating SS restraints...
    Processing helix  chain 'C' and resid 1346 through 1356
      removed outlier: 4.283A  pdb=" N   LEU C1351 " --> pdb=" O   LYS C1347 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1398 through 1405
    Processing helix  chain 'C' and resid 1424 through 1442
      removed outlier: 3.919A  pdb=" N   VAL C1428 " --> pdb=" O   GLY C1424 " (cutoff:3.500A)
      Proline residue:  C1433  - end of helix
    Processing helix  chain 'C' and resid 1458 through 1470
      removed outlier: 3.977A  pdb=" N   ARG C1462 " --> pdb=" O   ASP C1458 " (cutoff:3.500A)
      removed outlier: 5.060A  pdb=" N   ALA C1464 " --> pdb=" O   LYS C1460 " (cutoff:3.500A)
      removed outlier: 4.993A  pdb=" N   CYS C1465 " --> pdb=" O   GLN C1461 " (cutoff:3.500A)
      removed outlier: 4.391A  pdb=" N   THR C1470 " --> pdb=" O   MET C1466 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1498 through 1503
      removed outlier: 3.977A  pdb=" N   LYS C1502 " --> pdb=" O   ALA C1498 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1512 through 1516
      removed outlier: 4.042A  pdb=" N   ASP C1515 " --> pdb=" O   LYS C1512 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   GLN C1516 " --> pdb=" O   ILE C1513 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 1512 through 1516'
    Processing helix  chain 'C' and resid 1524 through 1538
      removed outlier: 3.866A  pdb=" N   VAL C1528 " --> pdb=" O   PRO C1524 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1550 through 1561
    Processing helix  chain 'C' and resid 1568 through 1580
      removed outlier: 3.583A  pdb=" N   GLY C1580 " --> pdb=" O   LEU C1576 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1587 through 1591
    Processing helix  chain 'C' and resid 1599 through 1605
      removed outlier: 3.643A  pdb=" N   LEU C1603 " --> pdb=" O   GLU C1599 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   CYS C1604 " --> pdb=" O   PRO C1600 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   LYS C1605 " --> pdb=" O   LYS C1601 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 1599 through 1605'
    Processing helix  chain 'C' and resid 1606 through 1612
    Processing helix  chain 'C' and resid 1704 through 1712
    Processing helix  chain 'C' and resid 1770 through 1791
      removed outlier: 4.120A  pdb=" N   ASP C1782 " --> pdb=" O   GLY C1778 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1792 through 1796
      removed outlier: 3.575A  pdb=" N   LEU C1795 " --> pdb=" O   PHE C1792 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1826 through 1837
      removed outlier: 4.793A  pdb=" N   LYS C1832 " --> pdb=" O   ASP C1828 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   GLY C1837 " --> pdb=" O   LYS C1833 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1871 through 1875
      removed outlier: 3.501A  pdb=" N   LEU C1875 " --> pdb=" O   ASN C1872 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1913 through 1925
      removed outlier: 3.997A  pdb=" N   LEU C1917 " --> pdb=" O   SER C1913 " (cutoff:3.500A)
      removed outlier: 4.298A  pdb=" N   VAL C1923 " --> pdb=" O   GLN C1919 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1955 through 1960
    Processing helix  chain 'C' and resid 1969 through 1974
    Processing helix  chain 'C' and resid 1976 through 1987
    Processing helix  chain 'C' and resid 2040 through 2045
      removed outlier: 3.883A  pdb=" N   ALA C2044 " --> pdb=" O   ALA C2040 " (cutoff:3.500A)
      removed outlier: 4.097A  pdb=" N   ARG C2045 " --> pdb=" O   PRO C2041 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 2040 through 2045'
    Processing helix  chain 'C' and resid 2055 through 2068
    Processing helix  chain 'C' and resid 2071 through 2077
    Processing helix  chain 'C' and resid 2079 through 2085
      removed outlier: 3.587A  pdb=" N   PHE C2083 " --> pdb=" O   PHE C2079 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 2094 through 2099
      removed outlier: 4.254A  pdb=" N   GLU C2098 " --> pdb=" O   ASP C2094 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   TYR C2099 " --> pdb=" O   PRO C2095 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 2094 through 2099'
    Processing helix  chain 'C' and resid 2107 through 2114
      removed outlier: 3.730A  pdb=" N   LYS C2112 " --> pdb=" O   GLU C2108 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   GLN C2113 " --> pdb=" O   LYS C2109 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 2124 through 2130
    Processing helix  chain 'C' and resid 2276 through 2282
      removed outlier: 3.653A  pdb=" N   VAL C2280 " --> pdb=" O   ASP C2277 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   LYS C2281 " --> pdb=" O   LYS C2278 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 2307 through 2315
      removed outlier: 5.849A  pdb=" N   ARG C2312 " --> pdb=" O   SER C2309 " (cutoff:3.500A)
      removed outlier: 5.421A  pdb=" N   ASN C2313 " --> pdb=" O   THR C2310 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 2348 through 2352
      removed outlier: 3.943A  pdb=" N   ASP C2351 " --> pdb=" O   ALA C2348 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 2391 through 2396
      removed outlier: 4.395A  pdb=" N   GLU C2395 " --> pdb=" O   PHE C2392 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 2499 through 2527
      removed outlier: 3.750A  pdb=" N   GLU C2508 " --> pdb=" O   VAL C2504 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   LYS C2515 " --> pdb=" O   ILE C2511 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   GLU C2516 " --> pdb=" O   GLU C2512 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   LEU C2517 " --> pdb=" O   VAL C2513 " (cutoff:3.500A)
      removed outlier: 4.242A  pdb=" N   GLU C2519 " --> pdb=" O   LYS C2515 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   ARG C2522 " --> pdb=" O   ALA C2518 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   THR C2524 " --> pdb=" O   LYS C2520 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   SER C2525 " --> pdb=" O   MET C2521 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   VAL C2526 " --> pdb=" O   ARG C2522 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 1330 through 1331
    Processing sheet with id=AA2, first strand: chain 'C' and resid 1372 through 1373
      removed outlier: 3.501A  pdb=" N   ASP C1372 " --> pdb=" O   ASP C1394 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 1547 through 1549
    Processing sheet with id=AA4, first strand: chain 'C' and resid 1761 through 1768
      removed outlier: 3.641A  pdb=" N   VAL C1767 " --> pdb=" O   ILE C1691 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   TRP C1811 " --> pdb=" O   LEU C1694 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 1739 through 1743
      removed outlier: 6.774A  pdb=" N   ALA C1746 " --> pdb=" O   TRP C1742 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 1840 through 1841
      removed outlier: 3.535A  pdb=" N   LEU C1840 " --> pdb=" O   ILE C1850 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ILE C1850 " --> pdb=" O   LEU C1840 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'C' and resid 1891 through 1893
      removed outlier: 3.875A  pdb=" N   ILE C1907 " --> pdb=" O   SER C1892 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   MET C1947 " --> pdb=" O   ALA C1904 " (cutoff:3.500A)
      removed outlier: 7.151A  pdb=" N   VAL C1946 " --> pdb=" O   LEU C1936 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 1990 through 1991
      removed outlier: 3.506A  pdb=" N   GLN C2022 " --> pdb=" O   ILE C1991 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 2000 through 2002
    Processing sheet with id=AB1, first strand: chain 'C' and resid 2140 through 2144
      removed outlier: 4.104A  pdb=" N   ARG C2142 " --> pdb=" O   VAL C2495 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   VAL C2495 " --> pdb=" O   ARG C2142 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   ILE C2144 " --> pdb=" O   LEU C2493 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   VAL C2472 " --> pdb=" O   THR C2494 " (cutoff:3.500A)
      removed outlier: 7.321A  pdb=" N   LEU C2471 " --> pdb=" O   MET C2458 " (cutoff:3.500A)
      removed outlier: 5.202A  pdb=" N   MET C2458 " --> pdb=" O   LEU C2471 " (cutoff:3.500A)
      removed outlier: 7.018A  pdb=" N   LEU C2473 " --> pdb=" O   ARG C2456 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   SER C2454 " --> pdb=" O   TYR C2475 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 2140 through 2144
      removed outlier: 4.104A  pdb=" N   ARG C2142 " --> pdb=" O   VAL C2495 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   VAL C2495 " --> pdb=" O   ARG C2142 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   ILE C2144 " --> pdb=" O   LEU C2493 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   VAL C2472 " --> pdb=" O   THR C2494 " (cutoff:3.500A)
      removed outlier: 4.338A  pdb=" N   ASN C2468 " --> pdb=" O   ALA C2461 " (cutoff:3.500A)
      removed outlier: 7.572A  pdb=" N   ALA C2461 " --> pdb=" O   ASN C2468 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 2154 through 2156
      removed outlier: 3.715A  pdb=" N   VAL C2156 " --> pdb=" O   TRP C2168 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   LEU C2169 " --> pdb=" O   SER C2180 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 2214 through 2216
    Processing sheet with id=AB5, first strand: chain 'C' and resid 2245 through 2247
      removed outlier: 3.803A  pdb=" N   THR C2267 " --> pdb=" O   LYS C2271 " (cutoff:3.500A)
      removed outlier: 4.762A  pdb=" N   LYS C2271 " --> pdb=" O   THR C2267 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 2322 through 2325
      removed outlier: 4.302A  pdb=" N   LYS C2334 " --> pdb=" O   SER C2325 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'C' and resid 2363 through 2365
      removed outlier: 6.233A  pdb=" N   VAL C2373 " --> pdb=" O   LEU C2386 " (cutoff:3.500A)
      removed outlier: 5.036A  pdb=" N   LEU C2386 " --> pdb=" O   VAL C2373 " (cutoff:3.500A)
      removed outlier: 7.322A  pdb=" N   VAL C2375 " --> pdb=" O   CYS C2384 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'C' and resid 2416 through 2419

    224 hydrogen bonds defined for protein.
    594 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: 1.42

  Time building geometry restraints manager: 0.77 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: 1222
        1.27 -     1.41: 1857
        1.41 -     1.54: 4628
        1.54 -     1.68: 58
        1.68 -     1.82: 59
  Bond restraints: 7824
  Sorted by residual:
  bond pdb=" C2  TVT C2602 "
       pdb=" N1  TVT C2602 "
    ideal  model  delta    sigma   weight residual
    1.336  1.448 -0.112 2.00e-02 2.50e+03 3.11e+01
  bond pdb=" C3  TVT C2602 "
       pdb=" N3  TVT C2602 "
    ideal  model  delta    sigma   weight residual
    1.350  1.456 -0.106 2.00e-02 2.50e+03 2.81e+01
  bond pdb=" C4  TVT C2602 "
       pdb=" N3  TVT C2602 "
    ideal  model  delta    sigma   weight residual
    1.386  1.454 -0.068 2.00e-02 2.50e+03 1.16e+01
  bond pdb=" C5  TVT C2602 "
       pdb=" N4  TVT C2602 "
    ideal  model  delta    sigma   weight residual
    1.355  1.303  0.052 2.00e-02 2.50e+03 6.78e+00
  bond pdb=" C   LEU C2500 "
       pdb=" N   PRO C2501 "
    ideal  model  delta    sigma   weight residual
    1.335  1.368 -0.033 1.30e-02 5.92e+03 6.43e+00
  ... (remaining 7819 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.30: 10468
        2.30 -     4.61: 220
        4.61 -     6.91: 34
        6.91 -     9.22: 9
        9.22 -    11.52: 1
  Bond angle restraints: 10732
  Sorted by residual:
  angle pdb=" CA  CYS C2139 "
        pdb=" CB  CYS C2139 "
        pdb=" SG  CYS C2139 "
      ideal   model   delta    sigma   weight residual
     114.40  125.92  -11.52 2.30e+00 1.89e-01 2.51e+01
  angle pdb=" C   ASN C1644 "
        pdb=" N   TYR C1645 "
        pdb=" CA  TYR C1645 "
      ideal   model   delta    sigma   weight residual
     121.70  130.03   -8.33 1.80e+00 3.09e-01 2.14e+01
  angle pdb=" C   CYS C2139 "
        pdb=" N   LEU C2140 "
        pdb=" CA  LEU C2140 "
      ideal   model   delta    sigma   weight residual
     122.64  114.49    8.15 1.77e+00 3.19e-01 2.12e+01
  angle pdb=" C   ARG C2163 "
        pdb=" N   ASN C2164 "
        pdb=" CA  ASN C2164 "
      ideal   model   delta    sigma   weight residual
     121.54  128.78   -7.24 1.91e+00 2.74e-01 1.44e+01
  angle pdb=" N   HIS C1405 "
        pdb=" CA  HIS C1405 "
        pdb=" C   HIS C1405 "
      ideal   model   delta    sigma   weight residual
     109.81  118.13   -8.32 2.21e+00 2.05e-01 1.42e+01
  ... (remaining 10727 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.93: 4112
       15.93 -    31.87: 402
       31.87 -    47.80: 83
       47.80 -    63.74: 12
       63.74 -    79.67: 4
  Dihedral angle restraints: 4613
    sinusoidal: 1460
      harmonic: 3153
  Sorted by residual:
  dihedral pdb=" CA  ARG C1957 "
           pdb=" C   ARG C1957 "
           pdb=" N   LEU C1958 "
           pdb=" CA  LEU C1958 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.68   29.32     0      5.00e+00 4.00e-02 3.44e+01
  dihedral pdb=" CA  TRP C2104 "
           pdb=" C   TRP C2104 "
           pdb=" N   PRO C2105 "
           pdb=" CA  PRO C2105 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -152.02  -27.98     0      5.00e+00 4.00e-02 3.13e+01
  dihedral pdb=" CA  CYS C2302 "
           pdb=" C   CYS C2302 "
           pdb=" N   LEU C2303 "
           pdb=" CA  LEU C2303 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.05  -27.95     0      5.00e+00 4.00e-02 3.12e+01
  ... (remaining 4610 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 993
       0.051 -    0.102: 269
       0.102 -    0.154: 65
       0.154 -    0.205: 9
       0.205 -    0.256: 2
  Chirality restraints: 1338
  Sorted by residual:
  chirality pdb=" CB  ILE C1339 "
            pdb=" CA  ILE C1339 "
            pdb=" CG1 ILE C1339 "
            pdb=" CG2 ILE C1339 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.39    0.26 2.00e-01 2.50e+01 1.64e+00
  chirality pdb=" CB  ILE C1715 "
            pdb=" CA  ILE C1715 "
            pdb=" CG1 ILE C1715 "
            pdb=" CG2 ILE C1715 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.43    0.21 2.00e-01 2.50e+01 1.11e+00
  chirality pdb=" CA  ILE C1765 "
            pdb=" N   ILE C1765 "
            pdb=" C   ILE C1765 "
            pdb=" CB  ILE C1765 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.17 2.00e-01 2.50e+01 7.43e-01
  ... (remaining 1335 not shown)

  Planarity restraints: 1339
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS C2502 "    0.018 2.00e-02 2.50e+03   3.57e-02 1.28e+01
        pdb=" C   HIS C2502 "   -0.062 2.00e-02 2.50e+03
        pdb=" O   HIS C2502 "    0.023 2.00e-02 2.50e+03
        pdb=" N   GLU C2503 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG C2514 "    0.017 2.00e-02 2.50e+03   3.30e-02 1.09e+01
        pdb=" C   ARG C2514 "   -0.057 2.00e-02 2.50e+03
        pdb=" O   ARG C2514 "    0.021 2.00e-02 2.50e+03
        pdb=" N   LYS C2515 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU C2508 "   -0.012 2.00e-02 2.50e+03   2.41e-02 5.79e+00
        pdb=" C   GLU C2508 "    0.042 2.00e-02 2.50e+03
        pdb=" O   GLU C2508 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   LYS C2509 "   -0.014 2.00e-02 2.50e+03
  ... (remaining 1336 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.78: 1626
        2.78 -     3.31: 7146
        3.31 -     3.84: 11417
        3.84 -     4.37: 12642
        4.37 -     4.90: 22214
  Nonbonded interactions: 55045
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN C2420 "
            pdb=" O   ILE C2498 "
     model   vdw
     2.256 3.120
  nonbonded pdb=" O   LEU C2146 "
            pdb=" NE2 GLN C2490 "
     model   vdw
     2.328 3.120
  nonbonded pdb=" O   SER C2244 "
            pdb=" OG1 THR C2267 "
     model   vdw
     2.334 3.040
  nonbonded pdb=" OH  TYR C1739 "
            pdb=" ND2 ASN C1741 "
     model   vdw
     2.335 3.120
  nonbonded pdb=" OH  TYR C1332 "
            pdb=" OG  SER C1579 "
     model   vdw
     2.349 3.040
  ... (remaining 55040 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.010
  Normalize map: mean=0, sd=1:             1.530
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.870
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.490
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.110
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.112   7824  Z= 0.198
  Angle     :  0.837  11.520  10732  Z= 0.427
  Chirality :  0.051   0.256   1338
  Planarity :  0.006   0.054   1339
  Dihedral  : 13.636  79.673   2561
  Min Nonbonded Distance : 2.256

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.00 %
    Favored  : 90.00 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  7.23 %
    Favored  : 92.63 %
  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: -5.52 (0.21), residues: 1060
  helix: -2.71 (0.27), residues: 251
  sheet: -4.20 (0.27), residues: 196
  loop : -4.07 (0.21), residues: 613

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C1957 
 TYR   0.023   0.001   TYR C1402 
 PHE   0.024   0.002   PHE C2451 
 TRP   0.015   0.001   TRP C1705 
 HIS   0.012   0.002   HIS C2510 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 ( 7824)
  covalent geometry    : angle       0.83699 (10732)
  hydrogen bonds       : bond        0.21279 (  218)
  hydrogen bonds       : angle       9.53268 (  594)

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 53
  time to evaluate  : 0.298 
Fit side-chains
  outliers start: 1
  outliers final: 0
  residues processed: 54
  average time/residue: 0.0633
  time to fit residues: 5.5026
Evaluate side-chains
  38 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 97 optimal weight:    5.9990
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.3980
   chunk 51 optimal weight:    0.7980
   chunk 100 optimal weight:    1.9990
   chunk 106 optimal weight:    1.9990
   chunk 38 optimal weight:    0.5980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** C1437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C1453 HIS
C1926 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.087775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.070687 restraints weight = 25901.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.072102 restraints weight = 17872.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.072966 restraints weight = 13795.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.073733 restraints weight = 11614.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.073998 restraints weight = 10233.681|
|-----------------------------------------------------------------------------|
r_work (final): 0.3218
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7962
moved from start:          0.1050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7824  Z= 0.117
  Angle     :  0.615   7.014  10732  Z= 0.312
  Chirality :  0.044   0.148   1338
  Planarity :  0.004   0.045   1339
  Dihedral  :  6.442  82.740   1151
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.40 %
    Favored  : 91.60 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  6.79 %
    Favored  : 93.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.13 %
    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: -4.23 (0.24), residues: 1060
  helix: -1.37 (0.31), residues: 259
  sheet: -3.64 (0.30), residues: 209
  loop : -3.25 (0.24), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C2514 
 TYR   0.015   0.001   TYR C1402 
 PHE   0.009   0.001   PHE C1877 
 TRP   0.007   0.001   TRP C1791 
 HIS   0.008   0.001   HIS C2510 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 7824)
  covalent geometry    : angle       0.61495 (10732)
  hydrogen bonds       : bond        0.03860 (  218)
  hydrogen bonds       : angle       6.05879 (  594)

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 53
  time to evaluate  : 0.300 
Fit side-chains
REVERT: C 1989 MET cc_start: 0.7981 (ptm) cc_final: 0.7733 (ptm)
REVERT: C 2459 MET cc_start: 0.7062 (ptp) cc_final: 0.6827 (ptm)
  outliers start: 1
  outliers final: 0
  residues processed: 54
  average time/residue: 0.0599
  time to fit residues: 5.3213
Evaluate side-chains
  35 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 61 optimal weight:    2.9990
   chunk 24 optimal weight:    0.7980
   chunk 20 optimal weight:   10.0000
   chunk 6 optimal weight:    0.7980
   chunk 99 optimal weight:    3.9990
   chunk 5 optimal weight:    0.5980
   chunk 63 optimal weight:    0.8980
   chunk 0 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   chunk 66 optimal weight:    0.6980
   chunk 27 optimal weight:    5.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** C1437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C2505 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.087814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.070694 restraints weight = 25909.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.072099 restraints weight = 17914.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.072856 restraints weight = 13839.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.073794 restraints weight = 11753.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.074058 restraints weight = 10233.334|
|-----------------------------------------------------------------------------|
r_work (final): 0.3222
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7965
moved from start:          0.1457

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7824  Z= 0.124
  Angle     :  0.595   7.258  10732  Z= 0.300
  Chirality :  0.044   0.149   1338
  Planarity :  0.004   0.043   1339
  Dihedral  :  5.923  81.537   1151
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.02 %
    Favored  : 91.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  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: -3.56 (0.25), residues: 1060
  helix: -0.66 (0.34), residues: 251
  sheet: -3.41 (0.31), residues: 206
  loop : -2.81 (0.25), residues: 603

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C1957 
 TYR   0.010   0.001   TYR C1733 
 PHE   0.016   0.001   PHE C1816 
 TRP   0.010   0.001   TRP C2426 
 HIS   0.006   0.001   HIS C2510 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 7824)
  covalent geometry    : angle       0.59537 (10732)
  hydrogen bonds       : bond        0.03309 (  218)
  hydrogen bonds       : angle       5.42987 (  594)

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.298 
Fit side-chains
REVERT: C 1989 MET cc_start: 0.8042 (ptm) cc_final: 0.7702 (ptm)
REVERT: C 2435 LEU cc_start: 0.9026 (tp) cc_final: 0.8816 (tt)
REVERT: C 2459 MET cc_start: 0.7316 (ptp) cc_final: 0.7058 (ptm)
  outliers start: 0
  outliers final: 0
  residues processed: 49
  average time/residue: 0.0626
  time to fit residues: 4.9021
Evaluate side-chains
  35 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 103 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   chunk 52 optimal weight:    0.1980
   chunk 51 optimal weight:    2.9990
   chunk 66 optimal weight:    0.7980
   chunk 81 optimal weight:    7.9990
   chunk 94 optimal weight:    1.9990
   chunk 100 optimal weight:    0.1980
   chunk 26 optimal weight:    0.6980
   chunk 39 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   overall best weight:    0.5782

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

Flipped N/Q/H residues before XYZ refinement:
** C1437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C1879 GLN
C1986 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.088222 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.070998 restraints weight = 26322.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.072453 restraints weight = 18245.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.073088 restraints weight = 14082.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.074072 restraints weight = 12151.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.074454 restraints weight = 10572.192|
|-----------------------------------------------------------------------------|
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7952
moved from start:          0.1600

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7824  Z= 0.107
  Angle     :  0.580   7.551  10732  Z= 0.291
  Chirality :  0.044   0.148   1338
  Planarity :  0.004   0.044   1339
  Dihedral  :  5.823  80.874   1151
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.83 %
    Favored  : 92.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  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: -3.23 (0.26), residues: 1060
  helix: -0.41 (0.34), residues: 252
  sheet: -3.15 (0.32), residues: 206
  loop : -2.62 (0.25), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C1707 
 TYR   0.010   0.001   TYR C1733 
 PHE   0.009   0.001   PHE C1877 
 TRP   0.011   0.001   TRP C2426 
 HIS   0.006   0.001   HIS C2510 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 7824)
  covalent geometry    : angle       0.57994 (10732)
  hydrogen bonds       : bond        0.03060 (  218)
  hydrogen bonds       : angle       5.14985 (  594)

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.238 
Fit side-chains
REVERT: C 1989 MET cc_start: 0.7931 (ptm) cc_final: 0.7584 (ptm)
REVERT: C 2435 LEU cc_start: 0.9028 (tp) cc_final: 0.8824 (tt)
REVERT: C 2459 MET cc_start: 0.7276 (ptp) cc_final: 0.5969 (ptm)
  outliers start: 0
  outliers final: 0
  residues processed: 46
  average time/residue: 0.0573
  time to fit residues: 4.2520
Evaluate side-chains
  34 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 73 optimal weight:    0.9980
   chunk 91 optimal weight:    6.9990
   chunk 14 optimal weight:    6.9990
   chunk 15 optimal weight:    3.9990
   chunk 11 optimal weight:    0.0170
   chunk 68 optimal weight:    0.0970
   chunk 38 optimal weight:    0.0170
   chunk 50 optimal weight:    0.9980
   chunk 88 optimal weight:    0.7980
   chunk 18 optimal weight:    0.7980
   chunk 12 optimal weight:    4.9990
   overall best weight:    0.3454

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

Flipped N/Q/H residues before XYZ refinement:
C1407 HIS
C1437 ASN
C2505 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.089562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.072584 restraints weight = 25945.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.074099 restraints weight = 17828.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.074984 restraints weight = 13636.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.075796 restraints weight = 11413.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.076212 restraints weight = 9996.872|
|-----------------------------------------------------------------------------|
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.1844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   7824  Z= 0.092
  Angle     :  0.559   7.167  10732  Z= 0.281
  Chirality :  0.043   0.144   1338
  Planarity :  0.004   0.042   1339
  Dihedral  :  5.814  79.346   1151
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.60 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  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: -2.97 (0.26), residues: 1060
  helix: -0.10 (0.35), residues: 252
  sheet: -2.92 (0.31), residues: 235
  loop : -2.46 (0.26), residues: 573

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C1957 
 TYR   0.010   0.001   TYR C1402 
 PHE   0.008   0.001   PHE C1877 
 TRP   0.061   0.002   TRP C2104 
 HIS   0.006   0.001   HIS C2510 

Details of bonding type rmsd
  covalent geometry    : bond        0.00210 ( 7824)
  covalent geometry    : angle       0.55857 (10732)
  hydrogen bonds       : bond        0.02947 (  218)
  hydrogen bonds       : angle       4.84625 (  594)

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.320 
Fit side-chains
REVERT: C 1989 MET cc_start: 0.8001 (ptm) cc_final: 0.7627 (ptm)
  outliers start: 0
  outliers final: 0
  residues processed: 54
  average time/residue: 0.0543
  time to fit residues: 4.8778
Evaluate side-chains
  34 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 57 optimal weight:    2.9990
   chunk 92 optimal weight:    9.9990
   chunk 76 optimal weight:    4.9990
   chunk 91 optimal weight:    0.9990
   chunk 18 optimal weight:    0.5980
   chunk 104 optimal weight:    7.9990
   chunk 28 optimal weight:    6.9990
   chunk 44 optimal weight:    0.6980
   chunk 47 optimal weight:    0.7980
   chunk 65 optimal weight:    0.5980
   chunk 81 optimal weight:    7.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
C1407 HIS
C1926 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.088603 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.071387 restraints weight = 25841.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.072825 restraints weight = 17978.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.073857 restraints weight = 13860.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.074367 restraints weight = 11573.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.074877 restraints weight = 10316.433|
|-----------------------------------------------------------------------------|
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7935
moved from start:          0.1907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7824  Z= 0.116
  Angle     :  0.576   7.216  10732  Z= 0.288
  Chirality :  0.044   0.145   1338
  Planarity :  0.004   0.042   1339
  Dihedral  :  5.612  80.166   1151
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.36 %
    Favored  : 92.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  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: -2.81 (0.26), residues: 1060
  helix:  0.03 (0.35), residues: 252
  sheet: -2.68 (0.32), residues: 234
  loop : -2.43 (0.26), residues: 574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C1398 
 TYR   0.011   0.001   TYR C1402 
 PHE   0.010   0.001   PHE C1877 
 TRP   0.031   0.001   TRP C2104 
 HIS   0.006   0.001   HIS C2510 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 7824)
  covalent geometry    : angle       0.57635 (10732)
  hydrogen bonds       : bond        0.02925 (  218)
  hydrogen bonds       : angle       4.77325 (  594)

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.200 
Fit side-chains
REVERT: C 1989 MET cc_start: 0.7984 (ptm) cc_final: 0.7697 (ptm)
  outliers start: 0
  outliers final: 0
  residues processed: 47
  average time/residue: 0.0534
  time to fit residues: 4.2974
Evaluate side-chains
  34 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 70 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9990
   chunk 78 optimal weight:    8.9990
   chunk 58 optimal weight:    2.9990
   chunk 99 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 16 optimal weight:    0.0370
   chunk 19 optimal weight:    0.7980
   chunk 13 optimal weight:    0.0270
   chunk 90 optimal weight:    9.9990
   chunk 89 optimal weight:   10.0000
   overall best weight:    0.7720

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

Flipped N/Q/H residues before XYZ refinement:
C1407 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.088875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.071787 restraints weight = 25746.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.073246 restraints weight = 17816.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.074125 restraints weight = 13719.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.074968 restraints weight = 11551.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.075134 restraints weight = 10080.915|
|-----------------------------------------------------------------------------|
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
moved from start:          0.1941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7824  Z= 0.116
  Angle     :  0.576   7.213  10732  Z= 0.288
  Chirality :  0.044   0.145   1338
  Planarity :  0.004   0.042   1339
  Dihedral  :  5.621  80.167   1151
  Min Nonbonded Distance : 1.958

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.36 %
    Favored  : 92.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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: -2.81 (0.26), residues: 1060
  helix:  0.03 (0.35), residues: 252
  sheet: -2.68 (0.32), residues: 234
  loop : -2.43 (0.26), residues: 574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C1398 
 TYR   0.011   0.001   TYR C1402 
 PHE   0.010   0.001   PHE C1877 
 TRP   0.031   0.001   TRP C2104 
 HIS   0.006   0.001   HIS C2510 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 7824)
  covalent geometry    : angle       0.57630 (10732)
  hydrogen bonds       : bond        0.02925 (  218)
  hydrogen bonds       : angle       4.77325 (  594)

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.359 
Fit side-chains
REVERT: C 1989 MET cc_start: 0.7985 (ptm) cc_final: 0.7696 (ptm)
  outliers start: 0
  outliers final: 0
  residues processed: 47
  average time/residue: 0.0550
  time to fit residues: 4.4248
Evaluate side-chains
  35 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 20 optimal weight:    0.4980
   chunk 104 optimal weight:    0.0670
   chunk 31 optimal weight:    0.0970
   chunk 38 optimal weight:    0.5980
   chunk 61 optimal weight:    2.9990
   chunk 15 optimal weight:    0.7980
   chunk 69 optimal weight:    0.7980
   chunk 95 optimal weight:    6.9990
   chunk 93 optimal weight:    0.9980
   chunk 21 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   overall best weight:    0.4116

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

Flipped N/Q/H residues before XYZ refinement:
C1407 HIS
C1926 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.088732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.071620 restraints weight = 25792.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.073056 restraints weight = 17848.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.074061 restraints weight = 13766.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.074554 restraints weight = 11522.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.074555 restraints weight = 10302.209|
|-----------------------------------------------------------------------------|
r_work (final): 0.3231
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7944
moved from start:          0.1937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7824  Z= 0.118
  Angle     :  0.576   7.149  10732  Z= 0.287
  Chirality :  0.043   0.144   1338
  Planarity :  0.004   0.042   1339
  Dihedral  :  5.742  80.182   1151
  Min Nonbonded Distance : 1.981

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.45 %
    Favored  : 92.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.14 %
    Favored  : 99.86 %
  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: -2.81 (0.26), residues: 1060
  helix:  0.03 (0.35), residues: 252
  sheet: -2.68 (0.32), residues: 234
  loop : -2.43 (0.26), residues: 574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C1398 
 TYR   0.010   0.001   TYR C1402 
 PHE   0.009   0.001   PHE C1877 
 TRP   0.028   0.001   TRP C2104 
 HIS   0.006   0.001   HIS C2510 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 7824)
  covalent geometry    : angle       0.57571 (10732)
  hydrogen bonds       : bond        0.02922 (  218)
  hydrogen bonds       : angle       4.77296 (  594)

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.288 
Fit side-chains
REVERT: C 1989 MET cc_start: 0.7988 (ptm) cc_final: 0.7702 (ptm)
  outliers start: 0
  outliers final: 0
  residues processed: 46
  average time/residue: 0.0430
  time to fit residues: 3.4166
Evaluate side-chains
  35 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 65 optimal weight:    0.8980
   chunk 74 optimal weight:    6.9990
   chunk 28 optimal weight:    0.8980
   chunk 71 optimal weight:    0.0980
   chunk 76 optimal weight:    0.9980
   chunk 97 optimal weight:    4.9990
   chunk 50 optimal weight:    0.8980
   chunk 49 optimal weight:    0.8980
   chunk 42 optimal weight:    0.0970
   chunk 56 optimal weight:    0.7980
   chunk 80 optimal weight:    5.9990
   overall best weight:    0.5578

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

Flipped N/Q/H residues before XYZ refinement:
C1407 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.088836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.071726 restraints weight = 25770.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.073192 restraints weight = 17837.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.074230 restraints weight = 13746.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.074764 restraints weight = 11442.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.075261 restraints weight = 10163.411|
|-----------------------------------------------------------------------------|
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7925
moved from start:          0.1941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   7824  Z= 0.121
  Angle     :  0.576   7.114  10732  Z= 0.287
  Chirality :  0.043   0.144   1338
  Planarity :  0.004   0.042   1339
  Dihedral  :  5.951  80.209   1151
  Min Nonbonded Distance : 1.996

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.45 %
    Favored  : 92.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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: -2.80 (0.26), residues: 1060
  helix:  0.03 (0.35), residues: 252
  sheet: -2.67 (0.32), residues: 234
  loop : -2.43 (0.26), residues: 574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C1398 
 TYR   0.010   0.001   TYR C1402 
 PHE   0.009   0.001   PHE C1877 
 TRP   0.027   0.001   TRP C2104 
 HIS   0.006   0.001   HIS C2510 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 7824)
  covalent geometry    : angle       0.57565 (10732)
  hydrogen bonds       : bond        0.02920 (  218)
  hydrogen bonds       : angle       4.77283 (  594)

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.250 
Fit side-chains
REVERT: C 1989 MET cc_start: 0.7988 (ptm) cc_final: 0.7698 (ptm)
  outliers start: 0
  outliers final: 0
  residues processed: 47
  average time/residue: 0.0588
  time to fit residues: 4.6741
Evaluate side-chains
  34 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 71 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.6980
   chunk 49 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 61 optimal weight:    3.9990
   chunk 22 optimal weight:   10.0000
   chunk 39 optimal weight:    0.3980
   chunk 60 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   chunk 28 optimal weight:    0.2980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
C1407 HIS
C1926 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.088267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.071079 restraints weight = 25723.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.072486 restraints weight = 17942.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.073355 restraints weight = 13884.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.074166 restraints weight = 11666.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 17)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.074539 restraints weight = 10311.464|
|-----------------------------------------------------------------------------|
r_work (final): 0.3232
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7943
moved from start:          0.2010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7824  Z= 0.128
  Angle     :  0.601   8.708  10732  Z= 0.296
  Chirality :  0.044   0.278   1338
  Planarity :  0.004   0.043   1339
  Dihedral  :  5.651  78.351   1151
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.55 %
    Favored  : 92.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.29 %
    Favored  : 99.71 %
  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: -2.68 (0.26), residues: 1060
  helix:  0.11 (0.35), residues: 252
  sheet: -2.51 (0.32), residues: 232
  loop : -2.38 (0.26), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C1957 
 TYR   0.012   0.001   TYR C1733 
 PHE   0.013   0.001   PHE C1575 
 TRP   0.019   0.001   TRP C2104 
 HIS   0.005   0.001   HIS C2510 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 7824)
  covalent geometry    : angle       0.60086 (10732)
  hydrogen bonds       : bond        0.02964 (  218)
  hydrogen bonds       : angle       4.75962 (  594)

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

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

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2120 Ramachandran restraints generated.
    1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.292 
Fit side-chains
REVERT: C 1989 MET cc_start: 0.8056 (ptm) cc_final: 0.7840 (ptm)
  outliers start: 0
  outliers final: 0
  residues processed: 46
  average time/residue: 0.0495
  time to fit residues: 3.9364
Evaluate side-chains
  34 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 65 optimal weight:    0.6980
   chunk 36 optimal weight:    1.9990
   chunk 85 optimal weight:    9.9990
   chunk 80 optimal weight:    5.9990
   chunk 61 optimal weight:    2.9990
   chunk 15 optimal weight:    0.6980
   chunk 102 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9990
   chunk 87 optimal weight:    2.9990
   chunk 9 optimal weight:    0.8980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
C1407 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.088476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.071278 restraints weight = 25859.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.072752 restraints weight = 17967.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.073686 restraints weight = 13849.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.074457 restraints weight = 11631.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.074852 restraints weight = 10211.451|
|-----------------------------------------------------------------------------|
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
moved from start:          0.2019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7824  Z= 0.128
  Angle     :  0.601   8.708  10732  Z= 0.296
  Chirality :  0.044   0.278   1338
  Planarity :  0.004   0.043   1339
  Dihedral  :  5.651  78.351   1151
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.55 %
    Favored  : 92.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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: -2.68 (0.26), residues: 1060
  helix:  0.11 (0.35), residues: 252
  sheet: -2.51 (0.32), residues: 232
  loop : -2.38 (0.26), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C1957 
 TYR   0.012   0.001   TYR C1733 
 PHE   0.013   0.001   PHE C1575 
 TRP   0.019   0.001   TRP C2104 
 HIS   0.005   0.001   HIS C2510 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 7824)
  covalent geometry    : angle       0.60086 (10732)
  hydrogen bonds       : bond        0.02964 (  218)
  hydrogen bonds       : angle       4.75962 (  594)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1132.56 seconds
wall clock time: 20 minutes 17.59 seconds (1217.59 seconds total)