Starting phenix.real_space_refine
on Sat Sep 12 01:12:20 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9oxi_70982/09_2026/9oxi_70982.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9oxi_70982/09_2026/9oxi_70982.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.72
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9oxi_70982/09_2026/9oxi_70982.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9oxi_70982/09_2026/9oxi_70982.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9oxi_70982/09_2026/9oxi_70982.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9oxi_70982/09_2026/9oxi_70982.cif"
  }
  resolution = 3.72
  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=   0.014
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      71      5.16       5
     C    7745      2.51       5
     N    2063      2.21       5
     O    2219      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 12100
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 12072
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1531, 12072
          Classifications: {'peptide': 1531}
          Incomplete info: {'truncation_to_alanine': 37}
          Link IDs: {'PCIS': 1, 'PTRANS': 72, 'TRANS': 1457}
          Chain breaks: 14
          Unresolved non-hydrogen bonds: 135
          Unresolved non-hydrogen angles: 167
          Unresolved non-hydrogen dihedrals: 115
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'ASN:plan1': 5, 'GLU:plan': 2, 'ARG:plan': 4, 'PHE:plan': 2, 'ASP:plan': 2, 'HIS:plan': 4, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 85
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'GDP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.67, per 1000 atoms: 0.22
  Number of scatterers: 12100
  At special positions: 0
  Unit cell: (100.045, 108.46, 152.405, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      71     16.00
     P       2     15.00
     O    2219      8.00
     N    2063      7.00
     C    7745      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: 0.91
  Conformation dependent library (CDL) restraints added in 540.9 milliseconds
  

  3002 Ramachandran restraints generated.
    1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2916

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 14 sheets defined
      30.0% alpha, 15.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.64
  Creating SS restraints...
    Processing helix  chain 'A' and resid 744 through 750
    Processing helix  chain 'A' and resid 757 through 763
    Processing helix  chain 'A' and resid 769 through 782
    Processing helix  chain 'A' and resid 784 through 788
    Processing helix  chain 'A' and resid 814 through 819
      removed outlier: 3.507A  pdb=" N   LEU A 818 " --> pdb=" O   GLU A 814 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   GLY A 819 " --> pdb=" O   PRO A 815 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 814 through 819'
    Processing helix  chain 'A' and resid 998 through 1002
      removed outlier: 3.754A  pdb=" N   SER A1001 " --> pdb=" O   ASP A 998 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   GLN A1002 " --> pdb=" O   ALA A 999 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 998 through 1002'
    Processing helix  chain 'A' and resid 1006 through 1011
    Processing helix  chain 'A' and resid 1027 through 1034
    Processing helix  chain 'A' and resid 1051 through 1057
      removed outlier: 3.594A  pdb=" N   LEU A1054 " --> pdb=" O   PRO A1051 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   MET A1057 " --> pdb=" O   LEU A1054 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1101 through 1106
    Processing helix  chain 'A' and resid 1189 through 1194
      removed outlier: 3.757A  pdb=" N   LEU A1193 " --> pdb=" O   PRO A1189 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   ASN A1194 " --> pdb=" O   GLU A1190 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1189 through 1194'
    Processing helix  chain 'A' and resid 1213 through 1217
    Processing helix  chain 'A' and resid 1240 through 1245
    Processing helix  chain 'A' and resid 1261 through 1267
    Processing helix  chain 'A' and resid 1285 through 1291
    Processing helix  chain 'A' and resid 1316 through 1328
    Processing helix  chain 'A' and resid 1346 through 1355
    Processing helix  chain 'A' and resid 1398 through 1402
      removed outlier: 3.521A  pdb=" N   TYR A1402 " --> pdb=" O   GLU A1399 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1404 through 1409
      removed outlier: 3.731A  pdb=" N   MET A1409 " --> pdb=" O   PRO A1406 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1426 through 1431
    Processing helix  chain 'A' and resid 1431 through 1442
      removed outlier: 3.679A  pdb=" N   LEU A1435 " --> pdb=" O   MET A1431 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1465 through 1471
      removed outlier: 3.948A  pdb=" N   LYS A1471 " --> pdb=" O   SER A1467 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1494 through 1509
      removed outlier: 4.851A  pdb=" N   THR A1503 " --> pdb=" O   LYS A1499 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   ASN A1506 " --> pdb=" O   LYS A1502 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1512 through 1516
      removed outlier: 4.150A  pdb=" N   ASP A1515 " --> pdb=" O   LYS A1512 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1525 through 1538
    Processing helix  chain 'A' and resid 1549 through 1560
    Processing helix  chain 'A' and resid 1568 through 1579
    Processing helix  chain 'A' and resid 1599 through 1613
      removed outlier: 3.500A  pdb=" N   LEU A1603 " --> pdb=" O   GLU A1599 " (cutoff:3.500A)
      removed outlier: 4.130A  pdb=" N   ILE A1610 " --> pdb=" O   ILE A1606 " (cutoff:3.500A)
      removed outlier: 4.954A  pdb=" N   LEU A1611 " --> pdb=" O   MET A1607 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   THR A1612 " --> pdb=" O   ALA A1608 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1643 through 1647
    Processing helix  chain 'A' and resid 1648 through 1656
    Processing helix  chain 'A' and resid 1669 through 1673
      removed outlier: 3.552A  pdb=" N   LEU A1673 " --> pdb=" O   PRO A1670 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1703 through 1713
      removed outlier: 3.752A  pdb=" N   ARG A1711 " --> pdb=" O   ARG A1707 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1770 through 1792
    Processing helix  chain 'A' and resid 1793 through 1796
    Processing helix  chain 'A' and resid 1829 through 1835
    Processing helix  chain 'A' and resid 1836 through 1840
      removed outlier: 4.132A  pdb=" N   LEU A1840 " --> pdb=" O   GLY A1837 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1851 through 1856
      removed outlier: 3.954A  pdb=" N   ILE A1855 " --> pdb=" O   PRO A1851 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1913 through 1925
    Processing helix  chain 'A' and resid 1954 through 1961
      removed outlier: 3.864A  pdb=" N   LEU A1958 " --> pdb=" O   SER A1954 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1969 through 1987
    Processing helix  chain 'A' and resid 1996 through 1998
      No H-bonds generated for 'chain 'A' and resid 1996 through 1998'
    Processing helix  chain 'A' and resid 2035 through 2039
      removed outlier: 4.167A  pdb=" N   ARG A2039 " --> pdb=" O   PRO A2036 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2040 through 2044
    Processing helix  chain 'A' and resid 2055 through 2068
    Processing helix  chain 'A' and resid 2070 through 2079
      removed outlier: 3.662A  pdb=" N   LYS A2078 " --> pdb=" O   VAL A2074 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2081 through 2086
      removed outlier: 4.297A  pdb=" N   GLU A2085 " --> pdb=" O   ASN A2081 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2094 through 2099
    Processing helix  chain 'A' and resid 2104 through 2115
    Processing helix  chain 'A' and resid 2127 through 2133
    Processing helix  chain 'A' and resid 2135 through 2139
    Processing helix  chain 'A' and resid 2389 through 2397
      removed outlier: 3.526A  pdb=" N   GLU A2395 " --> pdb=" O   HIS A2391 " (cutoff:3.500A)
      removed outlier: 4.221A  pdb=" N   VAL A2396 " --> pdb=" O   PHE A2392 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2499 through 2525
    Processing sheet with id=AA1, first strand: chain 'A' and resid 987 through 988
      removed outlier: 6.891A  pdb=" N   LEU A 987 " --> pdb=" O   GLU A1017 " (cutoff:3.500A)
      removed outlier: 6.836A  pdb=" N   LEU A1016 " --> pdb=" O   ASP A1041 " (cutoff:3.500A)
      removed outlier: 6.845A  pdb=" N   LEU A1040 " --> pdb=" O   ASP A1064 " (cutoff:3.500A)
      removed outlier: 6.973A  pdb=" N   LEU A1063 " --> pdb=" O   ASN A1089 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ILE A1113 " --> pdb=" O   PHE A1088 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   LEU A1090 " --> pdb=" O   ILE A1113 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   LEU A1134 " --> pdb=" O   SER A1159 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   ASP A1202 " --> pdb=" O   LEU A1178 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   HIS A1251 " --> pdb=" O   LEU A1225 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 1329 through 1330
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1375 through 1378
      removed outlier: 6.597A  pdb=" N   MET A1335 " --> pdb=" O   ASN A1391 " (cutoff:3.500A)
      removed outlier: 7.478A  pdb=" N   TRP A1393 " --> pdb=" O   MET A1335 " (cutoff:3.500A)
      removed outlier: 6.807A  pdb=" N   LEU A1337 " --> pdb=" O   TRP A1393 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   VAL A1418 " --> pdb=" O   VAL A1340 " (cutoff:3.500A)
      removed outlier: 8.610A  pdb=" N   ILE A1448 " --> pdb=" O   ALA A1413 " (cutoff:3.500A)
      removed outlier: 6.487A  pdb=" N   TYR A1415 " --> pdb=" O   ILE A1448 " (cutoff:3.500A)
      removed outlier: 7.446A  pdb=" N   VAL A1450 " --> pdb=" O   TYR A1415 " (cutoff:3.500A)
      removed outlier: 6.057A  pdb=" N   ALA A1417 " --> pdb=" O   VAL A1450 " (cutoff:3.500A)
      removed outlier: 6.055A  pdb=" N   VAL A1447 " --> pdb=" O   ILE A1482 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   ASP A1484 " --> pdb=" O   VAL A1447 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1547 through 1548
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1730 through 1734
      removed outlier: 4.045A  pdb=" N   TRP A1742 " --> pdb=" O   ALA A1746 " (cutoff:3.500A)
      removed outlier: 7.334A  pdb=" N   ALA A1746 " --> pdb=" O   TRP A1742 " (cutoff:3.500A)
      removed outlier: 6.081A  pdb=" N   TYR A1747 " --> pdb=" O   PRO A1768 " (cutoff:3.500A)
      removed outlier: 4.554A  pdb=" N   ILE A1692 " --> pdb=" O   LEU A1813 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1893 through 1898
    Processing sheet with id=AA7, first strand: chain 'A' and resid 2000 through 2002
    Processing sheet with id=AA8, first strand: chain 'A' and resid 2140 through 2145
      removed outlier: 6.573A  pdb=" N   LEU A2140 " --> pdb=" O   ASP A2497 " (cutoff:3.500A)
      removed outlier: 6.486A  pdb=" N   ASP A2497 " --> pdb=" O   LEU A2140 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   ARG A2142 " --> pdb=" O   VAL A2495 " (cutoff:3.500A)
      removed outlier: 6.266A  pdb=" N   TYR A2475 " --> pdb=" O   VAL A2455 " (cutoff:3.500A)
      removed outlier: 5.562A  pdb=" N   VAL A2455 " --> pdb=" O   TYR A2475 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 2152 through 2158
      removed outlier: 5.520A  pdb=" N   VAL A2152 " --> pdb=" O   GLY A2172 " (cutoff:3.500A)
      removed outlier: 7.108A  pdb=" N   GLY A2172 " --> pdb=" O   VAL A2152 " (cutoff:3.500A)
      removed outlier: 4.472A  pdb=" N   CYS A2154 " --> pdb=" O   GLY A2170 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 2199 through 2205
    Processing sheet with id=AB2, first strand: chain 'A' and resid 2245 through 2249
      removed outlier: 6.585A  pdb=" N   GLY A2266 " --> pdb=" O   THR A2246 " (cutoff:3.500A)
      removed outlier: 4.730A  pdb=" N   LEU A2248 " --> pdb=" O   LEU A2264 " (cutoff:3.500A)
      removed outlier: 6.894A  pdb=" N   LEU A2264 " --> pdb=" O   LEU A2248 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 2300 through 2303
      removed outlier: 4.059A  pdb=" N   CYS A2302 " --> pdb=" O   GLY A2318 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 2354 through 2358
      removed outlier: 7.214A  pdb=" N   ALA A2366 " --> pdb=" O   ILE A2355 " (cutoff:3.500A)
      removed outlier: 4.398A  pdb=" N   VAL A2357 " --> pdb=" O   TYR A2364 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   TYR A2364 " --> pdb=" O   VAL A2357 " (cutoff:3.500A)
      removed outlier: 4.540A  pdb=" N   LYS A2367 " --> pdb=" O   VAL A2372 " (cutoff:3.500A)
      removed outlier: 6.512A  pdb=" N   VAL A2372 " --> pdb=" O   LYS A2367 " (cutoff:3.500A)
      removed outlier: 6.077A  pdb=" N   ASP A2377 " --> pdb=" O   LEU A2383 " (cutoff:3.500A)
      removed outlier: 6.379A  pdb=" N   LEU A2383 " --> pdb=" O   ASP A2377 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 2414 through 2419
      removed outlier: 7.103A  pdb=" N   GLY A2428 " --> pdb=" O   LYS A2415 " (cutoff:3.500A)
      removed outlier: 4.563A  pdb=" N   LEU A2417 " --> pdb=" O   TRP A2426 " (cutoff:3.500A)
      removed outlier: 6.821A  pdb=" N   TRP A2426 " --> pdb=" O   LEU A2417 " (cutoff:3.500A)
      removed outlier: 5.046A  pdb=" N   LEU A2419 " --> pdb=" O   ALA A2424 " (cutoff:3.500A)
      removed outlier: 6.880A  pdb=" N   ALA A2424 " --> pdb=" O   LEU A2419 " (cutoff:3.500A)
      removed outlier: 6.024A  pdb=" N   ILE A2434 " --> pdb=" O   VAL A2447 " (cutoff:3.500A)
      removed outlier: 4.170A  pdb=" N   VAL A2447 " --> pdb=" O   ILE A2434 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   LEU A2436 " --> pdb=" O   ILE A2445 " (cutoff:3.500A)

    379 hydrogen bonds defined for protein.
    1002 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: 2.65

  Time building geometry restraints manager: 1.24 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3900
        1.34 -     1.46: 2063
        1.46 -     1.58: 6257
        1.58 -     1.70: 4
        1.70 -     1.82: 104
  Bond restraints: 12328
  Sorted by residual:
  bond pdb=" C5  GDP A2601 "
       pdb=" C4  GDP A2601 "
    ideal  model  delta    sigma   weight residual
    1.490  1.374  0.116 2.00e-02 2.50e+03 3.36e+01
  bond pdb=" C5  GDP A2601 "
       pdb=" C6  GDP A2601 "
    ideal  model  delta    sigma   weight residual
    1.490  1.408  0.082 2.00e-02 2.50e+03 1.67e+01
  bond pdb=" CB  PRO A1546 "
       pdb=" CG  PRO A1546 "
    ideal  model  delta    sigma   weight residual
    1.492  1.650 -0.158 5.00e-02 4.00e+02 1.00e+01
  bond pdb=" C6  GDP A2601 "
       pdb=" N1  GDP A2601 "
    ideal  model  delta    sigma   weight residual
    1.337  1.390 -0.053 2.00e-02 2.50e+03 7.00e+00
  bond pdb=" C8  GDP A2601 "
       pdb=" N7  GDP A2601 "
    ideal  model  delta    sigma   weight residual
    1.350  1.307  0.043 2.00e-02 2.50e+03 4.67e+00
  ... (remaining 12323 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.28: 16252
        2.28 -     4.56: 360
        4.56 -     6.84: 66
        6.84 -     9.12: 13
        9.12 -    11.40: 5
  Bond angle restraints: 16696
  Sorted by residual:
  angle pdb=" CA  PRO A1546 "
        pdb=" N   PRO A1546 "
        pdb=" CD  PRO A1546 "
      ideal   model   delta    sigma   weight residual
     112.00  100.60   11.40 1.40e+00 5.10e-01 6.63e+01
  angle pdb=" C   LYS A1502 "
        pdb=" N   THR A1503 "
        pdb=" CA  THR A1503 "
      ideal   model   delta    sigma   weight residual
     121.54  130.91   -9.37 1.91e+00 2.74e-01 2.40e+01
  angle pdb=" N   PRO A1546 "
        pdb=" CD  PRO A1546 "
        pdb=" CG  PRO A1546 "
      ideal   model   delta    sigma   weight residual
     103.20   97.41    5.79 1.50e+00 4.44e-01 1.49e+01
  angle pdb=" C3' GDP A2601 "
        pdb=" C2' GDP A2601 "
        pdb=" C1' GDP A2601 "
      ideal   model   delta    sigma   weight residual
     111.00  100.39   10.61 3.00e+00 1.11e-01 1.25e+01
  angle pdb=" C   GLY A1424 "
        pdb=" N   GLN A1425 "
        pdb=" CA  GLN A1425 "
      ideal   model   delta    sigma   weight residual
     121.54  127.93   -6.39 1.91e+00 2.74e-01 1.12e+01
  ... (remaining 16691 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.14: 7411
       35.14 -    70.28: 115
       70.28 -   105.42: 13
      105.42 -   140.56: 0
      140.56 -   175.69: 1
  Dihedral angle restraints: 7540
    sinusoidal: 3071
      harmonic: 4469
  Sorted by residual:
  dihedral pdb=" O2B GDP A2601 "
           pdb=" O3A GDP A2601 "
           pdb=" PB  GDP A2601 "
           pdb=" PA  GDP A2601 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00    4.31  175.69     1      2.00e+01 2.50e-03 4.79e+01
  dihedral pdb=" CA  PRO A2080 "
           pdb=" C   PRO A2080 "
           pdb=" N   ASN A2081 "
           pdb=" CA  ASN A2081 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.49  -27.51     0      5.00e+00 4.00e-02 3.03e+01
  dihedral pdb=" CA  ASN A1506 "
           pdb=" C   ASN A1506 "
           pdb=" N   GLU A1507 "
           pdb=" CA  GLU A1507 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.68   27.32     0      5.00e+00 4.00e-02 2.98e+01
  ... (remaining 7537 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.073: 1680
       0.073 -    0.147: 259
       0.147 -    0.220: 5
       0.220 -    0.293: 1
       0.293 -    0.366: 1
  Chirality restraints: 1946
  Sorted by residual:
  chirality pdb=" CB  ILE A 997 "
            pdb=" CA  ILE A 997 "
            pdb=" CG1 ILE A 997 "
            pdb=" CG2 ILE A 997 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.28    0.37 2.00e-01 2.50e+01 3.36e+00
  chirality pdb=" CB  ILE A1113 "
            pdb=" CA  ILE A1113 "
            pdb=" CG1 ILE A1113 "
            pdb=" CG2 ILE A1113 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.36    0.28 2.00e-01 2.50e+01 1.99e+00
  chirality pdb=" C3' GDP A2601 "
            pdb=" C4' GDP A2601 "
            pdb=" O3' GDP A2601 "
            pdb=" C2' GDP A2601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.51   -2.72    0.21 2.00e-01 2.50e+01 1.11e+00
  ... (remaining 1943 not shown)

  Planarity restraints: 2107
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A1050 "    0.069 5.00e-02 4.00e+02   1.06e-01 1.79e+01
        pdb=" N   PRO A1051 "   -0.183 5.00e-02 4.00e+02
        pdb=" CA  PRO A1051 "    0.057 5.00e-02 4.00e+02
        pdb=" CD  PRO A1051 "    0.057 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A1503 "   -0.019 2.00e-02 2.50e+03   3.73e-02 1.39e+01
        pdb=" C   THR A1503 "    0.065 2.00e-02 2.50e+03
        pdb=" O   THR A1503 "   -0.023 2.00e-02 2.50e+03
        pdb=" N   ILE A1504 "   -0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A1545 "   -0.061 5.00e-02 4.00e+02   8.57e-02 1.18e+01
        pdb=" N   PRO A1546 "    0.148 5.00e-02 4.00e+02
        pdb=" CA  PRO A1546 "   -0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO A1546 "   -0.045 5.00e-02 4.00e+02
  ... (remaining 2104 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.78: 2348
        2.78 -     3.31: 11393
        3.31 -     3.84: 19209
        3.84 -     4.37: 22582
        4.37 -     4.90: 38351
  Nonbonded interactions: 93883
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A2246 "
            pdb=" O   LEU A2300 "
     model   vdw
     2.256 3.040
  nonbonded pdb=" OG1 THR A2267 "
            pdb=" OD1 ASP A2269 "
     model   vdw
     2.282 3.040
  nonbonded pdb=" OD2 ASP A1077 "
            pdb=" OG1 THR A1079 "
     model   vdw
     2.282 3.040
  nonbonded pdb=" OG  SER A1934 "
            pdb=" OE2 GLU A1948 "
     model   vdw
     2.295 3.040
  nonbonded pdb=" OH  TYR A2249 "
            pdb=" OE1 GLU A2305 "
     model   vdw
     2.299 3.040
  ... (remaining 93878 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:             4.530
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     12.430
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.420
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7608
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.158  12328  Z= 0.179
  Angle     :  0.840  11.396  16696  Z= 0.425
  Chirality :  0.050   0.366   1946
  Planarity :  0.007   0.106   2107
  Dihedral  : 13.820 175.694   4624
  Min Nonbonded Distance : 2.256

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  8.99 %
    Favored  : 90.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.07 %
    Favored  : 99.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.37 %
    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: -2.14 (0.21), residues: 1501
  helix: -0.69 (0.26), residues: 364
  sheet: -1.22 (0.31), residues: 280
  loop : -1.85 (0.21), residues: 857

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 793 
 TYR   0.029   0.001   TYR A1649 
 PHE   0.052   0.002   PHE A2083 
 TRP   0.020   0.002   TRP A2104 
 HIS   0.006   0.001   HIS A1574 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00390 /  0.18 (12328)
  covalent geometry    : angle       0.83967 /  0.43 (16696)
  hydrogen bonds       : bond        0.17348 / 11.01 (  379)
  hydrogen bonds       : angle       7.13347 /  4.88 ( 1002)

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

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

  3002 Ramachandran restraints generated.
    1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3002 Ramachandran restraints generated.
    1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 177
  time to evaluate  : 0.472 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1162 MET cc_start: 0.7850 (ptp) cc_final: 0.7261 (ptp)
REVERT: A 1654 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7527 (tm-30)
REVERT: A 2079 PHE cc_start: 0.8058 (t80) cc_final: 0.7804 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 177
  average time/residue: 0.1104
  time to fit residues: 28.4529
Evaluate side-chains
  136 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 107 optimal weight:    0.9980
   chunk 10 optimal weight:    5.9990
   chunk 66 optimal weight:    3.9990
   chunk 130 optimal weight:    7.9990
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    0.6980
   chunk 77 optimal weight:    0.3980
   chunk 122 optimal weight:    0.2980
   chunk 91 optimal weight:    2.9990
   chunk 149 optimal weight:    0.7980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A1068 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4280 r_free = 0.4280 target = 0.169970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.125133 restraints weight = 21271.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.125106 restraints weight = 16299.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.125016 restraints weight = 13610.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.125316 restraints weight = 13738.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.125706 restraints weight = 12506.384|
|-----------------------------------------------------------------------------|
r_work (final): 0.3727
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7676
moved from start:          0.1147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067  12328  Z= 0.136
  Angle     :  0.629   8.473  16696  Z= 0.321
  Chirality :  0.045   0.184   1946
  Planarity :  0.005   0.067   2107
  Dihedral  :  6.539 167.091   1633
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  9.06 %
    Favored  : 90.74 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  :  6.68 %
    Favored  : 92.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.37 %
    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: -1.89 (0.21), residues: 1501
  helix: -0.12 (0.27), residues: 371
  sheet: -1.17 (0.31), residues: 274
  loop : -1.85 (0.21), residues: 856

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A2143 
 TYR   0.020   0.001   TYR A2064 
 PHE   0.017   0.001   PHE A2083 
 TRP   0.013   0.001   TRP A2104 
 HIS   0.004   0.001   HIS A1998 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00316 /  0.14 (12328)
  covalent geometry    : angle       0.62945 /  0.32 (16696)
  hydrogen bonds       : bond        0.03787 /  2.41 (  379)
  hydrogen bonds       : angle       5.42137 /  3.70 ( 1002)

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

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

  3002 Ramachandran restraints generated.
    1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3002 Ramachandran restraints generated.
    1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 156
  time to evaluate  : 0.465 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1017 GLU cc_start: 0.7760 (mp0) cc_final: 0.7423 (mp0)
REVERT: A 1162 MET cc_start: 0.7746 (ptp) cc_final: 0.7435 (ptp)
REVERT: A 1546 PRO cc_start: 0.9042 (Cg_endo) cc_final: 0.8638 (Cg_exo)
REVERT: A 1592 LEU cc_start: 0.7854 (tp) cc_final: 0.7591 (mt)
REVERT: A 1968 ARG cc_start: 0.7868 (mmt-90) cc_final: 0.7647 (mmt180)
REVERT: A 2079 PHE cc_start: 0.8077 (t80) cc_final: 0.7781 (t80)
REVERT: A 2082 GLU cc_start: 0.8032 (pp20) cc_final: 0.7374 (pp20)
  outliers start: 6
  outliers final: 4
  residues processed: 159
  average time/residue: 0.1008
  time to fit residues: 24.1680
Evaluate side-chains
  143 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 139
  time to evaluate  : 0.461 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1625 ILE
Chi-restraints excluded: chain A residue 1982 LEU
Chi-restraints excluded: chain A residue 2151 ILE
Chi-restraints excluded: chain A residue 2457 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 149 optimal weight:    1.9990
   chunk 31 optimal weight:    6.9990
   chunk 143 optimal weight:    0.7980
   chunk 108 optimal weight:    0.9990
   chunk 85 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 24 optimal weight:    9.9990
   chunk 45 optimal weight:    3.9990
   chunk 113 optimal weight:    0.9990
   chunk 61 optimal weight:    0.0870
   chunk 48 optimal weight:    0.0980
   overall best weight:    0.5962

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A2053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4269 r_free = 0.4269 target = 0.169194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.121335 restraints weight = 21348.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.123443 restraints weight = 16575.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.124058 restraints weight = 12542.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.124233 restraints weight = 12231.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.124479 restraints weight = 11925.335|
|-----------------------------------------------------------------------------|
r_work (final): 0.3707
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7707
moved from start:          0.1502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  12328  Z= 0.125
  Angle     :  0.600   7.768  16696  Z= 0.305
  Chirality :  0.044   0.146   1946
  Planarity :  0.005   0.071   2107
  Dihedral  :  6.227 158.673   1633
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  8.59 %
    Favored  : 91.21 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  :  8.91 %
    Favored  : 89.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.37 %
    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: -1.70 (0.22), residues: 1501
  helix:  0.27 (0.28), residues: 362
  sheet: -1.04 (0.32), residues: 268
  loop : -1.83 (0.21), residues: 871

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 793 
 TYR   0.016   0.001   TYR A2064 
 PHE   0.024   0.001   PHE A1050 
 TRP   0.012   0.001   TRP A1295 
 HIS   0.006   0.001   HIS A1998 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00290 /  0.13 (12328)
  covalent geometry    : angle       0.59976 /  0.30 (16696)
  hydrogen bonds       : bond        0.03251 /  2.06 (  379)
  hydrogen bonds       : angle       5.12478 /  3.50 ( 1002)

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

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

  3002 Ramachandran restraints generated.
    1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3002 Ramachandran restraints generated.
    1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 153
  time to evaluate  : 0.372 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1017 GLU cc_start: 0.7819 (mp0) cc_final: 0.7380 (mp0)
REVERT: A 1109 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8269 (mt)
REVERT: A 1168 MET cc_start: 0.8410 (mmm) cc_final: 0.8063 (mmm)
REVERT: A 1355 MET cc_start: 0.8455 (mmt) cc_final: 0.8097 (mmm)
REVERT: A 1431 MET cc_start: 0.8273 (OUTLIER) cc_final: 0.8059 (ttm)
REVERT: A 1592 LEU cc_start: 0.7764 (tp) cc_final: 0.7532 (mt)
REVERT: A 1968 ARG cc_start: 0.7964 (mmt-90) cc_final: 0.7713 (mmt180)
REVERT: A 2315 MET cc_start: 0.7059 (pmm) cc_final: 0.6611 (pmm)
REVERT: A 2388 ASP cc_start: 0.7203 (p0) cc_final: 0.6772 (t0)
  outliers start: 16
  outliers final: 10
  residues processed: 162
  average time/residue: 0.1025
  time to fit residues: 24.4428
Evaluate side-chains
  152 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 140
  time to evaluate  : 0.472 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1109 LEU
Chi-restraints excluded: chain A residue 1431 MET
Chi-restraints excluded: chain A residue 1519 VAL
Chi-restraints excluded: chain A residue 1625 ILE
Chi-restraints excluded: chain A residue 1631 VAL
Chi-restraints excluded: chain A residue 1652 LEU
Chi-restraints excluded: chain A residue 1947 MET
Chi-restraints excluded: chain A residue 1982 LEU
Chi-restraints excluded: chain A residue 2124 THR
Chi-restraints excluded: chain A residue 2151 ILE
Chi-restraints excluded: chain A residue 2358 VAL
Chi-restraints excluded: chain A residue 2457 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 148 optimal weight:    0.5980
   chunk 81 optimal weight:    0.3980
   chunk 36 optimal weight:    4.9990
   chunk 93 optimal weight:    0.8980
   chunk 31 optimal weight:    4.9990
   chunk 104 optimal weight:    0.6980
   chunk 129 optimal weight:    6.9990
   chunk 136 optimal weight:    4.9990
   chunk 8 optimal weight:    9.9990
   chunk 22 optimal weight:    7.9990
   chunk 85 optimal weight:    1.9990
   overall best weight:    0.9182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A1555 GLN
** A2053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.167085 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.119263 restraints weight = 21348.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.120609 restraints weight = 16384.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.120931 restraints weight = 13299.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.120843 restraints weight = 13101.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.121086 restraints weight = 12671.771|
|-----------------------------------------------------------------------------|
r_work (final): 0.3659
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7778
moved from start:          0.1837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  12328  Z= 0.160
  Angle     :  0.614   8.014  16696  Z= 0.312
  Chirality :  0.045   0.219   1946
  Planarity :  0.005   0.078   2107
  Dihedral  :  6.147 152.286   1633
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  9.66 %
    Favored  : 90.21 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 10.10 %
    Favored  : 88.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.37 %
    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: -1.71 (0.22), residues: 1501
  helix:  0.28 (0.28), residues: 365
  sheet: -1.10 (0.32), residues: 268
  loop : -1.84 (0.21), residues: 868

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A1552 
 TYR   0.012   0.001   TYR A2064 
 PHE   0.025   0.001   PHE A1050 
 TRP   0.012   0.001   TRP A2426 
 HIS   0.005   0.001   HIS A1998 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00381 /  0.16 (12328)
  covalent geometry    : angle       0.61353 /  0.31 (16696)
  hydrogen bonds       : bond        0.03270 /  2.07 (  379)
  hydrogen bonds       : angle       5.06762 /  3.48 ( 1002)

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

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

  3002 Ramachandran restraints generated.
    1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3002 Ramachandran restraints generated.
    1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 150
  time to evaluate  : 0.468 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  776 THR cc_start: 0.8923 (m) cc_final: 0.8610 (p)
REVERT: A  986 SER cc_start: 0.9104 (m) cc_final: 0.8789 (p)
REVERT: A 1017 GLU cc_start: 0.7863 (mp0) cc_final: 0.7386 (mp0)
REVERT: A 1109 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8351 (mt)
REVERT: A 1115 GLU cc_start: 0.7567 (pm20) cc_final: 0.7107 (pm20)
REVERT: A 1592 LEU cc_start: 0.7810 (tp) cc_final: 0.7581 (mt)
REVERT: A 1673 LEU cc_start: 0.8697 (tp) cc_final: 0.8404 (tp)
REVERT: A 2315 MET cc_start: 0.7160 (pmm) cc_final: 0.6767 (pmm)
  outliers start: 20
  outliers final: 12
  residues processed: 162
  average time/residue: 0.1064
  time to fit residues: 25.4257
Evaluate side-chains
  154 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 141
  time to evaluate  : 0.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1109 LEU
Chi-restraints excluded: chain A residue 1539 LYS
Chi-restraints excluded: chain A residue 1625 ILE
Chi-restraints excluded: chain A residue 1631 VAL
Chi-restraints excluded: chain A residue 1652 LEU
Chi-restraints excluded: chain A residue 1947 MET
Chi-restraints excluded: chain A residue 1959 LEU
Chi-restraints excluded: chain A residue 1982 LEU
Chi-restraints excluded: chain A residue 2124 THR
Chi-restraints excluded: chain A residue 2151 ILE
Chi-restraints excluded: chain A residue 2358 VAL
Chi-restraints excluded: chain A residue 2457 VAL
Chi-restraints excluded: chain A residue 2458 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 11 optimal weight:    8.9990
   chunk 44 optimal weight:    1.9990
   chunk 89 optimal weight:    0.5980
   chunk 5 optimal weight:    0.6980
   chunk 24 optimal weight:    0.5980
   chunk 114 optimal weight:    0.9990
   chunk 40 optimal weight:    4.9990
   chunk 142 optimal weight:    0.9990
   chunk 121 optimal weight:    1.9990
   chunk 93 optimal weight:    0.0000
   chunk 83 optimal weight:    1.9990
   overall best weight:    0.5786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A1216 HIS
A1405 HIS
** A1425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2391 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4255 r_free = 0.4255 target = 0.168068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.123623 restraints weight = 21416.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.123514 restraints weight = 14475.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.123112 restraints weight = 12428.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.123500 restraints weight = 13187.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.123866 restraints weight = 12038.143|
|-----------------------------------------------------------------------------|
r_work (final): 0.3703
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7710
moved from start:          0.1929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12328  Z= 0.124
  Angle     :  0.606   8.822  16696  Z= 0.306
  Chirality :  0.044   0.238   1946
  Planarity :  0.005   0.087   2107
  Dihedral  :  5.928 144.261   1633
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 9.48
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  9.06 %
    Favored  : 90.81 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 11.51 %
    Favored  : 87.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.37 %
    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: -1.63 (0.22), residues: 1501
  helix:  0.46 (0.28), residues: 364
  sheet: -1.12 (0.32), residues: 269
  loop : -1.81 (0.21), residues: 868

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 793 
 TYR   0.012   0.001   TYR A2064 
 PHE   0.028   0.001   PHE A1050 
 TRP   0.010   0.001   TRP A2426 
 HIS   0.008   0.001   HIS A2391 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00289 /  0.12 (12328)
  covalent geometry    : angle       0.60645 /  0.31 (16696)
  hydrogen bonds       : bond        0.03046 /  1.92 (  379)
  hydrogen bonds       : angle       4.94555 /  3.39 ( 1002)

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

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

  3002 Ramachandran restraints generated.
    1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3002 Ramachandran restraints generated.
    1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 150
  time to evaluate  : 0.499 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  773 LYS cc_start: 0.9239 (mmmt) cc_final: 0.8739 (mtmt)
REVERT: A  986 SER cc_start: 0.9029 (m) cc_final: 0.8722 (p)
REVERT: A 1017 GLU cc_start: 0.7803 (mp0) cc_final: 0.7318 (mp0)
REVERT: A 1050 PHE cc_start: 0.4724 (p90) cc_final: 0.4277 (p90)
REVERT: A 1109 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8315 (mt)
REVERT: A 1115 GLU cc_start: 0.7572 (pm20) cc_final: 0.7188 (pm20)
REVERT: A 1673 LEU cc_start: 0.8655 (tp) cc_final: 0.8336 (tt)
REVERT: A 2315 MET cc_start: 0.7260 (pmm) cc_final: 0.6924 (pmm)
  outliers start: 19
  outliers final: 15
  residues processed: 159
  average time/residue: 0.1043
  time to fit residues: 24.7271
Evaluate side-chains
  155 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 139
  time to evaluate  : 0.488 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1109 LEU
Chi-restraints excluded: chain A residue 1288 MET
Chi-restraints excluded: chain A residue 1539 LYS
Chi-restraints excluded: chain A residue 1592 LEU
Chi-restraints excluded: chain A residue 1625 ILE
Chi-restraints excluded: chain A residue 1631 VAL
Chi-restraints excluded: chain A residue 1652 LEU
Chi-restraints excluded: chain A residue 1788 MET
Chi-restraints excluded: chain A residue 1947 MET
Chi-restraints excluded: chain A residue 1959 LEU
Chi-restraints excluded: chain A residue 1982 LEU
Chi-restraints excluded: chain A residue 2124 THR
Chi-restraints excluded: chain A residue 2151 ILE
Chi-restraints excluded: chain A residue 2358 VAL
Chi-restraints excluded: chain A residue 2457 VAL
Chi-restraints excluded: chain A residue 2458 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 105 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   chunk 95 optimal weight:    0.0040
   chunk 23 optimal weight:    0.7980
   chunk 130 optimal weight:    6.9990
   chunk 46 optimal weight:    0.7980
   chunk 66 optimal weight:    1.9990
   chunk 63 optimal weight:    0.7980
   chunk 106 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 136 optimal weight:    5.9990
   overall best weight:    0.6792

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A1039 HIS
** A1425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.163761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.114497 restraints weight = 21497.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.117349 restraints weight = 15190.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.117300 restraints weight = 12566.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.117971 restraints weight = 11788.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.118342 restraints weight = 11695.516|
|-----------------------------------------------------------------------------|
r_work (final): 0.3604
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
moved from start:          0.2147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  12328  Z= 0.135
  Angle     :  0.618   9.345  16696  Z= 0.311
  Chirality :  0.044   0.245   1946
  Planarity :  0.005   0.088   2107
  Dihedral  :  5.786 136.070   1633
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 10.13
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  9.26 %
    Favored  : 90.61 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 12.55 %
    Favored  : 85.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.37 %
    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: -1.63 (0.22), residues: 1501
  helix:  0.49 (0.29), residues: 364
  sheet: -1.18 (0.31), residues: 269
  loop : -1.80 (0.21), residues: 868

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 793 
 TYR   0.011   0.001   TYR A1649 
 PHE   0.022   0.001   PHE A1050 
 TRP   0.010   0.001   TRP A2426 
 HIS   0.005   0.001   HIS A1574 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00317 /  0.13 (12328)
  covalent geometry    : angle       0.61836 /  0.31 (16696)
  hydrogen bonds       : bond        0.03076 /  1.93 (  379)
  hydrogen bonds       : angle       4.93554 /  3.40 ( 1002)

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

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

  3002 Ramachandran restraints generated.
    1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3002 Ramachandran restraints generated.
    1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 147
  time to evaluate  : 0.478 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  773 LYS cc_start: 0.8983 (mmmt) cc_final: 0.8344 (mtmt)
REVERT: A  986 SER cc_start: 0.9214 (m) cc_final: 0.8880 (p)
REVERT: A 1017 GLU cc_start: 0.7911 (mp0) cc_final: 0.7534 (mp0)
REVERT: A 1050 PHE cc_start: 0.4763 (p90) cc_final: 0.4378 (p90)
REVERT: A 1109 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8429 (mt)
REVERT: A 1115 GLU cc_start: 0.7699 (pm20) cc_final: 0.7304 (pm20)
REVERT: A 1592 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7520 (tp)
REVERT: A 1985 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7207 (mp)
  outliers start: 22
  outliers final: 16
  residues processed: 160
  average time/residue: 0.0917
  time to fit residues: 22.3630
Evaluate side-chains
  161 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 142
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1109 LEU
Chi-restraints excluded: chain A residue 1288 MET
Chi-restraints excluded: chain A residue 1343 THR
Chi-restraints excluded: chain A residue 1519 VAL
Chi-restraints excluded: chain A residue 1539 LYS
Chi-restraints excluded: chain A residue 1592 LEU
Chi-restraints excluded: chain A residue 1625 ILE
Chi-restraints excluded: chain A residue 1631 VAL
Chi-restraints excluded: chain A residue 1652 LEU
Chi-restraints excluded: chain A residue 1788 MET
Chi-restraints excluded: chain A residue 1947 MET
Chi-restraints excluded: chain A residue 1959 LEU
Chi-restraints excluded: chain A residue 1982 LEU
Chi-restraints excluded: chain A residue 1985 LEU
Chi-restraints excluded: chain A residue 2124 THR
Chi-restraints excluded: chain A residue 2151 ILE
Chi-restraints excluded: chain A residue 2358 VAL
Chi-restraints excluded: chain A residue 2457 VAL
Chi-restraints excluded: chain A residue 2458 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 106 optimal weight:    3.9990
   chunk 122 optimal weight:    0.6980
   chunk 91 optimal weight:    0.0870
   chunk 136 optimal weight:    4.9990
   chunk 149 optimal weight:    0.8980
   chunk 74 optimal weight:    1.9990
   chunk 139 optimal weight:    0.7980
   chunk 135 optimal weight:    0.9980
   chunk 56 optimal weight:    1.9990
   chunk 3 optimal weight:    6.9990
   chunk 12 optimal weight:    6.9990
   overall best weight:    0.6958

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A1062 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4252 r_free = 0.4252 target = 0.167450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.122388 restraints weight = 20944.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.121303 restraints weight = 15967.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.121883 restraints weight = 13413.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.122104 restraints weight = 13846.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.122503 restraints weight = 12093.874|
|-----------------------------------------------------------------------------|
r_work (final): 0.3679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7749
moved from start:          0.2259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12328  Z= 0.135
  Angle     :  0.621   9.328  16696  Z= 0.310
  Chirality :  0.044   0.250   1946
  Planarity :  0.005   0.091   2107
  Dihedral  :  5.639 125.377   1633
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  8.79 %
    Favored  : 91.07 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 13.81 %
    Favored  : 84.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.37 %
    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: -1.61 (0.22), residues: 1501
  helix:  0.51 (0.29), residues: 365
  sheet: -1.22 (0.31), residues: 268
  loop : -1.77 (0.21), residues: 868

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1847 
 TYR   0.010   0.001   TYR A1649 
 PHE   0.027   0.001   PHE A1026 
 TRP   0.010   0.001   TRP A2426 
 HIS   0.005   0.001   HIS A1998 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00317 /  0.13 (12328)
  covalent geometry    : angle       0.62066 /  0.31 (16696)
  hydrogen bonds       : bond        0.03046 /  1.91 (  379)
  hydrogen bonds       : angle       4.87387 /  3.35 ( 1002)

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

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

  3002 Ramachandran restraints generated.
    1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3002 Ramachandran restraints generated.
    1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 142
  time to evaluate  : 0.407 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  986 SER cc_start: 0.9182 (m) cc_final: 0.8850 (p)
REVERT: A 1017 GLU cc_start: 0.8127 (mp0) cc_final: 0.7643 (mp0)
REVERT: A 1050 PHE cc_start: 0.4527 (p90) cc_final: 0.4265 (p90)
REVERT: A 1057 MET cc_start: 0.7638 (mmm) cc_final: 0.6567 (tmm)
REVERT: A 1109 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8418 (mt)
REVERT: A 1115 GLU cc_start: 0.7652 (pm20) cc_final: 0.7280 (pm20)
REVERT: A 1168 MET cc_start: 0.8437 (mmm) cc_final: 0.8174 (mmp)
REVERT: A 1592 LEU cc_start: 0.7959 (tp) cc_final: 0.7602 (tp)
REVERT: A 1985 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7274 (mp)
  outliers start: 22
  outliers final: 17
  residues processed: 155
  average time/residue: 0.0948
  time to fit residues: 22.1010
Evaluate side-chains
  158 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 139
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1109 LEU
Chi-restraints excluded: chain A residue 1192 ILE
Chi-restraints excluded: chain A residue 1288 MET
Chi-restraints excluded: chain A residue 1343 THR
Chi-restraints excluded: chain A residue 1519 VAL
Chi-restraints excluded: chain A residue 1539 LYS
Chi-restraints excluded: chain A residue 1625 ILE
Chi-restraints excluded: chain A residue 1631 VAL
Chi-restraints excluded: chain A residue 1652 LEU
Chi-restraints excluded: chain A residue 1788 MET
Chi-restraints excluded: chain A residue 1947 MET
Chi-restraints excluded: chain A residue 1959 LEU
Chi-restraints excluded: chain A residue 1982 LEU
Chi-restraints excluded: chain A residue 1985 LEU
Chi-restraints excluded: chain A residue 2124 THR
Chi-restraints excluded: chain A residue 2151 ILE
Chi-restraints excluded: chain A residue 2358 VAL
Chi-restraints excluded: chain A residue 2457 VAL
Chi-restraints excluded: chain A residue 2458 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 89 optimal weight:    0.2980
   chunk 131 optimal weight:    5.9990
   chunk 43 optimal weight:    0.5980
   chunk 39 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9990
   chunk 152 optimal weight:    1.9990
   chunk 26 optimal weight:    6.9990
   chunk 62 optimal weight:    0.9990
   chunk 150 optimal weight:    0.5980
   chunk 72 optimal weight:    0.9990
   chunk 71 optimal weight:    4.9990
   overall best weight:    0.6984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A1062 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2453 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.163634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.119222 restraints weight = 21338.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.119805 restraints weight = 15200.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.119544 restraints weight = 13035.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.119626 restraints weight = 13424.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.119685 restraints weight = 12182.279|
|-----------------------------------------------------------------------------|
r_work (final): 0.3627
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7698
moved from start:          0.2412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  12328  Z= 0.135
  Angle     :  0.619   7.720  16696  Z= 0.311
  Chirality :  0.044   0.226   1946
  Planarity :  0.005   0.099   2107
  Dihedral  :  5.544 117.965   1633
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 9.44
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  9.39 %
    Favored  : 90.47 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 13.88 %
    Favored  : 84.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.37 %
    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 (0.22), residues: 1501
  helix:  0.52 (0.29), residues: 365
  sheet: -1.20 (0.32), residues: 268
  loop : -1.77 (0.21), residues: 868

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 793 
 TYR   0.010   0.001   TYR A1649 
 PHE   0.017   0.001   PHE A1050 
 TRP   0.010   0.001   TRP A2426 
 HIS   0.005   0.001   HIS A1574 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00320 /  0.14 (12328)
  covalent geometry    : angle       0.61893 /  0.31 (16696)
  hydrogen bonds       : bond        0.03055 /  1.92 (  379)
  hydrogen bonds       : angle       4.83938 /  3.33 ( 1002)

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

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

  3002 Ramachandran restraints generated.
    1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3002 Ramachandran restraints generated.
    1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 143
  time to evaluate  : 0.463 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  986 SER cc_start: 0.9218 (m) cc_final: 0.8902 (p)
REVERT: A  987 LEU cc_start: 0.7184 (mp) cc_final: 0.6802 (mp)
REVERT: A 1017 GLU cc_start: 0.8214 (mp0) cc_final: 0.7727 (mp0)
REVERT: A 1050 PHE cc_start: 0.4504 (p90) cc_final: 0.4298 (p90)
REVERT: A 1109 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8458 (mt)
REVERT: A 1115 GLU cc_start: 0.7670 (pm20) cc_final: 0.7261 (pm20)
REVERT: A 1551 LYS cc_start: 0.8719 (tptt) cc_final: 0.8404 (ttmm)
REVERT: A 1592 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7568 (tp)
REVERT: A 1985 LEU cc_start: 0.7502 (OUTLIER) cc_final: 0.7180 (mp)
  outliers start: 25
  outliers final: 15
  residues processed: 156
  average time/residue: 0.1026
  time to fit residues: 24.0646
Evaluate side-chains
  161 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 143
  time to evaluate  : 0.531 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1109 LEU
Chi-restraints excluded: chain A residue 1192 ILE
Chi-restraints excluded: chain A residue 1343 THR
Chi-restraints excluded: chain A residue 1519 VAL
Chi-restraints excluded: chain A residue 1539 LYS
Chi-restraints excluded: chain A residue 1592 LEU
Chi-restraints excluded: chain A residue 1625 ILE
Chi-restraints excluded: chain A residue 1631 VAL
Chi-restraints excluded: chain A residue 1652 LEU
Chi-restraints excluded: chain A residue 1788 MET
Chi-restraints excluded: chain A residue 1947 MET
Chi-restraints excluded: chain A residue 1982 LEU
Chi-restraints excluded: chain A residue 1985 LEU
Chi-restraints excluded: chain A residue 2124 THR
Chi-restraints excluded: chain A residue 2151 ILE
Chi-restraints excluded: chain A residue 2358 VAL
Chi-restraints excluded: chain A residue 2457 VAL
Chi-restraints excluded: chain A residue 2458 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 111 optimal weight:    0.0010
   chunk 10 optimal weight:    0.0980
   chunk 30 optimal weight:    0.8980
   chunk 146 optimal weight:    0.5980
   chunk 14 optimal weight:    2.9990
   chunk 24 optimal weight:    0.2980
   chunk 54 optimal weight:    0.6980
   chunk 87 optimal weight:    0.0370
   chunk 137 optimal weight:    8.9990
   chunk 81 optimal weight:    0.0470
   chunk 13 optimal weight:    0.7980
   overall best weight:    0.0962

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A1062 ASN
A1425 GLN
** A2053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4306 r_free = 0.4306 target = 0.172248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.124183 restraints weight = 21054.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.127981 restraints weight = 15046.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.128084 restraints weight = 11876.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.128889 restraints weight = 11136.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.129150 restraints weight = 10949.676|
|-----------------------------------------------------------------------------|
r_work (final): 0.3771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7633
moved from start:          0.2386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  12328  Z= 0.099
  Angle     :  0.595  11.319  16696  Z= 0.297
  Chirality :  0.043   0.184   1946
  Planarity :  0.005   0.100   2107
  Dihedral  :  5.211 107.943   1633
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  8.46 %
    Favored  : 91.41 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 14.92 %
    Favored  : 84.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.37 %
    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: -1.41 (0.22), residues: 1501
  helix:  0.78 (0.29), residues: 362
  sheet: -1.11 (0.32), residues: 266
  loop : -1.69 (0.21), residues: 873

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1847 
 TYR   0.008   0.001   TYR A1992 
 PHE   0.031   0.001   PHE A1026 
 TRP   0.009   0.001   TRP A1295 
 HIS   0.004   0.001   HIS A1998 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00214 /  0.10 (12328)
  covalent geometry    : angle       0.59534 /  0.30 (16696)
  hydrogen bonds       : bond        0.02703 /  1.70 (  379)
  hydrogen bonds       : angle       4.69812 /  3.20 ( 1002)

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

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

  3002 Ramachandran restraints generated.
    1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3002 Ramachandran restraints generated.
    1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 163
  time to evaluate  : 0.519 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  773 LYS cc_start: 0.9039 (mmmt) cc_final: 0.8297 (mtmt)
REVERT: A  986 SER cc_start: 0.9149 (m) cc_final: 0.8812 (p)
REVERT: A  987 LEU cc_start: 0.7055 (mp) cc_final: 0.6713 (mp)
REVERT: A 1014 GLU cc_start: 0.7754 (tp30) cc_final: 0.7385 (tp30)
REVERT: A 1017 GLU cc_start: 0.8179 (mp0) cc_final: 0.7667 (mp0)
REVERT: A 1057 MET cc_start: 0.7933 (mmm) cc_final: 0.6845 (tmm)
REVERT: A 1115 GLU cc_start: 0.7519 (pm20) cc_final: 0.7108 (pm20)
REVERT: A 1420 ASP cc_start: 0.8045 (t0) cc_final: 0.7751 (t0)
REVERT: A 1592 LEU cc_start: 0.7809 (tp) cc_final: 0.7593 (mt)
REVERT: A 2263 LEU cc_start: 0.6922 (tt) cc_final: 0.6499 (tt)
REVERT: A 2335 LEU cc_start: 0.7381 (tp) cc_final: 0.7012 (mt)
  outliers start: 14
  outliers final: 7
  residues processed: 170
  average time/residue: 0.1256
  time to fit residues: 31.3679
Evaluate side-chains
  151 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 144
  time to evaluate  : 0.503 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1343 THR
Chi-restraints excluded: chain A residue 1519 VAL
Chi-restraints excluded: chain A residue 1947 MET
Chi-restraints excluded: chain A residue 2107 VAL
Chi-restraints excluded: chain A residue 2151 ILE
Chi-restraints excluded: chain A residue 2359 VAL
Chi-restraints excluded: chain A residue 2457 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 139 optimal weight:    0.7980
   chunk 132 optimal weight:    0.8980
   chunk 144 optimal weight:    2.9990
   chunk 151 optimal weight:    0.7980
   chunk 74 optimal weight:    0.6980
   chunk 122 optimal weight:    4.9990
   chunk 54 optimal weight:    0.0870
   chunk 47 optimal weight:    0.6980
   chunk 92 optimal weight:    0.9980
   chunk 110 optimal weight:    0.0870
   overall best weight:    0.4736

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A1039 HIS
** A1062 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1571 HIS
** A2053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2178 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.166246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.117343 restraints weight = 21378.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.118804 restraints weight = 17539.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.119622 restraints weight = 13748.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.120016 restraints weight = 12762.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.120187 restraints weight = 12525.209|
|-----------------------------------------------------------------------------|
r_work (final): 0.3648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7701
moved from start:          0.2565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12328  Z= 0.118
  Angle     :  0.627  10.828  16696  Z= 0.310
  Chirality :  0.044   0.194   1946
  Planarity :  0.005   0.108   2107
  Dihedral  :  5.234 105.019   1633
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  8.99 %
    Favored  : 90.87 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 15.81 %
    Favored  : 83.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.37 %
    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: -1.42 (0.22), residues: 1501
  helix:  0.67 (0.29), residues: 365
  sheet: -1.18 (0.31), residues: 271
  loop : -1.62 (0.22), residues: 865

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG A2176 
 TYR   0.012   0.001   TYR A1992 
 PHE   0.014   0.001   PHE A2324 
 TRP   0.008   0.001   TRP A1705 
 HIS   0.005   0.001   HIS A1998 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00273 /  0.12 (12328)
  covalent geometry    : angle       0.62710 /  0.31 (16696)
  hydrogen bonds       : bond        0.02841 /  1.79 (  379)
  hydrogen bonds       : angle       4.67452 /  3.20 ( 1002)

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

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

  3002 Ramachandran restraints generated.
    1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3002 Ramachandran restraints generated.
    1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 144
  time to evaluate  : 0.502 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  773 LYS cc_start: 0.9052 (mmmt) cc_final: 0.8306 (mtmt)
REVERT: A  986 SER cc_start: 0.9205 (m) cc_final: 0.8850 (p)
REVERT: A  987 LEU cc_start: 0.7150 (mp) cc_final: 0.6734 (mp)
REVERT: A 1014 GLU cc_start: 0.7817 (tp30) cc_final: 0.7513 (tp30)
REVERT: A 1017 GLU cc_start: 0.8120 (mp0) cc_final: 0.7601 (mp0)
REVERT: A 1057 MET cc_start: 0.7941 (mmm) cc_final: 0.6780 (tmm)
REVERT: A 1115 GLU cc_start: 0.7574 (pm20) cc_final: 0.7179 (pm20)
REVERT: A 1592 LEU cc_start: 0.7939 (tp) cc_final: 0.7685 (mt)
REVERT: A 2263 LEU cc_start: 0.7026 (tt) cc_final: 0.6732 (tt)
  outliers start: 10
  outliers final: 8
  residues processed: 151
  average time/residue: 0.0980
  time to fit residues: 22.1423
Evaluate side-chains
  149 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 141
  time to evaluate  : 0.484 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1343 THR
Chi-restraints excluded: chain A residue 1519 VAL
Chi-restraints excluded: chain A residue 1631 VAL
Chi-restraints excluded: chain A residue 1947 MET
Chi-restraints excluded: chain A residue 2107 VAL
Chi-restraints excluded: chain A residue 2151 ILE
Chi-restraints excluded: chain A residue 2439 LEU
Chi-restraints excluded: chain A residue 2457 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 28 optimal weight:    5.9990
   chunk 55 optimal weight:    0.8980
   chunk 41 optimal weight:    0.5980
   chunk 81 optimal weight:    0.5980
   chunk 20 optimal weight:    0.8980
   chunk 139 optimal weight:    0.9980
   chunk 113 optimal weight:    0.9990
   chunk 1 optimal weight:    0.0060
   chunk 137 optimal weight:    2.9990
   chunk 118 optimal weight:    2.9990
   chunk 96 optimal weight:    1.9990
   overall best weight:    0.5996

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A1062 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4272 r_free = 0.4272 target = 0.169398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.123292 restraints weight = 21304.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.124459 restraints weight = 15411.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.124294 restraints weight = 12711.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.124423 restraints weight = 12625.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.124736 restraints weight = 12145.309|
|-----------------------------------------------------------------------------|
r_work (final): 0.3712
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7709
moved from start:          0.2615

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12328  Z= 0.128
  Angle     :  0.635  10.644  16696  Z= 0.314
  Chirality :  0.044   0.168   1946
  Planarity :  0.005   0.111   2107
  Dihedral  :  5.247 102.845   1633
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 9.27
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  9.26 %
    Favored  : 90.61 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 15.81 %
    Favored  : 83.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.37 %
    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: -1.45 (0.22), residues: 1501
  helix:  0.61 (0.29), residues: 366
  sheet: -1.16 (0.32), residues: 266
  loop : -1.65 (0.21), residues: 869

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A2176 
 TYR   0.011   0.001   TYR A1992 
 PHE   0.026   0.001   PHE A1026 
 TRP   0.008   0.001   TRP A2426 
 HIS   0.005   0.001   HIS A1998 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00298 /  0.13 (12328)
  covalent geometry    : angle       0.63461 /  0.31 (16696)
  hydrogen bonds       : bond        0.02912 /  1.84 (  379)
  hydrogen bonds       : angle       4.68850 /  3.22 ( 1002)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2167.14 seconds
wall clock time: 38 minutes 13.27 seconds (2293.27 seconds total)