Starting phenix.real_space_refine
on Tue Jan 13 16:57:24 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8u7h_41982/01_2026/8u7h_41982.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8u7h_41982/01_2026/8u7h_41982.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8u7h_41982/01_2026/8u7h_41982.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8u7h_41982/01_2026/8u7h_41982.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8u7h_41982/01_2026/8u7h_41982.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8u7h_41982/01_2026/8u7h_41982.cif"
  }
  resolution = 3.8
  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=  -0.000 sd=   0.069
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    5062      2.51       5
     N    1355      2.21       5
     O    1405      1.98       5
     F       4      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7870
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "C"
      Number of atoms: 7811
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1111, 7811
          Classifications: {'peptide': 1111}
          Incomplete info: {'truncation_to_alanine': 281}
          Link IDs: {'PTRANS': 50, 'TRANS': 1060}
          Chain breaks: 10
          Unresolved non-hydrogen bonds: 1094
          Unresolved non-hydrogen angles: 1334
          Unresolved non-hydrogen dihedrals: 901
          Unresolved non-hydrogen chiralities: 43
          Planarities with less than four sites: {'ASN:plan1': 19, 'GLN:plan1': 19, 'ASP:plan': 33, 'ARG:plan': 29, 'GLU:plan': 50, 'PHE:plan': 11, 'TYR:plan': 3, 'HIS:plan': 8}
          Unresolved non-hydrogen planarities: 704
    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: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'A0T': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.13, per 1000 atoms: 0.27
  Number of scatterers: 7870
  At special positions: 0
  Unit cell: (72.9855, 96.8175, 142.992, 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       4      9.00
     O    1405      8.00
     N    1355      7.00
     C    5062      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: 0.71
  Conformation dependent library (CDL) restraints added in 376.9 milliseconds
  

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2104

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 16 sheets defined
      29.8% alpha, 17.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.36
  Creating SS restraints...
    Processing helix  chain 'C' and resid 1346 through 1355
    Processing helix  chain 'C' and resid 1398 through 1405
      removed outlier: 4.386A  pdb=" N   SER C1403 " --> pdb=" O   GLU C1400 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1424 through 1442
      removed outlier: 3.949A  pdb=" N   VAL C1428 " --> pdb=" O   GLY C1424 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   ASP C1429 " --> pdb=" O   GLN C1425 " (cutoff:3.500A)
      Proline residue:  C1433  - end of helix
      removed outlier: 3.673A  pdb=" N   ALA C1440 " --> pdb=" O   PHE C1436 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1453 through 1457
      removed outlier: 3.546A  pdb=" N   VAL C1456 " --> pdb=" O   HIS C1453 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1458 through 1470
      removed outlier: 3.792A  pdb=" N   ARG C1462 " --> pdb=" O   ASP C1458 " (cutoff:3.500A)
      removed outlier: 4.156A  pdb=" N   ALA C1464 " --> pdb=" O   LYS C1460 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   CYS C1465 " --> pdb=" O   GLN C1461 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   THR C1470 " --> pdb=" O   MET C1466 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1498 through 1508
      removed outlier: 3.599A  pdb=" N   LYS C1502 " --> pdb=" O   ALA C1498 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1524 through 1541
      removed outlier: 3.718A  pdb=" N   VAL C1528 " --> pdb=" O   PRO C1524 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   SER C1536 " --> pdb=" O   LYS C1532 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   LYS C1539 " --> pdb=" O   LEU C1535 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1549 through 1560
      removed outlier: 3.666A  pdb=" N   LEU C1553 " --> pdb=" O   ASP C1549 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   ARG C1558 " --> pdb=" O   LEU C1554 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1568 through 1580
    Processing helix  chain 'C' and resid 1599 through 1604
      removed outlier: 4.155A  pdb=" N   LEU C1603 " --> pdb=" O   GLU C1599 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   CYS C1604 " --> pdb=" O   PRO C1600 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 1599 through 1604'
    Processing helix  chain 'C' and resid 1605 through 1612
      removed outlier: 4.087A  pdb=" N   THR C1612 " --> pdb=" O   ALA C1608 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1629 through 1633
    Processing helix  chain 'C' and resid 1646 through 1650
    Processing helix  chain 'C' and resid 1703 through 1712
      removed outlier: 3.833A  pdb=" N   ARG C1707 " --> pdb=" O   GLY C1703 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1770 through 1791
      removed outlier: 3.628A  pdb=" N   GLN C1779 " --> pdb=" O   ILE C1775 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   ASP C1782 " --> pdb=" O   GLY C1778 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1826 through 1837
      removed outlier: 3.848A  pdb=" N   LYS C1832 " --> pdb=" O   ASP C1828 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   GLY C1837 " --> pdb=" O   LYS C1833 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1871 through 1875
    Processing helix  chain 'C' and resid 1913 through 1922
      removed outlier: 3.797A  pdb=" N   LEU C1917 " --> pdb=" O   SER C1913 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1962 through 1966
      removed outlier: 3.588A  pdb=" N   LEU C1966 " --> pdb=" O   LYS C1963 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1969 through 1987
      removed outlier: 3.982A  pdb=" N   ALA C1975 " --> pdb=" O   GLN C1971 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   VAL C1978 " --> pdb=" O   ILE C1974 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 2040 through 2045
      removed outlier: 3.592A  pdb=" N   ALA C2044 " --> pdb=" O   ALA C2040 " (cutoff:3.500A)
      removed outlier: 3.826A  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 2051 through 2054
    Processing helix  chain 'C' and resid 2055 through 2068
      removed outlier: 3.572A  pdb=" N   THR C2068 " --> pdb=" O   TYR C2064 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 2070 through 2078
      removed outlier: 3.557A  pdb=" N   VAL C2074 " --> pdb=" O   GLY C2070 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   LYS C2078 " --> pdb=" O   VAL C2074 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 2079 through 2086
      removed outlier: 4.243A  pdb=" N   LEU C2086 " --> pdb=" O   GLU C2082 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 2107 through 2112
    Processing helix  chain 'C' and resid 2118 through 2122
    Processing helix  chain 'C' and resid 2124 through 2133
      removed outlier: 3.506A  pdb=" N   ILE C2131 " --> pdb=" O   GLN C2127 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 2134 through 2140
      removed outlier: 3.995A  pdb=" N   VAL C2138 " --> pdb=" O   SER C2134 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 2208 through 2211
    Processing helix  chain 'C' and resid 2278 through 2281
      removed outlier: 4.521A  pdb=" N   LYS C2281 " --> pdb=" O   LYS C2278 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 2278 through 2281'
    Processing helix  chain 'C' and resid 2311 through 2314
    Processing helix  chain 'C' and resid 2389 through 2394
    Processing helix  chain 'C' and resid 2499 through 2526
      removed outlier: 3.676A  pdb=" N   GLN C2505 " --> pdb=" O   PRO C2501 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   VAL C2526 " --> pdb=" O   ARG C2522 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 1373 through 1374
      removed outlier: 3.631A  pdb=" N   LEU C1388 " --> pdb=" O   ILE C1378 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 1373 through 1374
      removed outlier: 7.058A  pdb=" N   MET C1335 " --> pdb=" O   ASN C1391 " (cutoff:3.500A)
      removed outlier: 8.181A  pdb=" N   TRP C1393 " --> pdb=" O   MET C1335 " (cutoff:3.500A)
      removed outlier: 6.815A  pdb=" N   LEU C1337 " --> pdb=" O   TRP C1393 " (cutoff:3.500A)
      removed outlier: 9.566A  pdb=" N   LEU C1414 " --> pdb=" O   ARG C1334 " (cutoff:3.500A)
      removed outlier: 7.303A  pdb=" N   LYS C1336 " --> pdb=" O   LEU C1414 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 1418 through 1420
      removed outlier: 6.748A  pdb=" N   TYR C1419 " --> pdb=" O   THR C1452 " (cutoff:3.500A)
      removed outlier: 8.256A  pdb=" N   VAL C1447 " --> pdb=" O   ARG C1483 " (cutoff:3.500A)
      removed outlier: 6.906A  pdb=" N   TYR C1485 " --> pdb=" O   VAL C1447 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   LEU C1449 " --> pdb=" O   TYR C1485 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 1751 through 1752
      removed outlier: 4.911A  pdb=" N   ILE C1692 " --> pdb=" O   LEU C1813 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   LEU C1813 " --> pdb=" O   ILE C1692 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 1730 through 1731
      removed outlier: 3.823A  pdb=" N   LEU C1740 " --> pdb=" O   CYS C1748 " (cutoff:3.500A)
      removed outlier: 6.874A  pdb=" N   ALA C1746 " --> pdb=" O   TRP C1742 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 1894 through 1898
      removed outlier: 3.615A  pdb=" N   GLU C1901 " --> pdb=" O   TYR C1898 " (cutoff:3.500A)
      removed outlier: 7.190A  pdb=" N   MET C1944 " --> pdb=" O   ALA C1938 " (cutoff:3.500A)
      removed outlier: 5.100A  pdb=" N   ALA C1938 " --> pdb=" O   MET C1944 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   VAL C1946 " --> pdb=" O   LEU C1936 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 1953 through 1954
      removed outlier: 3.991A  pdb=" N   GLY C1953 " --> pdb=" O   LEU C2002 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 1990 through 1991
      removed outlier: 3.514A  pdb=" N   GLN C2022 " --> pdb=" O   ILE C1991 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 2142 through 2145
      removed outlier: 3.685A  pdb=" N   ARG C2142 " --> pdb=" O   VAL C2495 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   VAL C2495 " --> pdb=" O   ARG C2142 " (cutoff:3.500A)
      removed outlier: 6.627A  pdb=" N   LYS C2467 " --> pdb=" O   GLN C2462 " (cutoff:3.500A)
      removed outlier: 6.070A  pdb=" N   GLN C2462 " --> pdb=" O   LYS C2467 " (cutoff:3.500A)
      removed outlier: 6.941A  pdb=" N   VAL C2469 " --> pdb=" O   THR C2460 " (cutoff:3.500A)
      removed outlier: 4.649A  pdb=" N   THR C2460 " --> pdb=" O   VAL C2469 " (cutoff:3.500A)
      removed outlier: 6.972A  pdb=" N   LEU C2471 " --> pdb=" O   MET C2458 " (cutoff:3.500A)
      removed outlier: 4.686A  pdb=" N   MET C2458 " --> pdb=" O   LEU C2471 " (cutoff:3.500A)
      removed outlier: 6.738A  pdb=" N   LEU C2473 " --> pdb=" O   ARG C2456 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   SER C2454 " --> pdb=" O   TYR C2475 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 2152 through 2156
      removed outlier: 3.806A  pdb=" N   CYS C2154 " --> pdb=" O   GLY C2170 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   VAL C2156 " --> pdb=" O   TRP C2168 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   TRP C2168 " --> pdb=" O   VAL C2156 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 2199 through 2207
    Processing sheet with id=AB3, first strand: chain 'C' and resid 2245 through 2247
      removed outlier: 6.504A  pdb=" N   GLY C2266 " --> pdb=" O   THR C2246 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   LEU C2263 " --> pdb=" O   PHE C2275 " (cutoff:3.500A)
      removed outlier: 4.344A  pdb=" N   THR C2267 " --> pdb=" O   LYS C2271 " (cutoff:3.500A)
      removed outlier: 4.697A  pdb=" N   LYS C2271 " --> pdb=" O   THR C2267 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   LEU C2272 " --> pdb=" O   LEU C2291 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 2316 through 2318
      removed outlier: 4.380A  pdb=" N   LYS C2334 " --> pdb=" O   SER C2325 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 2354 through 2359
      removed outlier: 6.809A  pdb=" N   ALA C2366 " --> pdb=" O   ILE C2355 " (cutoff:3.500A)
      removed outlier: 4.218A  pdb=" N   VAL C2357 " --> pdb=" O   TYR C2364 " (cutoff:3.500A)
      removed outlier: 6.735A  pdb=" N   TYR C2364 " --> pdb=" O   VAL C2357 " (cutoff:3.500A)
      removed outlier: 5.231A  pdb=" N   LYS C2367 " --> pdb=" O   VAL C2372 " (cutoff:3.500A)
      removed outlier: 7.013A  pdb=" N   VAL C2372 " --> pdb=" O   LYS C2367 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   ILE C2387 " --> pdb=" O   VAL C2373 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   GLY C2385 " --> pdb=" O   VAL C2375 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 2416 through 2419
    Processing sheet with id=AB7, first strand: chain 'C' and resid 2434 through 2437
      removed outlier: 3.783A  pdb=" N   ARG C2446 " --> pdb=" O   LEU C2436 " (cutoff:3.500A)

    255 hydrogen bonds defined for protein.
    678 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: 1.51

  Time building geometry restraints manager: 0.93 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1260
        1.30 -     1.43: 1972
        1.43 -     1.56: 4729
        1.56 -     1.69: 4
        1.69 -     1.82: 59
  Bond restraints: 8024
  Sorted by residual:
  bond pdb=" CA  CYS C2139 "
       pdb=" C   CYS C2139 "
    ideal  model  delta    sigma   weight residual
    1.524  1.566 -0.042 7.00e-03 2.04e+04 3.58e+01
  bond pdb=" C19 A0T C2602 "
       pdb=" N21 A0T C2602 "
    ideal  model  delta    sigma   weight residual
    1.347  1.465 -0.118 2.00e-02 2.50e+03 3.50e+01
  bond pdb=" C04 A0T C2602 "
       pdb=" N03 A0T C2602 "
    ideal  model  delta    sigma   weight residual
    1.336  1.452 -0.116 2.00e-02 2.50e+03 3.39e+01
  bond pdb=" C   LEU C2140 "
       pdb=" O   LEU C2140 "
    ideal  model  delta    sigma   weight residual
    1.235  1.170  0.065 1.26e-02 6.30e+03 2.69e+01
  bond pdb=" C08 A0T C2602 "
       pdb=" N10 A0T C2602 "
    ideal  model  delta    sigma   weight residual
    1.360  1.462 -0.102 2.00e-02 2.50e+03 2.61e+01
  ... (remaining 8019 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.92: 10561
        1.92 -     3.83: 347
        3.83 -     5.75: 74
        5.75 -     7.66: 18
        7.66 -     9.58: 7
  Bond angle restraints: 11007
  Sorted by residual:
  angle pdb=" CA  CYS C2139 "
        pdb=" C   CYS C2139 "
        pdb=" N   LEU C2140 "
      ideal   model   delta    sigma   weight residual
     118.24  125.99   -7.75 1.18e+00 7.18e-01 4.32e+01
  angle pdb=" CA  CYS C2139 "
        pdb=" C   CYS C2139 "
        pdb=" O   CYS C2139 "
      ideal   model   delta    sigma   weight residual
     119.98  112.92    7.06 1.21e+00 6.83e-01 3.41e+01
  angle pdb=" N   LEU C2140 "
        pdb=" CA  LEU C2140 "
        pdb=" CB  LEU C2140 "
      ideal   model   delta    sigma   weight residual
     110.49  118.26   -7.77 1.69e+00 3.50e-01 2.11e+01
  angle pdb=" CA  VAL C2138 "
        pdb=" C   VAL C2138 "
        pdb=" N   CYS C2139 "
      ideal   model   delta    sigma   weight residual
     118.13  111.86    6.27 1.37e+00 5.33e-01 2.10e+01
  angle pdb=" N   LEU C2140 "
        pdb=" CA  LEU C2140 "
        pdb=" C   LEU C2140 "
      ideal   model   delta    sigma   weight residual
     110.80  102.17    8.63 2.13e+00 2.20e-01 1.64e+01
  ... (remaining 11002 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.80: 4490
       21.80 -    43.61: 228
       43.61 -    65.41: 21
       65.41 -    87.22: 2
       87.22 -   109.02: 2
  Dihedral angle restraints: 4743
    sinusoidal: 1509
      harmonic: 3234
  Sorted by residual:
  dihedral pdb=" CA  TYR C1666 "
           pdb=" C   TYR C1666 "
           pdb=" N   LEU C1667 "
           pdb=" CA  LEU C1667 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.08  -23.92     0      5.00e+00 4.00e-02 2.29e+01
  dihedral pdb=" C   CYS C2139 "
           pdb=" N   CYS C2139 "
           pdb=" CA  CYS C2139 "
           pdb=" CB  CYS C2139 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -133.30   10.70     0      2.50e+00 1.60e-01 1.83e+01
  dihedral pdb=" CA  ASN C2468 "
           pdb=" C   ASN C2468 "
           pdb=" N   VAL C2469 "
           pdb=" CA  VAL C2469 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.51   20.49     0      5.00e+00 4.00e-02 1.68e+01
  ... (remaining 4740 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.065: 1117
       0.065 -    0.130: 220
       0.130 -    0.194: 27
       0.194 -    0.259: 2
       0.259 -    0.324: 2
  Chirality restraints: 1368
  Sorted by residual:
  chirality pdb=" CA  CYS C2139 "
            pdb=" N   CYS C2139 "
            pdb=" C   CYS C2139 "
            pdb=" CB  CYS C2139 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.62e+00
  chirality pdb=" CB  VAL C2314 "
            pdb=" CA  VAL C2314 "
            pdb=" CG1 VAL C2314 "
            pdb=" CG2 VAL C2314 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.31   -0.32 2.00e-01 2.50e+01 2.57e+00
  chirality pdb=" CB  ILE C1680 "
            pdb=" CA  ILE C1680 "
            pdb=" CG1 ILE C1680 "
            pdb=" CG2 ILE C1680 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.39    0.25 2.00e-01 2.50e+01 1.61e+00
  ... (remaining 1365 not shown)

  Planarity restraints: 1380
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL C2138 "    0.043 2.00e-02 2.50e+03   8.71e-02 7.59e+01
        pdb=" C   VAL C2138 "   -0.151 2.00e-02 2.50e+03
        pdb=" O   VAL C2138 "    0.059 2.00e-02 2.50e+03
        pdb=" N   CYS C2139 "    0.049 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP C1785 "    0.020 2.00e-02 2.50e+03   4.03e-02 1.63e+01
        pdb=" C   ASP C1785 "   -0.070 2.00e-02 2.50e+03
        pdb=" O   ASP C1785 "    0.026 2.00e-02 2.50e+03
        pdb=" N   SER C1786 "    0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL C2504 "    0.017 2.00e-02 2.50e+03   3.47e-02 1.21e+01
        pdb=" C   VAL C2504 "   -0.060 2.00e-02 2.50e+03
        pdb=" O   VAL C2504 "    0.023 2.00e-02 2.50e+03
        pdb=" N   GLN C2505 "    0.020 2.00e-02 2.50e+03
  ... (remaining 1377 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.78: 1735
        2.78 -     3.31: 7313
        3.31 -     3.84: 12069
        3.84 -     4.37: 13731
        4.37 -     4.90: 23650
  Nonbonded interactions: 58498
  Sorted by model distance:
  nonbonded pdb=" OG1 THR C2158 "
            pdb=" O   SER C2166 "
     model   vdw
     2.256 3.040
  nonbonded pdb=" O   ILE C1505 "
            pdb=" OG  SER C1508 "
     model   vdw
     2.281 3.040
  nonbonded pdb=" OG  SER C2370 "
            pdb=" O   VAL C2372 "
     model   vdw
     2.300 3.040
  nonbonded pdb=" O   CYS C2139 "
            pdb=" C   LEU C2140 "
     model   vdw
     2.307 3.270
  nonbonded pdb=" O   THR C1912 "
            pdb=" NH1 ARG C1943 "
     model   vdw
     2.311 3.120
  ... (remaining 58493 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:                  0.000
  Normalize map: mean=0, sd=1:             1.290
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.820
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  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:             0.010
  Load rotamer database and sin/cos tables:1.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.560
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
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   0.118   8024  Z= 0.251
  Angle     :  0.867   9.577  11007  Z= 0.453
  Chirality :  0.053   0.324   1368
  Planarity :  0.006   0.087   1380
  Dihedral  : 13.287 109.019   2639
  Min Nonbonded Distance : 2.256

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  7.81 %
    Favored  : 92.10 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  5.05 %
    Favored  : 94.67 %
  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: -4.54 (0.22), residues: 1089
  helix: -2.35 (0.26), residues: 271
  sheet: -3.60 (0.28), residues: 221
  loop : -3.15 (0.23), residues: 597

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C1943 
 TYR   0.010   0.001   TYR C1984 
 PHE   0.020   0.001   PHE C1650 
 TRP   0.020   0.001   TRP C1734 
 HIS   0.009   0.001   HIS C2510 

Details of bonding type rmsd
  covalent geometry    : bond        0.00461 ( 8024)
  covalent geometry    : angle       0.86741 (11007)
  hydrogen bonds       : bond        0.19320 (  253)
  hydrogen bonds       : angle       8.33247 (  678)

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

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

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 91
  time to evaluate  : 0.319 
Fit side-chains
REVERT: C 1338 MET cc_start: 0.7354 (mmt) cc_final: 0.7124 (mtt)
REVERT: C 1402 TYR cc_start: 0.8169 (m-10) cc_final: 0.7737 (m-80)
REVERT: C 1409 MET cc_start: 0.8401 (mtm) cc_final: 0.8142 (mtp)
REVERT: C 1486 HIS cc_start: 0.8132 (m-70) cc_final: 0.7684 (m90)
REVERT: C 1738 ILE cc_start: 0.9159 (tp) cc_final: 0.8894 (tp)
REVERT: C 2023 TYR cc_start: 0.7690 (m-80) cc_final: 0.7468 (t80)
REVERT: C 2227 ILE cc_start: 0.9154 (mp) cc_final: 0.8906 (mt)
REVERT: C 2249 TYR cc_start: 0.7359 (t80) cc_final: 0.6430 (t80)
  outliers start: 2
  outliers final: 1
  residues processed: 93
  average time/residue: 0.0822
  time to fit residues: 11.0501
Evaluate side-chains
  67 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 66
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue 2140 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 108 optimal weight:    0.0070
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.6980
   chunk 100 optimal weight:    5.9990
   chunk 106 optimal weight:    0.9990
   overall best weight:    0.7002

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

Flipped N/Q/H residues before XYZ refinement:
C1405 HIS
C2476 ASN
C2490 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.114897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.091199 restraints weight = 17822.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.092524 restraints weight = 12071.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.093288 restraints weight = 10150.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.094636 restraints weight = 8528.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.094632 restraints weight = 7694.433|
|-----------------------------------------------------------------------------|
r_work (final): 0.3317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7871
moved from start:          0.1244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8024  Z= 0.140
  Angle     :  0.648   6.540  11007  Z= 0.318
  Chirality :  0.045   0.142   1368
  Planarity :  0.004   0.052   1380
  Dihedral  :  5.947  55.733   1188
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.89 %
    Favored  : 93.11 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 12.20 %
    Favored  : 85.83 %
  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: -3.32 (0.24), residues: 1089
  helix: -0.71 (0.31), residues: 272
  sheet: -3.03 (0.31), residues: 217
  loop : -2.65 (0.24), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C1943 
 TYR   0.009   0.001   TYR C1527 
 PHE   0.008   0.001   PHE C1650 
 TRP   0.012   0.001   TRP C1705 
 HIS   0.004   0.001   HIS C2510 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 8024)
  covalent geometry    : angle       0.64787 (11007)
  hydrogen bonds       : bond        0.03577 (  253)
  hydrogen bonds       : angle       5.50885 (  678)

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

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

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 74
  time to evaluate  : 0.296 
Fit side-chains
REVERT: C 1338 MET cc_start: 0.7410 (mmt) cc_final: 0.7002 (mtt)
REVERT: C 1486 HIS cc_start: 0.7872 (m-70) cc_final: 0.7565 (m90)
REVERT: C 2249 TYR cc_start: 0.7038 (t80) cc_final: 0.6491 (t80)
REVERT: C 2429 THR cc_start: 0.8652 (p) cc_final: 0.8385 (t)
  outliers start: 14
  outliers final: 7
  residues processed: 81
  average time/residue: 0.0697
  time to fit residues: 8.6739
Evaluate side-chains
  72 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 65
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue 1339 ILE
Chi-restraints excluded: chain C residue 1519 VAL
Chi-restraints excluded: chain C residue 1713 LEU
Chi-restraints excluded: chain C residue 1877 PHE
Chi-restraints excluded: chain C residue 1925 CYS
Chi-restraints excluded: chain C residue 2086 LEU
Chi-restraints excluded: chain C residue 2417 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 97 optimal weight:    1.9990
   chunk 25 optimal weight:    0.0670
   chunk 104 optimal weight:    3.9990
   chunk 79 optimal weight:    1.9990
   chunk 64 optimal weight:    0.0570
   chunk 31 optimal weight:    2.9990
   chunk 28 optimal weight:    9.9990
   chunk 16 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   chunk 105 optimal weight:    2.9990
   overall best weight:    1.2242

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

Flipped N/Q/H residues before XYZ refinement:
C1783 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.112393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.089266 restraints weight = 17598.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.090775 restraints weight = 12756.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.091387 restraints weight = 10163.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.091683 restraints weight = 8907.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.091756 restraints weight = 8349.895|
|-----------------------------------------------------------------------------|
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7943
moved from start:          0.1719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   8024  Z= 0.203
  Angle     :  0.689   8.820  11007  Z= 0.334
  Chirality :  0.045   0.152   1368
  Planarity :  0.004   0.056   1380
  Dihedral  :  5.774  57.413   1186
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.63 %
    Favored  : 91.37 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 15.99 %
    Favored  : 81.77 %
  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: -3.05 (0.25), residues: 1089
  helix: -0.30 (0.32), residues: 273
  sheet: -2.93 (0.31), residues: 220
  loop : -2.55 (0.25), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C1732 
 TYR   0.018   0.002   TYR C1666 
 PHE   0.008   0.001   PHE C1762 
 TRP   0.016   0.001   TRP C1705 
 HIS   0.004   0.001   HIS C2510 

Details of bonding type rmsd
  covalent geometry    : bond        0.00489 ( 8024)
  covalent geometry    : angle       0.68886 (11007)
  hydrogen bonds       : bond        0.03547 (  253)
  hydrogen bonds       : angle       5.16380 (  678)

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

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

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 67
  time to evaluate  : 0.295 
Fit side-chains
REVERT: C 1869 MET cc_start: 0.7934 (mmt) cc_final: 0.7645 (mmm)
REVERT: C 2042 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.7745 (pt0)
REVERT: C 2249 TYR cc_start: 0.7096 (t80) cc_final: 0.6449 (t80)
REVERT: C 2429 THR cc_start: 0.8679 (p) cc_final: 0.8444 (t)
  outliers start: 16
  outliers final: 9
  residues processed: 79
  average time/residue: 0.0669
  time to fit residues: 8.2083
Evaluate side-chains
  71 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 61
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue 1339 ILE
Chi-restraints excluded: chain C residue 1519 VAL
Chi-restraints excluded: chain C residue 1543 ILE
Chi-restraints excluded: chain C residue 1691 ILE
Chi-restraints excluded: chain C residue 1713 LEU
Chi-restraints excluded: chain C residue 1877 PHE
Chi-restraints excluded: chain C residue 1925 CYS
Chi-restraints excluded: chain C residue 2042 GLU
Chi-restraints excluded: chain C residue 2380 THR
Chi-restraints excluded: chain C residue 2417 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 16 optimal weight:    0.7980
   chunk 4 optimal weight:    1.9990
   chunk 104 optimal weight:    0.7980
   chunk 66 optimal weight:    0.8980
   chunk 49 optimal weight:    1.9990
   chunk 50 optimal weight:    0.0470
   chunk 71 optimal weight:    0.4980
   chunk 2 optimal weight:    0.8980
   chunk 24 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9990
   overall best weight:    0.6078

-------------------------------------------------------------------------------
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 = 0.3640 r_free = 0.3640 target = 0.114548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.091248 restraints weight = 17830.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.093416 restraints weight = 12977.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.093818 restraints weight = 9347.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.093947 restraints weight = 9120.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.094104 restraints weight = 8327.836|
|-----------------------------------------------------------------------------|
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7883
moved from start:          0.1879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8024  Z= 0.120
  Angle     :  0.602   8.064  11007  Z= 0.290
  Chirality :  0.043   0.147   1368
  Planarity :  0.004   0.056   1380
  Dihedral  :  5.400  52.085   1186
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.43 %
    Favored  : 93.57 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 17.11 %
    Favored  : 79.94 %
  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: -2.54 (0.25), residues: 1089
  helix:  0.19 (0.33), residues: 273
  sheet: -2.58 (0.32), residues: 214
  loop : -2.30 (0.25), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C1677 
 TYR   0.007   0.001   TYR C1527 
 PHE   0.008   0.001   PHE C1890 
 TRP   0.012   0.001   TRP C1705 
 HIS   0.005   0.001   HIS C2510 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 8024)
  covalent geometry    : angle       0.60174 (11007)
  hydrogen bonds       : bond        0.02877 (  253)
  hydrogen bonds       : angle       4.74949 (  678)

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

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

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 65
  time to evaluate  : 0.320 
Fit side-chains
REVERT: C 1869 MET cc_start: 0.7837 (mmt) cc_final: 0.7530 (mmm)
REVERT: C 2042 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.7678 (pt0)
REVERT: C 2249 TYR cc_start: 0.7206 (t80) cc_final: 0.6736 (t80)
REVERT: C 2359 VAL cc_start: 0.8040 (OUTLIER) cc_final: 0.7839 (m)
REVERT: C 2429 THR cc_start: 0.8577 (p) cc_final: 0.8322 (t)
  outliers start: 21
  outliers final: 13
  residues processed: 83
  average time/residue: 0.0582
  time to fit residues: 7.8343
Evaluate side-chains
  76 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 61
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue 1339 ILE
Chi-restraints excluded: chain C residue 1500 LEU
Chi-restraints excluded: chain C residue 1543 ILE
Chi-restraints excluded: chain C residue 1669 VAL
Chi-restraints excluded: chain C residue 1713 LEU
Chi-restraints excluded: chain C residue 1763 LEU
Chi-restraints excluded: chain C residue 1877 PHE
Chi-restraints excluded: chain C residue 1884 LEU
Chi-restraints excluded: chain C residue 1925 CYS
Chi-restraints excluded: chain C residue 1935 LEU
Chi-restraints excluded: chain C residue 2004 THR
Chi-restraints excluded: chain C residue 2042 GLU
Chi-restraints excluded: chain C residue 2359 VAL
Chi-restraints excluded: chain C residue 2417 LEU
Chi-restraints excluded: chain C residue 2457 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 20 optimal weight:    0.0070
   chunk 106 optimal weight:    2.9990
   chunk 15 optimal weight:    0.7980
   chunk 36 optimal weight:    1.9990
   chunk 24 optimal weight:    4.9990
   chunk 94 optimal weight:    3.9990
   chunk 54 optimal weight:    0.6980
   chunk 56 optimal weight:    0.0770
   chunk 70 optimal weight:    9.9990
   chunk 95 optimal weight:    0.5980
   chunk 9 optimal weight:    2.9990
   overall best weight:    0.4356

-------------------------------------------------------------------------------
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 = 0.3657 r_free = 0.3657 target = 0.115662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.091491 restraints weight = 17717.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.093532 restraints weight = 12089.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.094877 restraints weight = 9359.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.095836 restraints weight = 7892.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.096336 restraints weight = 7027.227|
|-----------------------------------------------------------------------------|
r_work (final): 0.3355
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7825
moved from start:          0.2044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045   8024  Z= 0.104
  Angle     :  0.588   8.617  11007  Z= 0.281
  Chirality :  0.043   0.165   1368
  Planarity :  0.004   0.055   1380
  Dihedral  :  5.157  48.227   1186
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.06 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 19.21 %
    Favored  : 77.56 %
  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: -2.16 (0.26), residues: 1089
  helix:  0.31 (0.33), residues: 282
  sheet: -2.32 (0.33), residues: 221
  loop : -1.98 (0.26), residues: 586

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C1771 
 TYR   0.007   0.001   TYR C2475 
 PHE   0.007   0.001   PHE C1890 
 TRP   0.011   0.001   TRP C1705 
 HIS   0.005   0.001   HIS C2510 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 8024)
  covalent geometry    : angle       0.58761 (11007)
  hydrogen bonds       : bond        0.02597 (  253)
  hydrogen bonds       : angle       4.46679 (  678)

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

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

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 64
  time to evaluate  : 0.379 
Fit side-chains
REVERT: C 1679 VAL cc_start: 0.7662 (OUTLIER) cc_final: 0.7393 (m)
REVERT: C 1702 MET cc_start: 0.8890 (mtp) cc_final: 0.8648 (mtm)
REVERT: C 1869 MET cc_start: 0.7771 (mmt) cc_final: 0.7473 (mmm)
REVERT: C 2042 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.8053 (pt0)
REVERT: C 2249 TYR cc_start: 0.7236 (t80) cc_final: 0.6780 (t80)
REVERT: C 2429 THR cc_start: 0.8506 (p) cc_final: 0.8262 (t)
  outliers start: 23
  outliers final: 14
  residues processed: 83
  average time/residue: 0.0642
  time to fit residues: 8.2773
Evaluate side-chains
  77 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 61
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue 1339 ILE
Chi-restraints excluded: chain C residue 1500 LEU
Chi-restraints excluded: chain C residue 1519 VAL
Chi-restraints excluded: chain C residue 1543 ILE
Chi-restraints excluded: chain C residue 1669 VAL
Chi-restraints excluded: chain C residue 1679 VAL
Chi-restraints excluded: chain C residue 1713 LEU
Chi-restraints excluded: chain C residue 1763 LEU
Chi-restraints excluded: chain C residue 1877 PHE
Chi-restraints excluded: chain C residue 1884 LEU
Chi-restraints excluded: chain C residue 1925 CYS
Chi-restraints excluded: chain C residue 2004 THR
Chi-restraints excluded: chain C residue 2042 GLU
Chi-restraints excluded: chain C residue 2280 VAL
Chi-restraints excluded: chain C residue 2417 LEU
Chi-restraints excluded: chain C residue 2457 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 66 optimal weight:    0.0030
   chunk 110 optimal weight:    0.9980
   chunk 85 optimal weight:   10.0000
   chunk 27 optimal weight:    0.4980
   chunk 39 optimal weight:    0.0020
   chunk 51 optimal weight:    0.9990
   chunk 87 optimal weight:   10.0000
   chunk 100 optimal weight:    5.9990
   chunk 97 optimal weight:    0.9990
   chunk 99 optimal weight:    0.9980
   chunk 82 optimal weight:    6.9990
   overall best weight:    0.4998

-------------------------------------------------------------------------------
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 = 0.3657 r_free = 0.3657 target = 0.115651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.091500 restraints weight = 17580.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.093460 restraints weight = 12200.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.094645 restraints weight = 9533.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.095800 restraints weight = 8102.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.096267 restraints weight = 7153.830|
|-----------------------------------------------------------------------------|
r_work (final): 0.3354
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7824
moved from start:          0.2202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8024  Z= 0.107
  Angle     :  0.572   8.911  11007  Z= 0.276
  Chirality :  0.043   0.136   1368
  Planarity :  0.004   0.055   1380
  Dihedral  :  5.025  47.602   1186
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.06 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 19.21 %
    Favored  : 77.56 %
  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: -2.02 (0.26), residues: 1089
  helix:  0.44 (0.33), residues: 283
  sheet: -2.31 (0.32), residues: 234
  loop : -1.83 (0.26), residues: 572

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C1957 
 TYR   0.008   0.001   TYR C1894 
 PHE   0.007   0.001   PHE C2324 
 TRP   0.011   0.001   TRP C1705 
 HIS   0.005   0.001   HIS C2510 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 8024)
  covalent geometry    : angle       0.57171 (11007)
  hydrogen bonds       : bond        0.02553 (  253)
  hydrogen bonds       : angle       4.36138 (  678)

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

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

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 61
  time to evaluate  : 0.315 
Fit side-chains
REVERT: C 1679 VAL cc_start: 0.7679 (OUTLIER) cc_final: 0.7415 (m)
REVERT: C 1702 MET cc_start: 0.8889 (mtp) cc_final: 0.8635 (mtm)
REVERT: C 2042 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.8055 (pt0)
REVERT: C 2249 TYR cc_start: 0.7138 (t80) cc_final: 0.6790 (t80)
REVERT: C 2429 THR cc_start: 0.8352 (p) cc_final: 0.8081 (t)
  outliers start: 23
  outliers final: 17
  residues processed: 80
  average time/residue: 0.0637
  time to fit residues: 7.9846
Evaluate side-chains
  79 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 60
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue 1339 ILE
Chi-restraints excluded: chain C residue 1500 LEU
Chi-restraints excluded: chain C residue 1519 VAL
Chi-restraints excluded: chain C residue 1543 ILE
Chi-restraints excluded: chain C residue 1669 VAL
Chi-restraints excluded: chain C residue 1679 VAL
Chi-restraints excluded: chain C residue 1713 LEU
Chi-restraints excluded: chain C residue 1731 ARG
Chi-restraints excluded: chain C residue 1763 LEU
Chi-restraints excluded: chain C residue 1877 PHE
Chi-restraints excluded: chain C residue 1884 LEU
Chi-restraints excluded: chain C residue 1922 VAL
Chi-restraints excluded: chain C residue 1925 CYS
Chi-restraints excluded: chain C residue 2004 THR
Chi-restraints excluded: chain C residue 2042 GLU
Chi-restraints excluded: chain C residue 2280 VAL
Chi-restraints excluded: chain C residue 2293 ILE
Chi-restraints excluded: chain C residue 2417 LEU
Chi-restraints excluded: chain C residue 2457 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 76 optimal weight:    3.9990
   chunk 57 optimal weight:    2.9990
   chunk 105 optimal weight:    2.9990
   chunk 44 optimal weight:    0.0980
   chunk 37 optimal weight:    0.7980
   chunk 82 optimal weight:    5.9990
   chunk 85 optimal weight:    8.9990
   chunk 9 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 29 optimal weight:    0.0020
   overall best weight:    0.9792

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

Flipped N/Q/H residues before XYZ refinement:
C2476 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.113679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.090818 restraints weight = 17874.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.091672 restraints weight = 12480.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.092023 restraints weight = 10061.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.092375 restraints weight = 9402.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.092522 restraints weight = 8873.056|
|-----------------------------------------------------------------------------|
r_work (final): 0.3278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
moved from start:          0.2294

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8024  Z= 0.164
  Angle     :  0.621   7.996  11007  Z= 0.300
  Chirality :  0.044   0.134   1368
  Planarity :  0.004   0.055   1380
  Dihedral  :  5.179  50.369   1186
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.62 %
    Favored  : 92.38 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 19.50 %
    Favored  : 77.14 %
  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: -2.05 (0.26), residues: 1089
  helix:  0.44 (0.33), residues: 283
  sheet: -2.30 (0.32), residues: 239
  loop : -1.88 (0.26), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C1957 
 TYR   0.015   0.002   TYR C1666 
 PHE   0.008   0.001   PHE C2324 
 TRP   0.014   0.001   TRP C1705 
 HIS   0.004   0.001   HIS C2510 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 ( 8024)
  covalent geometry    : angle       0.62074 (11007)
  hydrogen bonds       : bond        0.02915 (  253)
  hydrogen bonds       : angle       4.47462 (  678)

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

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

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 62
  time to evaluate  : 0.301 
Fit side-chains
REVERT: C 1679 VAL cc_start: 0.7795 (OUTLIER) cc_final: 0.7514 (m)
REVERT: C 1982 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.8869 (mp)
REVERT: C 2042 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8142 (pt0)
REVERT: C 2249 TYR cc_start: 0.7118 (t80) cc_final: 0.6574 (t80)
REVERT: C 2427 ILE cc_start: 0.9353 (mt) cc_final: 0.8940 (tp)
  outliers start: 24
  outliers final: 19
  residues processed: 82
  average time/residue: 0.0641
  time to fit residues: 8.2589
Evaluate side-chains
  81 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 59
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue 1339 ILE
Chi-restraints excluded: chain C residue 1500 LEU
Chi-restraints excluded: chain C residue 1519 VAL
Chi-restraints excluded: chain C residue 1543 ILE
Chi-restraints excluded: chain C residue 1669 VAL
Chi-restraints excluded: chain C residue 1679 VAL
Chi-restraints excluded: chain C residue 1691 ILE
Chi-restraints excluded: chain C residue 1713 LEU
Chi-restraints excluded: chain C residue 1731 ARG
Chi-restraints excluded: chain C residue 1763 LEU
Chi-restraints excluded: chain C residue 1877 PHE
Chi-restraints excluded: chain C residue 1884 LEU
Chi-restraints excluded: chain C residue 1922 VAL
Chi-restraints excluded: chain C residue 1925 CYS
Chi-restraints excluded: chain C residue 1935 LEU
Chi-restraints excluded: chain C residue 1982 LEU
Chi-restraints excluded: chain C residue 2004 THR
Chi-restraints excluded: chain C residue 2042 GLU
Chi-restraints excluded: chain C residue 2280 VAL
Chi-restraints excluded: chain C residue 2293 ILE
Chi-restraints excluded: chain C residue 2417 LEU
Chi-restraints excluded: chain C residue 2457 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 9 optimal weight:    0.7980
   chunk 79 optimal weight:    7.9990
   chunk 53 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   chunk 80 optimal weight:    1.9990
   chunk 62 optimal weight:    0.0570
   chunk 56 optimal weight:    0.9990
   chunk 93 optimal weight:    0.9990
   chunk 86 optimal weight:   10.0000
   chunk 104 optimal weight:    0.2980
   chunk 35 optimal weight:    2.9990
   overall best weight:    0.6302

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

Flipped N/Q/H residues before XYZ refinement:
C2118 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.114719 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.090589 restraints weight = 17646.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.092570 restraints weight = 12161.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.093928 restraints weight = 9444.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.094720 restraints weight = 8000.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.095492 restraints weight = 7168.953|
|-----------------------------------------------------------------------------|
r_work (final): 0.3341
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
moved from start:          0.2392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8024  Z= 0.123
  Angle     :  0.607  10.663  11007  Z= 0.288
  Chirality :  0.043   0.127   1368
  Planarity :  0.004   0.055   1380
  Dihedral  :  5.047  46.688   1186
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.43 %
    Favored  : 93.57 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 19.21 %
    Favored  : 77.14 %
  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: -1.87 (0.26), residues: 1089
  helix:  0.56 (0.33), residues: 283
  sheet: -2.14 (0.32), residues: 236
  loop : -1.78 (0.27), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C2413 
 TYR   0.009   0.001   TYR C1894 
 PHE   0.006   0.001   PHE C2324 
 TRP   0.011   0.001   TRP C1705 
 HIS   0.005   0.001   HIS C2510 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 8024)
  covalent geometry    : angle       0.60744 (11007)
  hydrogen bonds       : bond        0.02666 (  253)
  hydrogen bonds       : angle       4.37614 (  678)

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

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

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 59
  time to evaluate  : 0.316 
Fit side-chains
REVERT: C 1646 MET cc_start: 0.7889 (mmp) cc_final: 0.7667 (mmt)
REVERT: C 1702 MET cc_start: 0.8958 (mtm) cc_final: 0.8757 (mtm)
REVERT: C 1982 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.8846 (mp)
REVERT: C 2115 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8807 (mt)
REVERT: C 2249 TYR cc_start: 0.7079 (t80) cc_final: 0.6623 (t80)
  outliers start: 26
  outliers final: 18
  residues processed: 80
  average time/residue: 0.0628
  time to fit residues: 7.9880
Evaluate side-chains
  77 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 57
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue 1339 ILE
Chi-restraints excluded: chain C residue 1500 LEU
Chi-restraints excluded: chain C residue 1519 VAL
Chi-restraints excluded: chain C residue 1543 ILE
Chi-restraints excluded: chain C residue 1669 VAL
Chi-restraints excluded: chain C residue 1713 LEU
Chi-restraints excluded: chain C residue 1763 LEU
Chi-restraints excluded: chain C residue 1877 PHE
Chi-restraints excluded: chain C residue 1884 LEU
Chi-restraints excluded: chain C residue 1922 VAL
Chi-restraints excluded: chain C residue 1925 CYS
Chi-restraints excluded: chain C residue 1935 LEU
Chi-restraints excluded: chain C residue 1982 LEU
Chi-restraints excluded: chain C residue 2004 THR
Chi-restraints excluded: chain C residue 2115 LEU
Chi-restraints excluded: chain C residue 2280 VAL
Chi-restraints excluded: chain C residue 2293 ILE
Chi-restraints excluded: chain C residue 2380 THR
Chi-restraints excluded: chain C residue 2417 LEU
Chi-restraints excluded: chain C residue 2457 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 76 optimal weight:    4.9990
   chunk 87 optimal weight:   10.0000
   chunk 90 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9990
   chunk 50 optimal weight:    0.6980
   chunk 81 optimal weight:    0.7980
   chunk 27 optimal weight:    4.9990
   chunk 49 optimal weight:    1.9990
   chunk 48 optimal weight:    0.0170
   chunk 20 optimal weight:    0.9990
   chunk 25 optimal weight:    0.6980
   overall best weight:    0.5618

-------------------------------------------------------------------------------
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 = 0.3650 r_free = 0.3650 target = 0.115322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.090678 restraints weight = 17770.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.092662 restraints weight = 12032.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.094177 restraints weight = 9347.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.095015 restraints weight = 7814.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.095478 restraints weight = 6957.302|
|-----------------------------------------------------------------------------|
r_work (final): 0.3336
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7841
moved from start:          0.2478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8024  Z= 0.117
  Angle     :  0.593   8.861  11007  Z= 0.284
  Chirality :  0.043   0.130   1368
  Planarity :  0.004   0.055   1380
  Dihedral  :  4.951  45.881   1186
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.61 %
    Favored  : 93.39 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 19.35 %
    Favored  : 77.42 %
  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: -1.75 (0.26), residues: 1089
  helix:  0.72 (0.34), residues: 280
  sheet: -2.04 (0.33), residues: 239
  loop : -1.74 (0.26), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C2413 
 TYR   0.016   0.001   TYR C1666 
 PHE   0.006   0.001   PHE C2324 
 TRP   0.011   0.001   TRP C1705 
 HIS   0.005   0.001   HIS C2510 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 8024)
  covalent geometry    : angle       0.59323 (11007)
  hydrogen bonds       : bond        0.02551 (  253)
  hydrogen bonds       : angle       4.31284 (  678)

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

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

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 60
  time to evaluate  : 0.305 
Fit side-chains
REVERT: C 1646 MET cc_start: 0.7958 (mmp) cc_final: 0.7678 (mmt)
REVERT: C 1702 MET cc_start: 0.8964 (mtm) cc_final: 0.8761 (mtm)
REVERT: C 1982 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.8852 (mp)
REVERT: C 2115 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8820 (mt)
REVERT: C 2249 TYR cc_start: 0.7038 (t80) cc_final: 0.6590 (t80)
  outliers start: 23
  outliers final: 19
  residues processed: 80
  average time/residue: 0.0659
  time to fit residues: 8.2973
Evaluate side-chains
  79 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 58
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue 1339 ILE
Chi-restraints excluded: chain C residue 1500 LEU
Chi-restraints excluded: chain C residue 1519 VAL
Chi-restraints excluded: chain C residue 1543 ILE
Chi-restraints excluded: chain C residue 1669 VAL
Chi-restraints excluded: chain C residue 1713 LEU
Chi-restraints excluded: chain C residue 1763 LEU
Chi-restraints excluded: chain C residue 1877 PHE
Chi-restraints excluded: chain C residue 1884 LEU
Chi-restraints excluded: chain C residue 1922 VAL
Chi-restraints excluded: chain C residue 1925 CYS
Chi-restraints excluded: chain C residue 1935 LEU
Chi-restraints excluded: chain C residue 1982 LEU
Chi-restraints excluded: chain C residue 2004 THR
Chi-restraints excluded: chain C residue 2115 LEU
Chi-restraints excluded: chain C residue 2136 GLU
Chi-restraints excluded: chain C residue 2280 VAL
Chi-restraints excluded: chain C residue 2293 ILE
Chi-restraints excluded: chain C residue 2380 THR
Chi-restraints excluded: chain C residue 2417 LEU
Chi-restraints excluded: chain C residue 2457 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 47 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9990
   chunk 83 optimal weight:    6.9990
   chunk 9 optimal weight:    0.6980
   chunk 96 optimal weight:    0.4980
   chunk 0 optimal weight:    2.9990
   chunk 44 optimal weight:    0.7980
   chunk 56 optimal weight:    0.0010
   chunk 48 optimal weight:    0.4980
   chunk 5 optimal weight:    0.2980
   chunk 55 optimal weight:    0.6980
   overall best weight:    0.3986

-------------------------------------------------------------------------------
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 = 0.3661 r_free = 0.3661 target = 0.115975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.091936 restraints weight = 17561.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.093945 restraints weight = 12063.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.095127 restraints weight = 9335.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.096248 restraints weight = 7921.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.096864 restraints weight = 7009.693|
|-----------------------------------------------------------------------------|
r_work (final): 0.3362
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.2557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   8024  Z= 0.099
  Angle     :  0.591   9.148  11007  Z= 0.280
  Chirality :  0.043   0.129   1368
  Planarity :  0.004   0.056   1380
  Dihedral  :  4.859  45.551   1186
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.97 %
    Favored  : 94.03 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 19.92 %
    Favored  : 77.14 %
  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: -1.66 (0.27), residues: 1089
  helix:  0.66 (0.33), residues: 289
  sheet: -1.94 (0.33), residues: 240
  loop : -1.66 (0.27), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C2413 
 TYR   0.009   0.001   TYR C1894 
 PHE   0.006   0.001   PHE C2324 
 TRP   0.010   0.001   TRP C1734 
 HIS   0.005   0.001   HIS C2510 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 8024)
  covalent geometry    : angle       0.59112 (11007)
  hydrogen bonds       : bond        0.02428 (  253)
  hydrogen bonds       : angle       4.22165 (  678)

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

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

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 61
  time to evaluate  : 0.323 
Fit side-chains
REVERT: C 1646 MET cc_start: 0.7936 (mmp) cc_final: 0.7720 (mmt)
REVERT: C 1982 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8868 (mp)
REVERT: C 2249 TYR cc_start: 0.6750 (t80) cc_final: 0.6377 (t80)
  outliers start: 21
  outliers final: 18
  residues processed: 78
  average time/residue: 0.0596
  time to fit residues: 7.5975
Evaluate side-chains
  79 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 60
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue 1339 ILE
Chi-restraints excluded: chain C residue 1500 LEU
Chi-restraints excluded: chain C residue 1519 VAL
Chi-restraints excluded: chain C residue 1543 ILE
Chi-restraints excluded: chain C residue 1669 VAL
Chi-restraints excluded: chain C residue 1713 LEU
Chi-restraints excluded: chain C residue 1877 PHE
Chi-restraints excluded: chain C residue 1884 LEU
Chi-restraints excluded: chain C residue 1922 VAL
Chi-restraints excluded: chain C residue 1925 CYS
Chi-restraints excluded: chain C residue 1982 LEU
Chi-restraints excluded: chain C residue 2004 THR
Chi-restraints excluded: chain C residue 2136 GLU
Chi-restraints excluded: chain C residue 2280 VAL
Chi-restraints excluded: chain C residue 2293 ILE
Chi-restraints excluded: chain C residue 2417 LEU
Chi-restraints excluded: chain C residue 2429 THR
Chi-restraints excluded: chain C residue 2457 VAL
Chi-restraints excluded: chain C residue 2470 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 39 optimal weight:    0.7980
   chunk 17 optimal weight:    0.0050
   chunk 43 optimal weight:    4.9990
   chunk 16 optimal weight:    0.7980
   chunk 107 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9980
   chunk 18 optimal weight:    3.9990
   chunk 59 optimal weight:    0.6980
   chunk 109 optimal weight:    0.9990
   chunk 69 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   overall best weight:    0.6594

-------------------------------------------------------------------------------
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 = 0.3650 r_free = 0.3650 target = 0.115282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.091163 restraints weight = 17609.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.093149 restraints weight = 12208.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.094513 restraints weight = 9525.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.095219 restraints weight = 8020.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.095793 restraints weight = 7190.364|
|-----------------------------------------------------------------------------|
r_work (final): 0.3345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
moved from start:          0.2607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8024  Z= 0.126
  Angle     :  0.606   8.725  11007  Z= 0.287
  Chirality :  0.043   0.130   1368
  Planarity :  0.004   0.056   1380
  Dihedral  :  4.902  44.522   1186
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.80 %
    Favored  : 93.20 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 19.92 %
    Favored  : 77.14 %
  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: -1.60 (0.27), residues: 1089
  helix:  0.77 (0.33), residues: 285
  sheet: -1.88 (0.33), residues: 239
  loop : -1.66 (0.27), residues: 565

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C2413 
 TYR   0.017   0.001   TYR C1666 
 PHE   0.007   0.001   PHE C2324 
 TRP   0.014   0.001   TRP C1705 
 HIS   0.005   0.001   HIS C2510 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 8024)
  covalent geometry    : angle       0.60590 (11007)
  hydrogen bonds       : bond        0.02562 (  253)
  hydrogen bonds       : angle       4.23087 (  678)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1265.05 seconds
wall clock time: 22 minutes 35.54 seconds (1355.54 seconds total)