Starting phenix.real_space_refine
on Wed Jan 14 03:40:29 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tzh_41759/01_2026/8tzh_41759.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tzh_41759/01_2026/8tzh_41759.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8tzh_41759/01_2026/8tzh_41759.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tzh_41759/01_2026/8tzh_41759.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tzh_41759/01_2026/8tzh_41759.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tzh_41759/01_2026/8tzh_41759.cif"
  }
  resolution = 3.9
  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=   0.012
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      62      5.16       5
     C    7440      2.51       5
     N    1973      2.21       5
     O    2115      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11592
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "B"
      Number of atoms: 926
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 926
          Classifications: {'peptide': 121}
          Link IDs: {'PTRANS': 4, 'TRANS': 116}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 10610
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1485, 10610
          Classifications: {'peptide': 1485}
          Incomplete info: {'truncation_to_alanine': 308}
          Link IDs: {'PTRANS': 68, 'TRANS': 1416}
          Chain breaks: 38
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 1229
          Unresolved non-hydrogen angles: 1494
          Unresolved non-hydrogen dihedrals: 1021
          Unresolved non-hydrogen chiralities: 60
          Planarities with less than four sites: {'TYR:plan': 6, 'PHE:plan': 15, 'ASP:plan': 16, 'GLU:plan': 56, 'GLN:plan1': 31, 'HIS:plan': 4, 'ASN:plan1': 20, 'ARG:plan': 25}
          Unresolved non-hydrogen planarities: 732
    Chain: "A"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 56
          Unusual residues: {'A1N': 1, 'GDP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 2.74, per 1000 atoms: 0.24
  Number of scatterers: 11592
  At special positions: 0
  Unit cell: (106.59, 96.305, 145.86, 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      62     16.00
     P       2     15.00
     O    2115      8.00
     N    1973      7.00
     C    7440      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.95
  Conformation dependent library (CDL) restraints added in 560.4 milliseconds
  

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3060

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 18 sheets defined
      36.9% alpha, 10.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.53
  Creating SS restraints...
    Processing helix  chain 'B' and resid 51 through 60
      removed outlier: 3.624A  pdb=" N   LEU B  55 " --> pdb=" O   THR B  51 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 61 through 70
    Processing helix  chain 'B' and resid 84 through 93
    Processing helix  chain 'B' and resid 94 through 105
      removed outlier: 3.659A  pdb=" N   VAL B  98 " --> pdb=" O   HIS B  94 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 117 through 125
    Processing helix  chain 'B' and resid 127 through 136
    Processing helix  chain 'B' and resid 150 through 159
    Processing helix  chain 'B' and resid 160 through 169
      removed outlier: 3.676A  pdb=" N   VAL B 166 " --> pdb=" O   ASP B 162 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   LYS B 169 " --> pdb=" O   GLU B 165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 628 through 638
      removed outlier: 4.240A  pdb=" N   VAL A 632 " --> pdb=" O   ALA A 628 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 642 through 648
    Processing helix  chain 'A' and resid 650 through 650
      No H-bonds generated for 'chain 'A' and resid 650 through 650'
    Processing helix  chain 'A' and resid 651 through 655
      removed outlier: 3.776A  pdb=" N   ILE A 655 " --> pdb=" O   THR A 651 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 651 through 655'
    Processing helix  chain 'A' and resid 670 through 681
    Processing helix  chain 'A' and resid 689 through 700
      removed outlier: 3.568A  pdb=" N   LEU A 694 " --> pdb=" O   GLN A 690 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 709 through 719
      removed outlier: 4.360A  pdb=" N   GLN A 719 " --> pdb=" O   ARG A 715 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 721 through 731
    Processing helix  chain 'A' and resid 744 through 751
    Processing helix  chain 'A' and resid 754 through 764
      removed outlier: 3.759A  pdb=" N   VAL A 758 " --> pdb=" O   SER A 754 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 767 through 781
      removed outlier: 4.174A  pdb=" N   GLY A 780 " --> pdb=" O   THR A 776 " (cutoff:3.500A)
      removed outlier: 4.269A  pdb=" N   LYS A 781 " --> pdb=" O   ILE A 777 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 785 through 795
    Processing helix  chain 'A' and resid 814 through 819
      removed outlier: 3.730A  pdb=" N   GLY A 819 " --> pdb=" O   SER A 816 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 835 through 847
    Processing helix  chain 'A' and resid 1008 through 1013
      removed outlier: 4.072A  pdb=" N   HIS A1012 " --> pdb=" O   HIS A1009 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1027 through 1034
      removed outlier: 3.952A  pdb=" N   CYS A1031 " --> pdb=" O   PRO A1027 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1053 through 1057
    Processing helix  chain 'A' and resid 1101 through 1106
    Processing helix  chain 'A' and resid 1189 through 1195
      removed outlier: 3.630A  pdb=" N   LEU A1193 " --> pdb=" O   PRO A1189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1213 through 1218
      removed outlier: 3.650A  pdb=" N   TRP A1217 " --> pdb=" O   GLY A1213 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   LYS A1218 " --> pdb=" O   PRO A1214 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1213 through 1218'
    Processing helix  chain 'A' and resid 1261 through 1267
    Processing helix  chain 'A' and resid 1285 through 1291
    Processing helix  chain 'A' and resid 1315 through 1328
    Processing helix  chain 'A' and resid 1347 through 1354
    Processing helix  chain 'A' and resid 1398 through 1408
      removed outlier: 4.341A  pdb=" N   SER A1403 " --> pdb=" O   GLU A1400 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   THR A1404 " --> pdb=" O   PHE A1401 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   HIS A1405 " --> pdb=" O   TYR A1402 " (cutoff:3.500A)
      Proline residue:  A1406  - end of helix
    Processing helix  chain 'A' and resid 1420 through 1423
    Processing helix  chain 'A' and resid 1424 through 1431
      removed outlier: 3.795A  pdb=" N   VAL A1428 " --> pdb=" O   GLY A1424 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   ASP A1429 " --> pdb=" O   GLN A1425 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1431 through 1442
      removed outlier: 3.904A  pdb=" N   LEU A1435 " --> pdb=" O   MET A1431 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1465 through 1473
      removed outlier: 3.961A  pdb=" N   ILE A1469 " --> pdb=" O   CYS A1465 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1496 through 1510
    Processing helix  chain 'A' and resid 1525 through 1540
      removed outlier: 3.893A  pdb=" N   LYS A1539 " --> pdb=" O   LEU A1535 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   ASN A1540 " --> pdb=" O   SER A1536 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1550 through 1557
      removed outlier: 3.804A  pdb=" N   LEU A1554 " --> pdb=" O   ARG A1550 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   VAL A1557 " --> pdb=" O   LEU A1553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1567 through 1579
      removed outlier: 4.148A  pdb=" N   HIS A1571 " --> pdb=" O   ASN A1567 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1599 through 1607
      removed outlier: 3.734A  pdb=" N   LEU A1603 " --> pdb=" O   GLU A1599 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1608 through 1612
    Processing helix  chain 'A' and resid 1645 through 1657
      removed outlier: 4.425A  pdb=" N   LYS A1651 " --> pdb=" O   SER A1647 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1704 through 1712
      removed outlier: 4.434A  pdb=" N   ASN A1710 " --> pdb=" O   SER A1706 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1770 through 1792
    Processing helix  chain 'A' and resid 1828 through 1835
    Processing helix  chain 'A' and resid 1852 through 1856
    Processing helix  chain 'A' and resid 1915 through 1925
      removed outlier: 3.567A  pdb=" N   GLN A1919 " --> pdb=" O   ARG A1915 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1954 through 1962
    Processing helix  chain 'A' and resid 1967 through 1988
      removed outlier: 3.972A  pdb=" N   HIS A1972 " --> pdb=" O   ARG A1968 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2053 through 2069
      removed outlier: 3.662A  pdb=" N   TYR A2057 " --> pdb=" O   GLN A2053 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2079 through 2084
      removed outlier: 3.658A  pdb=" N   PHE A2083 " --> pdb=" O   PRO A2080 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2094 through 2100
    Processing helix  chain 'A' and resid 2107 through 2115
      removed outlier: 3.731A  pdb=" N   LYS A2112 " --> pdb=" O   GLU A2108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2124 through 2133
    Processing helix  chain 'A' and resid 2134 through 2139
      removed outlier: 3.641A  pdb=" N   VAL A2138 " --> pdb=" O   SER A2134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2346 through 2351
      removed outlier: 3.668A  pdb=" N   SER A2350 " --> pdb=" O   TYR A2346 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2389 through 2396
    Processing helix  chain 'A' and resid 2499 through 2522
      removed outlier: 4.011A  pdb=" N   ARG A2522 " --> pdb=" O   ALA A2518 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 796 through 797
    Processing sheet with id=AA2, first strand: chain 'A' and resid 986 through 988
      removed outlier: 6.638A  pdb=" N   LEU A 987 " --> pdb=" O   GLU A1017 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1063 through 1065
      removed outlier: 7.741A  pdb=" N   LEU A1063 " --> pdb=" O   ASN A1089 " (cutoff:3.500A)
      removed outlier: 6.503A  pdb=" N   PHE A1088 " --> pdb=" O   ILE A1113 " (cutoff:3.500A)
      removed outlier: 6.289A  pdb=" N   ILE A1133 " --> pdb=" O   LEU A1112 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1177 through 1179
      removed outlier: 3.779A  pdb=" N   ASP A1202 " --> pdb=" O   LEU A1178 " (cutoff:3.500A)
      removed outlier: 7.146A  pdb=" N   LEU A1250 " --> pdb=" O   ASP A1274 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1329 through 1331
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1335 through 1339
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1415 through 1416
      removed outlier: 7.070A  pdb=" N   TYR A1415 " --> pdb=" O   ILE A1448 " (cutoff:3.500A)
      removed outlier: 7.607A  pdb=" N   VAL A1450 " --> pdb=" O   TYR A1415 " (cutoff:3.500A)
      removed outlier: 6.464A  pdb=" N   VAL A1447 " --> pdb=" O   ASP A1484 " (cutoff:3.500A)
      removed outlier: 8.256A  pdb=" N   HIS A1486 " --> pdb=" O   VAL A1447 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   LEU A1449 " --> pdb=" O   HIS A1486 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1547 through 1549
    Processing sheet with id=AA9, first strand: chain 'A' and resid 1690 through 1694
      removed outlier: 6.891A  pdb=" N   TYR A1747 " --> pdb=" O   PRO A1768 " (cutoff:3.500A)
      removed outlier: 6.447A  pdb=" N   ALA A1746 " --> pdb=" O   TRP A1742 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 1840 through 1841
    Processing sheet with id=AB2, first strand: chain 'A' and resid 1884 through 1887
      removed outlier: 7.188A  pdb=" N   VAL A1893 " --> pdb=" O   LEU A1885 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   VAL A1946 " --> pdb=" O   LEU A1936 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 2000 through 2002
    Processing sheet with id=AB4, first strand: chain 'A' and resid 2140 through 2145
      removed outlier: 6.768A  pdb=" N   LEU A2140 " --> pdb=" O   ASP A2497 " (cutoff:3.500A)
      removed outlier: 6.365A  pdb=" N   ASP A2497 " --> pdb=" O   LEU A2140 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   ARG A2142 " --> pdb=" O   VAL A2495 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   TRP A2496 " --> pdb=" O   MET A2470 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   MET A2459 " --> pdb=" O   LEU A2471 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 2155 through 2156
      removed outlier: 4.097A  pdb=" N   TRP A2168 " --> pdb=" O   VAL A2156 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 2247 through 2249
      removed outlier: 3.547A  pdb=" N   CYS A2247 " --> pdb=" O   GLY A2266 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 2300 through 2304
      removed outlier: 3.852A  pdb=" N   CYS A2302 " --> pdb=" O   GLY A2318 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'A' and resid 2354 through 2359
      removed outlier: 3.595A  pdb=" N   TYR A2364 " --> pdb=" O   VAL A2358 " (cutoff:3.500A)
      removed outlier: 4.999A  pdb=" N   LYS A2367 " --> pdb=" O   VAL A2372 " (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   VAL A2372 " --> pdb=" O   LYS A2367 " (cutoff:3.500A)
      removed outlier: 5.941A  pdb=" N   ASP A2377 " --> pdb=" O   LEU A2383 " (cutoff:3.500A)
      removed outlier: 6.425A  pdb=" N   LEU A2383 " --> pdb=" O   ASP A2377 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'A' and resid 2414 through 2420
      removed outlier: 6.775A  pdb=" N   GLY A2428 " --> pdb=" O   LYS A2415 " (cutoff:3.500A)
      removed outlier: 4.635A  pdb=" N   LEU A2417 " --> pdb=" O   TRP A2426 " (cutoff:3.500A)
      removed outlier: 6.722A  pdb=" N   TRP A2426 " --> pdb=" O   LEU A2417 " (cutoff:3.500A)
      removed outlier: 4.866A  pdb=" N   LEU A2419 " --> pdb=" O   ALA A2424 " (cutoff:3.500A)
      removed outlier: 6.888A  pdb=" N   ALA A2424 " --> pdb=" O   LEU A2419 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   ARG A2446 " --> pdb=" O   LEU A2436 " (cutoff:3.500A)
      removed outlier: 6.349A  pdb=" N   ASP A2438 " --> pdb=" O   LEU A2444 " (cutoff:3.500A)
      removed outlier: 6.293A  pdb=" N   LEU A2444 " --> pdb=" O   ASP A2438 " (cutoff:3.500A)

    407 hydrogen bonds defined for protein.
    1107 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: 2.49

  Time building geometry restraints manager: 1.23 seconds

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

  Histogram of bond lengths:
        1.14 -     1.27: 1906
        1.27 -     1.41: 2706
        1.41 -     1.54: 7063
        1.54 -     1.68: 27
        1.68 -     1.82: 88
  Bond restraints: 11790
  Sorted by residual:
  bond pdb=" C11 A1N A2601 "
       pdb=" N4  A1N A2601 "
    ideal  model  delta    sigma   weight residual
    1.319  1.138  0.181 2.00e-02 2.50e+03 8.19e+01
  bond pdb=" C11 A1N A2601 "
       pdb=" C21 A1N A2601 "
    ideal  model  delta    sigma   weight residual
    1.428  1.309  0.119 2.00e-02 2.50e+03 3.51e+01
  bond pdb=" C20 A1N A2601 "
       pdb=" C21 A1N A2601 "
    ideal  model  delta    sigma   weight residual
    1.405  1.290  0.115 2.00e-02 2.50e+03 3.29e+01
  bond pdb=" C7  A1N A2601 "
       pdb=" C8  A1N A2601 "
    ideal  model  delta    sigma   weight residual
    1.409  1.297  0.112 2.00e-02 2.50e+03 3.13e+01
  bond pdb=" C7  A1N A2601 "
       pdb=" N3  A1N A2601 "
    ideal  model  delta    sigma   weight residual
    1.342  1.232  0.110 2.00e-02 2.50e+03 3.04e+01
  ... (remaining 11785 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.15: 15916
        3.15 -     6.30: 154
        6.30 -     9.46: 24
        9.46 -    12.61: 3
       12.61 -    15.76: 5
  Bond angle restraints: 16102
  Sorted by residual:
  angle pdb=" C   SER A1889 "
        pdb=" CA  SER A1889 "
        pdb=" CB  SER A1889 "
      ideal   model   delta    sigma   weight residual
     116.54  109.97    6.57 1.15e+00 7.56e-01 3.26e+01
  angle pdb=" C19 A1N A2601 "
        pdb=" C16 A1N A2601 "
        pdb=" O2  A1N A2601 "
      ideal   model   delta    sigma   weight residual
     117.13  102.39   14.74 3.00e+00 1.11e-01 2.41e+01
  angle pdb=" C21 A1N A2601 "
        pdb=" C11 A1N A2601 "
        pdb=" N4  A1N A2601 "
      ideal   model   delta    sigma   weight residual
     110.25  123.92  -13.67 3.00e+00 1.11e-01 2.08e+01
  angle pdb=" CA  LEU A2115 "
        pdb=" CB  LEU A2115 "
        pdb=" CG  LEU A2115 "
      ideal   model   delta    sigma   weight residual
     116.30  132.06  -15.76 3.50e+00 8.16e-02 2.03e+01
  angle pdb=" N   ASP A2017 "
        pdb=" CA  ASP A2017 "
        pdb=" C   ASP A2017 "
      ideal   model   delta    sigma   weight residual
     110.35  116.65   -6.30 1.40e+00 5.10e-01 2.02e+01
  ... (remaining 16097 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.74: 6873
       35.74 -    71.48: 122
       71.48 -   107.22: 11
      107.22 -   142.97: 2
      142.97 -   178.71: 2
  Dihedral angle restraints: 7010
    sinusoidal: 2352
      harmonic: 4658
  Sorted by residual:
  dihedral pdb=" O2B GDP A2602 "
           pdb=" O3A GDP A2602 "
           pdb=" PB  GDP A2602 "
           pdb=" PA  GDP A2602 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00    1.29  178.71     1      2.00e+01 2.50e-03 4.80e+01
  dihedral pdb=" CA  HIS B  94 "
           pdb=" C   HIS B  94 "
           pdb=" N   LEU B  95 "
           pdb=" CA  LEU B  95 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -153.09  -26.91     0      5.00e+00 4.00e-02 2.90e+01
  dihedral pdb=" CA  ARG A1941 "
           pdb=" C   ARG A1941 "
           pdb=" N   PRO A1942 "
           pdb=" CA  PRO A1942 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.62   25.38     0      5.00e+00 4.00e-02 2.58e+01
  ... (remaining 7007 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.061: 1698
       0.061 -    0.122: 280
       0.122 -    0.183: 26
       0.183 -    0.243: 1
       0.243 -    0.304: 2
  Chirality restraints: 2007
  Sorted by residual:
  chirality pdb=" CG  LEU A 635 "
            pdb=" CB  LEU A 635 "
            pdb=" CD1 LEU A 635 "
            pdb=" CD2 LEU A 635 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.29   -0.30 2.00e-01 2.50e+01 2.32e+00
  chirality pdb=" CA  ASP A2017 "
            pdb=" N   ASP A2017 "
            pdb=" C   ASP A2017 "
            pdb=" CB  ASP A2017 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.22e+00
  chirality pdb=" CB  ILE A1933 "
            pdb=" CA  ILE A1933 "
            pdb=" CG1 ILE A1933 "
            pdb=" CG2 ILE A1933 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.20 2.00e-01 2.50e+01 9.67e-01
  ... (remaining 2004 not shown)

  Planarity restraints: 2012
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A1941 "    0.090 5.00e-02 4.00e+02   1.37e-01 2.99e+01
        pdb=" N   PRO A1942 "   -0.237 5.00e-02 4.00e+02
        pdb=" CA  PRO A1942 "    0.073 5.00e-02 4.00e+02
        pdb=" CD  PRO A1942 "    0.073 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 676 "    0.019 2.00e-02 2.50e+03   2.04e-02 7.29e+00
        pdb=" CG  PHE A 676 "   -0.047 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 676 "    0.016 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 676 "    0.005 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 676 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 676 "    0.008 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 676 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 754 "    0.043 5.00e-02 4.00e+02   6.63e-02 7.04e+00
        pdb=" N   PRO A 755 "   -0.115 5.00e-02 4.00e+02
        pdb=" CA  PRO A 755 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO A 755 "    0.037 5.00e-02 4.00e+02
  ... (remaining 2009 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 865
        2.73 -     3.28: 12242
        3.28 -     3.82: 19040
        3.82 -     4.36: 21259
        4.36 -     4.90: 36277
  Nonbonded interactions: 89683
  Sorted by model distance:
  nonbonded pdb=" O   THR A2321 "
            pdb=" OG1 THR A2338 "
     model   vdw
     2.192 3.040
  nonbonded pdb=" OG1 THR A2246 "
            pdb=" O   LEU A2300 "
     model   vdw
     2.200 3.040
  nonbonded pdb=" O   LEU A 631 "
            pdb=" OG  SER A 634 "
     model   vdw
     2.214 3.040
  nonbonded pdb=" N   GLU B  96 "
            pdb=" OE1 GLU B  96 "
     model   vdw
     2.221 3.120
  nonbonded pdb=" OD1 ASN A1135 "
            pdb=" OG  SER A1159 "
     model   vdw
     2.223 3.040
  ... (remaining 89678 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.150
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     12.390
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.020
  Load rotamer database and sin/cos tables:1.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7437
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.181  11791  Z= 0.233
  Angle     :  0.841  15.761  16102  Z= 0.429
  Chirality :  0.045   0.304   2007
  Planarity :  0.005   0.137   2012
  Dihedral  : 15.562 178.706   3950
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 15.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.28 %
    Favored  : 91.72 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  : 18.29 %
    Favored  : 80.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.76 (0.22), residues: 1522
  helix:  0.52 (0.24), residues: 504
  sheet: -1.57 (0.34), residues: 223
  loop : -2.24 (0.21), residues: 795

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A2514 
 TYR   0.016   0.001   TYR A1992 
 PHE   0.047   0.002   PHE A 676 
 TRP   0.034   0.002   TRP A2426 
 HIS   0.008   0.001   HIS A 677 

Details of bonding type rmsd
  covalent geometry    : bond        0.00461 (11790)
  covalent geometry    : angle       0.84126 (16102)
  hydrogen bonds       : bond        0.16676 (  407)
  hydrogen bonds       : angle       6.95957 ( 1107)
  Misc. bond           : bond        0.00110 (    1)

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

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

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 119
  time to evaluate  : 0.426 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1402 TYR cc_start: 0.8066 (m-10) cc_final: 0.7333 (m-80)
REVERT: A 2017 ASP cc_start: 0.8806 (OUTLIER) cc_final: 0.8545 (p0)
  outliers start: 10
  outliers final: 5
  residues processed: 128
  average time/residue: 0.0871
  time to fit residues: 17.3925
Evaluate side-chains
  117 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 111
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1924 LEU
Chi-restraints excluded: chain A residue 1958 LEU
Chi-restraints excluded: chain A residue 2017 ASP
Chi-restraints excluded: chain A residue 2035 THR
Chi-restraints excluded: chain A residue 2096 VAL
Chi-restraints excluded: chain A residue 2357 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 98 optimal weight:    0.1980
   chunk 107 optimal weight:    0.3980
   chunk 10 optimal weight:    8.9990
   chunk 66 optimal weight:    1.9990
   chunk 130 optimal weight:    0.9980
   chunk 124 optimal weight:    0.9990
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    4.9990
   chunk 122 optimal weight:    0.4980
   chunk 91 optimal weight:    0.0050
   chunk 149 optimal weight:    1.9990
   overall best weight:    0.4194

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

Flipped N/Q/H residues before XYZ refinement:
** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 721 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 747 GLN
A 800 ASN
A1021 ASN
A1411 GLN
A1741 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.112569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.092729 restraints weight = 34049.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.092822 restraints weight = 23782.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.093295 restraints weight = 24001.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.094726 restraints weight = 17523.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.094767 restraints weight = 14024.625|
|-----------------------------------------------------------------------------|
r_work (final): 0.3593
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7399
moved from start:          0.0855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  11791  Z= 0.115
  Angle     :  0.657  11.520  16102  Z= 0.314
  Chirality :  0.044   0.243   2007
  Planarity :  0.005   0.098   2012
  Dihedral  :  7.541 145.702   1674
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 11.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.49 %
    Favored  : 92.51 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 18.29 %
    Favored  : 78.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.72 (0.22), residues: 1522
  helix:  0.48 (0.23), residues: 531
  sheet: -1.65 (0.35), residues: 212
  loop : -2.22 (0.22), residues: 779

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 793 
 TYR   0.015   0.001   TYR A1402 
 PHE   0.018   0.001   PHE A 676 
 TRP   0.017   0.001   TRP A2426 
 HIS   0.006   0.001   HIS B  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 (11790)
  covalent geometry    : angle       0.65692 (16102)
  hydrogen bonds       : bond        0.03553 (  407)
  hydrogen bonds       : angle       5.36385 ( 1107)
  Misc. bond           : bond        0.00244 (    1)

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

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

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 131
  time to evaluate  : 0.686 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  165 GLU cc_start: 0.9068 (mt-10) cc_final: 0.8864 (mt-10)
REVERT: A  761 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7886 (mm)
REVERT: A 1288 MET cc_start: 0.8296 (mmp) cc_final: 0.7981 (mmp)
  outliers start: 33
  outliers final: 14
  residues processed: 159
  average time/residue: 0.0807
  time to fit residues: 20.7236
Evaluate side-chains
  131 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 116
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  761 LEU
Chi-restraints excluded: chain A residue 1299 LEU
Chi-restraints excluded: chain A residue 1410 THR
Chi-restraints excluded: chain A residue 1767 VAL
Chi-restraints excluded: chain A residue 1954 SER
Chi-restraints excluded: chain A residue 1982 LEU
Chi-restraints excluded: chain A residue 2012 ILE
Chi-restraints excluded: chain A residue 2018 TYR
Chi-restraints excluded: chain A residue 2096 VAL
Chi-restraints excluded: chain A residue 2216 VAL
Chi-restraints excluded: chain A residue 2303 LEU
Chi-restraints excluded: chain A residue 2356 THR
Chi-restraints excluded: chain A residue 2396 VAL
Chi-restraints excluded: chain A residue 2416 THR
Chi-restraints excluded: chain A residue 2457 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 100 optimal weight:    0.9980
   chunk 106 optimal weight:    8.9990
   chunk 48 optimal weight:    6.9990
   chunk 87 optimal weight:    3.9990
   chunk 126 optimal weight:    0.7980
   chunk 10 optimal weight:    6.9990
   chunk 80 optimal weight:    8.9990
   chunk 128 optimal weight:    9.9990
   chunk 34 optimal weight:    5.9990
   chunk 78 optimal weight:    0.9990
   chunk 75 optimal weight:    2.9990
   overall best weight:    1.9586

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

Flipped N/Q/H residues before XYZ refinement:
** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 747 GLN
** A1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A2490 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.107447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.087560 restraints weight = 34733.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.088406 restraints weight = 24771.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.088815 restraints weight = 25099.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.089250 restraints weight = 17518.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.089498 restraints weight = 15880.977|
|-----------------------------------------------------------------------------|
r_work (final): 0.3493
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7557
moved from start:          0.1551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  11791  Z= 0.222
  Angle     :  0.724  12.521  16102  Z= 0.358
  Chirality :  0.047   0.286   2007
  Planarity :  0.005   0.075   2012
  Dihedral  :  7.045 145.270   1666
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 15.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.59 %
    Favored  : 90.41 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 20.78 %
    Favored  : 74.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -1.82 (0.22), residues: 1522
  helix:  0.46 (0.23), residues: 525
  sheet: -1.98 (0.34), residues: 219
  loop : -2.22 (0.22), residues: 778

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A2514 
 TYR   0.030   0.002   TYR A1733 
 PHE   0.016   0.002   PHE A1762 
 TRP   0.033   0.002   TRP A2426 
 HIS   0.013   0.002   HIS B  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00511 (11790)
  covalent geometry    : angle       0.72380 (16102)
  hydrogen bonds       : bond        0.03789 (  407)
  hydrogen bonds       : angle       5.32922 ( 1107)
  Misc. bond           : bond        0.00254 (    1)

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

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

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 118
  time to evaluate  : 0.457 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  761 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7899 (mm)
REVERT: A 2132 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8182 (mm)
REVERT: A 2426 TRP cc_start: 0.7650 (m-10) cc_final: 0.7169 (m-10)
REVERT: A 2444 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8352 (tt)
REVERT: A 2470 MET cc_start: 0.7531 (ptp) cc_final: 0.7212 (ptp)
REVERT: A 2521 MET cc_start: 0.8583 (mmp) cc_final: 0.8236 (mmp)
  outliers start: 48
  outliers final: 30
  residues processed: 161
  average time/residue: 0.0781
  time to fit residues: 20.3678
Evaluate side-chains
  142 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 109
  time to evaluate  : 0.488 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  132 GLU
Chi-restraints excluded: chain A residue  761 LEU
Chi-restraints excluded: chain A residue  796 LEU
Chi-restraints excluded: chain A residue 1080 VAL
Chi-restraints excluded: chain A residue 1299 LEU
Chi-restraints excluded: chain A residue 1339 ILE
Chi-restraints excluded: chain A residue 1392 VAL
Chi-restraints excluded: chain A residue 1410 THR
Chi-restraints excluded: chain A residue 1414 LEU
Chi-restraints excluded: chain A residue 1449 LEU
Chi-restraints excluded: chain A residue 1762 PHE
Chi-restraints excluded: chain A residue 1765 ILE
Chi-restraints excluded: chain A residue 1767 VAL
Chi-restraints excluded: chain A residue 1958 LEU
Chi-restraints excluded: chain A residue 1967 THR
Chi-restraints excluded: chain A residue 1982 LEU
Chi-restraints excluded: chain A residue 1986 HIS
Chi-restraints excluded: chain A residue 2012 ILE
Chi-restraints excluded: chain A residue 2018 TYR
Chi-restraints excluded: chain A residue 2035 THR
Chi-restraints excluded: chain A residue 2088 ILE
Chi-restraints excluded: chain A residue 2096 VAL
Chi-restraints excluded: chain A residue 2132 LEU
Chi-restraints excluded: chain A residue 2141 THR
Chi-restraints excluded: chain A residue 2216 VAL
Chi-restraints excluded: chain A residue 2301 MET
Chi-restraints excluded: chain A residue 2323 ILE
Chi-restraints excluded: chain A residue 2356 THR
Chi-restraints excluded: chain A residue 2370 SER
Chi-restraints excluded: chain A residue 2396 VAL
Chi-restraints excluded: chain A residue 2416 THR
Chi-restraints excluded: chain A residue 2444 LEU
Chi-restraints excluded: chain A residue 2457 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 146 optimal weight:    2.9990
   chunk 48 optimal weight:    4.9990
   chunk 129 optimal weight:    6.9990
   chunk 101 optimal weight:    0.9980
   chunk 56 optimal weight:    0.4980
   chunk 78 optimal weight:    0.9990
   chunk 85 optimal weight:    0.8980
   chunk 40 optimal weight:    4.9990
   chunk 3 optimal weight:    3.9990
   chunk 97 optimal weight:    0.9980
   chunk 42 optimal weight:    4.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
B  94 HIS
** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1486 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.109423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.089530 restraints weight = 34898.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.090098 restraints weight = 24902.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.090516 restraints weight = 26696.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.091311 restraints weight = 17678.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.091582 restraints weight = 15631.693|
|-----------------------------------------------------------------------------|
r_work (final): 0.3534
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7492
moved from start:          0.1616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  11791  Z= 0.130
  Angle     :  0.653  10.899  16102  Z= 0.317
  Chirality :  0.044   0.236   2007
  Planarity :  0.005   0.060   2012
  Dihedral  :  6.763 144.591   1666
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 12.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.15 %
    Favored  : 91.85 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 22.91 %
    Favored  : 73.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: 1522
  helix:  0.54 (0.23), residues: 530
  sheet: -1.90 (0.35), residues: 217
  loop : -2.16 (0.22), residues: 775

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1918 
 TYR   0.016   0.002   TYR A1733 
 PHE   0.031   0.001   PHE A 676 
 TRP   0.018   0.001   TRP A2426 
 HIS   0.007   0.001   HIS B  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 (11790)
  covalent geometry    : angle       0.65310 (16102)
  hydrogen bonds       : bond        0.03236 (  407)
  hydrogen bonds       : angle       5.07550 ( 1107)
  Misc. bond           : bond        0.00217 (    1)

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

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

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 125
  time to evaluate  : 0.465 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  761 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7816 (mm)
REVERT: A 2426 TRP cc_start: 0.7684 (m-10) cc_final: 0.7263 (m-10)
REVERT: A 2521 MET cc_start: 0.8559 (mmp) cc_final: 0.8267 (mmp)
  outliers start: 43
  outliers final: 28
  residues processed: 162
  average time/residue: 0.0808
  time to fit residues: 20.9237
Evaluate side-chains
  141 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 112
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   46 ASP
Chi-restraints excluded: chain B residue  132 GLU
Chi-restraints excluded: chain A residue  761 LEU
Chi-restraints excluded: chain A residue  796 LEU
Chi-restraints excluded: chain A residue 1080 VAL
Chi-restraints excluded: chain A residue 1177 ILE
Chi-restraints excluded: chain A residue 1299 LEU
Chi-restraints excluded: chain A residue 1339 ILE
Chi-restraints excluded: chain A residue 1410 THR
Chi-restraints excluded: chain A residue 1449 LEU
Chi-restraints excluded: chain A residue 1733 TYR
Chi-restraints excluded: chain A residue 1762 PHE
Chi-restraints excluded: chain A residue 1765 ILE
Chi-restraints excluded: chain A residue 1767 VAL
Chi-restraints excluded: chain A residue 1784 ILE
Chi-restraints excluded: chain A residue 1917 LEU
Chi-restraints excluded: chain A residue 1924 LEU
Chi-restraints excluded: chain A residue 1949 LEU
Chi-restraints excluded: chain A residue 1958 LEU
Chi-restraints excluded: chain A residue 1986 HIS
Chi-restraints excluded: chain A residue 2015 ILE
Chi-restraints excluded: chain A residue 2018 TYR
Chi-restraints excluded: chain A residue 2088 ILE
Chi-restraints excluded: chain A residue 2096 VAL
Chi-restraints excluded: chain A residue 2216 VAL
Chi-restraints excluded: chain A residue 2323 ILE
Chi-restraints excluded: chain A residue 2356 THR
Chi-restraints excluded: chain A residue 2416 THR
Chi-restraints excluded: chain A residue 2457 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 127 optimal weight:    2.9990
   chunk 144 optimal weight:    0.0000
   chunk 157 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   chunk 150 optimal weight:    4.9990
   chunk 89 optimal weight:    7.9990
   chunk 155 optimal weight:    6.9990
   chunk 60 optimal weight:    0.0020
   chunk 147 optimal weight:    0.4980
   chunk 136 optimal weight:    0.0050
   chunk 32 optimal weight:    7.9990
   overall best weight:    0.5008

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

Flipped N/Q/H residues before XYZ refinement:
** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 992 ASN
** A1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1206 ASN
** A1929 HIS ** 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 = 0.3878 r_free = 0.3878 target = 0.110753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.090581 restraints weight = 34483.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.090807 restraints weight = 24505.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.091388 restraints weight = 24685.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.092153 restraints weight = 17782.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.092382 restraints weight = 16014.675|
|-----------------------------------------------------------------------------|
r_work (final): 0.3552
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7464
moved from start:          0.1749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  11791  Z= 0.109
  Angle     :  0.639  13.881  16102  Z= 0.305
  Chirality :  0.044   0.238   2007
  Planarity :  0.004   0.057   2012
  Dihedral  :  6.510 144.388   1666
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 11.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.28 %
    Favored  : 91.72 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 22.47 %
    Favored  : 73.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -1.56 (0.22), residues: 1522
  helix:  0.67 (0.24), residues: 525
  sheet: -1.69 (0.37), residues: 195
  loop : -2.11 (0.22), residues: 802

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A2477 
 TYR   0.016   0.001   TYR A1092 
 PHE   0.025   0.001   PHE A 676 
 TRP   0.012   0.001   TRP A2426 
 HIS   0.007   0.001   HIS B  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 (11790)
  covalent geometry    : angle       0.63891 (16102)
  hydrogen bonds       : bond        0.02891 (  407)
  hydrogen bonds       : angle       4.85553 ( 1107)
  Misc. bond           : bond        0.00212 (    1)

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

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

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 128
  time to evaluate  : 0.454 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   66 GLU cc_start: 0.8693 (mm-30) cc_final: 0.8113 (mm-30)
REVERT: B   95 LEU cc_start: 0.9032 (pt) cc_final: 0.8595 (tp)
REVERT: A  761 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7769 (mm)
REVERT: A 1168 MET cc_start: 0.8164 (tmm) cc_final: 0.7944 (tmm)
REVERT: A 1198 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8282 (mt)
REVERT: A 1497 LEU cc_start: 0.8468 (mm) cc_final: 0.8257 (pt)
REVERT: A 2444 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8153 (tt)
REVERT: A 2521 MET cc_start: 0.8616 (mmp) cc_final: 0.8298 (mmt)
  outliers start: 46
  outliers final: 36
  residues processed: 168
  average time/residue: 0.0769
  time to fit residues: 20.9703
Evaluate side-chains
  151 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 112
  time to evaluate  : 0.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   99 GLU
Chi-restraints excluded: chain B residue  132 GLU
Chi-restraints excluded: chain A residue  724 MET
Chi-restraints excluded: chain A residue  761 LEU
Chi-restraints excluded: chain A residue 1008 VAL
Chi-restraints excluded: chain A residue 1080 VAL
Chi-restraints excluded: chain A residue 1174 SER
Chi-restraints excluded: chain A residue 1177 ILE
Chi-restraints excluded: chain A residue 1185 PHE
Chi-restraints excluded: chain A residue 1198 LEU
Chi-restraints excluded: chain A residue 1299 LEU
Chi-restraints excluded: chain A residue 1410 THR
Chi-restraints excluded: chain A residue 1449 LEU
Chi-restraints excluded: chain A residue 1733 TYR
Chi-restraints excluded: chain A residue 1765 ILE
Chi-restraints excluded: chain A residue 1767 VAL
Chi-restraints excluded: chain A residue 1784 ILE
Chi-restraints excluded: chain A residue 1924 LEU
Chi-restraints excluded: chain A residue 1949 LEU
Chi-restraints excluded: chain A residue 1954 SER
Chi-restraints excluded: chain A residue 1958 LEU
Chi-restraints excluded: chain A residue 1967 THR
Chi-restraints excluded: chain A residue 1982 LEU
Chi-restraints excluded: chain A residue 1986 HIS
Chi-restraints excluded: chain A residue 2015 ILE
Chi-restraints excluded: chain A residue 2018 TYR
Chi-restraints excluded: chain A residue 2035 THR
Chi-restraints excluded: chain A residue 2088 ILE
Chi-restraints excluded: chain A residue 2096 VAL
Chi-restraints excluded: chain A residue 2216 VAL
Chi-restraints excluded: chain A residue 2301 MET
Chi-restraints excluded: chain A residue 2303 LEU
Chi-restraints excluded: chain A residue 2356 THR
Chi-restraints excluded: chain A residue 2370 SER
Chi-restraints excluded: chain A residue 2375 VAL
Chi-restraints excluded: chain A residue 2387 ILE
Chi-restraints excluded: chain A residue 2416 THR
Chi-restraints excluded: chain A residue 2444 LEU
Chi-restraints excluded: chain A residue 2457 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 157 optimal weight:    2.9990
   chunk 154 optimal weight:    3.9990
   chunk 156 optimal weight:    0.7980
   chunk 22 optimal weight:    8.9990
   chunk 66 optimal weight:    0.6980
   chunk 59 optimal weight:    3.9990
   chunk 129 optimal weight:    1.9990
   chunk 134 optimal weight:    8.9990
   chunk 102 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9980
   chunk 135 optimal weight:    0.2980
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1929 HIS ** 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 = 0.3867 r_free = 0.3867 target = 0.109965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.090029 restraints weight = 34586.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.090335 restraints weight = 26148.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.090953 restraints weight = 23703.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.091910 restraints weight = 17852.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.092062 restraints weight = 16145.783|
|-----------------------------------------------------------------------------|
r_work (final): 0.3545
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7481
moved from start:          0.1922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  11791  Z= 0.134
  Angle     :  0.655  12.379  16102  Z= 0.314
  Chirality :  0.044   0.260   2007
  Planarity :  0.004   0.056   2012
  Dihedral  :  6.445 144.414   1666
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 12.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.41 %
    Favored  : 91.59 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 22.91 %
    Favored  : 72.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -1.58 (0.22), residues: 1522
  helix:  0.68 (0.24), residues: 524
  sheet: -1.75 (0.36), residues: 202
  loop : -2.12 (0.22), residues: 796

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A2514 
 TYR   0.016   0.002   TYR A1092 
 PHE   0.024   0.001   PHE A 676 
 TRP   0.015   0.001   TRP A2426 
 HIS   0.007   0.001   HIS A1926 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 (11790)
  covalent geometry    : angle       0.65459 (16102)
  hydrogen bonds       : bond        0.02979 (  407)
  hydrogen bonds       : angle       4.91270 ( 1107)
  Misc. bond           : bond        0.00204 (    1)

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

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

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 119
  time to evaluate  : 0.484 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   66 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8083 (mm-30)
REVERT: B   95 LEU cc_start: 0.9012 (pt) cc_final: 0.8573 (tp)
REVERT: A  761 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7801 (mm)
REVERT: A 1168 MET cc_start: 0.8086 (OUTLIER) cc_final: 0.7844 (tmm)
REVERT: A 1198 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8264 (mt)
REVERT: A 2426 TRP cc_start: 0.7792 (OUTLIER) cc_final: 0.7476 (m-10)
REVERT: A 2444 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8168 (tt)
REVERT: A 2521 MET cc_start: 0.8674 (mmp) cc_final: 0.8260 (mmt)
  outliers start: 50
  outliers final: 38
  residues processed: 163
  average time/residue: 0.0800
  time to fit residues: 20.8119
Evaluate side-chains
  151 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 108
  time to evaluate  : 0.447 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   99 GLU
Chi-restraints excluded: chain B residue  132 GLU
Chi-restraints excluded: chain A residue  724 MET
Chi-restraints excluded: chain A residue  761 LEU
Chi-restraints excluded: chain A residue 1008 VAL
Chi-restraints excluded: chain A residue 1080 VAL
Chi-restraints excluded: chain A residue 1168 MET
Chi-restraints excluded: chain A residue 1177 ILE
Chi-restraints excluded: chain A residue 1185 PHE
Chi-restraints excluded: chain A residue 1198 LEU
Chi-restraints excluded: chain A residue 1299 LEU
Chi-restraints excluded: chain A residue 1339 ILE
Chi-restraints excluded: chain A residue 1410 THR
Chi-restraints excluded: chain A residue 1428 VAL
Chi-restraints excluded: chain A residue 1449 LEU
Chi-restraints excluded: chain A residue 1733 TYR
Chi-restraints excluded: chain A residue 1762 PHE
Chi-restraints excluded: chain A residue 1765 ILE
Chi-restraints excluded: chain A residue 1767 VAL
Chi-restraints excluded: chain A residue 1784 ILE
Chi-restraints excluded: chain A residue 1917 LEU
Chi-restraints excluded: chain A residue 1924 LEU
Chi-restraints excluded: chain A residue 1949 LEU
Chi-restraints excluded: chain A residue 1958 LEU
Chi-restraints excluded: chain A residue 1967 THR
Chi-restraints excluded: chain A residue 1986 HIS
Chi-restraints excluded: chain A residue 2015 ILE
Chi-restraints excluded: chain A residue 2018 TYR
Chi-restraints excluded: chain A residue 2035 THR
Chi-restraints excluded: chain A residue 2088 ILE
Chi-restraints excluded: chain A residue 2096 VAL
Chi-restraints excluded: chain A residue 2216 VAL
Chi-restraints excluded: chain A residue 2301 MET
Chi-restraints excluded: chain A residue 2323 ILE
Chi-restraints excluded: chain A residue 2356 THR
Chi-restraints excluded: chain A residue 2370 SER
Chi-restraints excluded: chain A residue 2375 VAL
Chi-restraints excluded: chain A residue 2387 ILE
Chi-restraints excluded: chain A residue 2396 VAL
Chi-restraints excluded: chain A residue 2416 THR
Chi-restraints excluded: chain A residue 2426 TRP
Chi-restraints excluded: chain A residue 2444 LEU
Chi-restraints excluded: chain A residue 2457 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 25 optimal weight:    0.6980
   chunk 22 optimal weight:    5.9990
   chunk 136 optimal weight:    9.9990
   chunk 115 optimal weight:    0.2980
   chunk 84 optimal weight:    1.9990
   chunk 149 optimal weight:    4.9990
   chunk 78 optimal weight:    0.7980
   chunk 61 optimal weight:    5.9990
   chunk 26 optimal weight:    0.9990
   chunk 31 optimal weight:    7.9990
   chunk 37 optimal weight:    8.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 720 ASN
** A1437 ASN ** 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 = 0.3864 r_free = 0.3864 target = 0.109767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.089791 restraints weight = 34358.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.090287 restraints weight = 25723.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.090808 restraints weight = 23559.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.091920 restraints weight = 17587.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.092028 restraints weight = 15647.049|
|-----------------------------------------------------------------------------|
r_work (final): 0.3542
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7481
moved from start:          0.2071

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  11791  Z= 0.133
  Angle     :  0.654  12.217  16102  Z= 0.314
  Chirality :  0.044   0.270   2007
  Planarity :  0.004   0.056   2012
  Dihedral  :  6.369 144.369   1666
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 12.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.41 %
    Favored  : 91.59 %
  Rotamer:
    Outliers :  4.88 %
    Allowed  : 22.29 %
    Favored  : 72.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -1.56 (0.22), residues: 1522
  helix:  0.66 (0.24), residues: 524
  sheet: -1.90 (0.36), residues: 211
  loop : -2.02 (0.22), residues: 787

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A2514 
 TYR   0.015   0.002   TYR A1092 
 PHE   0.026   0.001   PHE A 676 
 TRP   0.017   0.001   TRP A2426 
 HIS   0.007   0.001   HIS A1926 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 (11790)
  covalent geometry    : angle       0.65419 (16102)
  hydrogen bonds       : bond        0.02978 (  407)
  hydrogen bonds       : angle       4.87755 ( 1107)
  Misc. bond           : bond        0.00177 (    1)

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

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

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 122
  time to evaluate  : 0.474 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   66 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8187 (mm-30)
REVERT: B   95 LEU cc_start: 0.8984 (pt) cc_final: 0.8606 (tp)
REVERT: A  761 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7807 (mm)
REVERT: A  835 ILE cc_start: 0.8396 (mp) cc_final: 0.8190 (tt)
REVERT: A 1168 MET cc_start: 0.8099 (OUTLIER) cc_final: 0.7748 (tmm)
REVERT: A 1198 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8340 (mt)
REVERT: A 1955 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.7446 (tt)
REVERT: A 2132 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8189 (mm)
REVERT: A 2426 TRP cc_start: 0.7797 (OUTLIER) cc_final: 0.7496 (m-10)
REVERT: A 2521 MET cc_start: 0.8655 (mmp) cc_final: 0.8292 (mmt)
  outliers start: 55
  outliers final: 38
  residues processed: 171
  average time/residue: 0.0790
  time to fit residues: 21.6822
Evaluate side-chains
  156 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 112
  time to evaluate  : 0.415 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   99 GLU
Chi-restraints excluded: chain B residue  132 GLU
Chi-restraints excluded: chain B residue  152 PHE
Chi-restraints excluded: chain A residue  761 LEU
Chi-restraints excluded: chain A residue 1008 VAL
Chi-restraints excluded: chain A residue 1080 VAL
Chi-restraints excluded: chain A residue 1168 MET
Chi-restraints excluded: chain A residue 1174 SER
Chi-restraints excluded: chain A residue 1177 ILE
Chi-restraints excluded: chain A residue 1185 PHE
Chi-restraints excluded: chain A residue 1198 LEU
Chi-restraints excluded: chain A residue 1299 LEU
Chi-restraints excluded: chain A residue 1339 ILE
Chi-restraints excluded: chain A residue 1410 THR
Chi-restraints excluded: chain A residue 1428 VAL
Chi-restraints excluded: chain A residue 1449 LEU
Chi-restraints excluded: chain A residue 1733 TYR
Chi-restraints excluded: chain A residue 1762 PHE
Chi-restraints excluded: chain A residue 1765 ILE
Chi-restraints excluded: chain A residue 1767 VAL
Chi-restraints excluded: chain A residue 1784 ILE
Chi-restraints excluded: chain A residue 1810 LYS
Chi-restraints excluded: chain A residue 1924 LEU
Chi-restraints excluded: chain A residue 1949 LEU
Chi-restraints excluded: chain A residue 1955 LEU
Chi-restraints excluded: chain A residue 1958 LEU
Chi-restraints excluded: chain A residue 1967 THR
Chi-restraints excluded: chain A residue 1986 HIS
Chi-restraints excluded: chain A residue 2018 TYR
Chi-restraints excluded: chain A residue 2035 THR
Chi-restraints excluded: chain A residue 2088 ILE
Chi-restraints excluded: chain A residue 2096 VAL
Chi-restraints excluded: chain A residue 2132 LEU
Chi-restraints excluded: chain A residue 2216 VAL
Chi-restraints excluded: chain A residue 2301 MET
Chi-restraints excluded: chain A residue 2323 ILE
Chi-restraints excluded: chain A residue 2356 THR
Chi-restraints excluded: chain A residue 2370 SER
Chi-restraints excluded: chain A residue 2375 VAL
Chi-restraints excluded: chain A residue 2387 ILE
Chi-restraints excluded: chain A residue 2396 VAL
Chi-restraints excluded: chain A residue 2416 THR
Chi-restraints excluded: chain A residue 2426 TRP
Chi-restraints excluded: chain A residue 2457 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 61 optimal weight:    0.3980
   chunk 138 optimal weight:    6.9990
   chunk 141 optimal weight:   20.0000
   chunk 37 optimal weight:    8.9990
   chunk 101 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9980
   chunk 153 optimal weight:    0.9990
   chunk 117 optimal weight:    0.0980
   chunk 121 optimal weight:    0.0980
   chunk 84 optimal weight:    6.9990
   chunk 104 optimal weight:    6.9990
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
** A1929 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1977 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.114610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.095909 restraints weight = 35925.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.096062 restraints weight = 26043.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.096858 restraints weight = 24923.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.098041 restraints weight = 18283.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.098169 restraints weight = 16056.033|
|-----------------------------------------------------------------------------|
r_work (final): 0.3675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7446
moved from start:          0.2217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  11791  Z= 0.107
  Angle     :  0.647  15.403  16102  Z= 0.305
  Chirality :  0.044   0.334   2007
  Planarity :  0.004   0.056   2012
  Dihedral  :  6.213 144.276   1666
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 11.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.82 %
    Favored  : 92.18 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 23.62 %
    Favored  : 72.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -1.46 (0.22), residues: 1522
  helix:  0.77 (0.24), residues: 520
  sheet: -1.83 (0.36), residues: 210
  loop : -1.98 (0.22), residues: 792

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A2514 
 TYR   0.016   0.001   TYR A1092 
 PHE   0.023   0.001   PHE A 676 
 TRP   0.013   0.001   TRP A2426 
 HIS   0.007   0.001   HIS A1926 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 (11790)
  covalent geometry    : angle       0.64710 (16102)
  hydrogen bonds       : bond        0.02760 (  407)
  hydrogen bonds       : angle       4.74301 ( 1107)
  Misc. bond           : bond        0.00157 (    1)

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

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

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 118
  time to evaluate  : 0.371 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   66 GLU cc_start: 0.8712 (mm-30) cc_final: 0.8183 (mm-30)
REVERT: B   95 LEU cc_start: 0.8967 (pt) cc_final: 0.8654 (tp)
REVERT: A  761 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7776 (mm)
REVERT: A 1198 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8215 (mt)
REVERT: A 1497 LEU cc_start: 0.8389 (mm) cc_final: 0.8153 (pt)
REVERT: A 2426 TRP cc_start: 0.7627 (OUTLIER) cc_final: 0.7395 (m-10)
REVERT: A 2521 MET cc_start: 0.8518 (mmp) cc_final: 0.8149 (mmt)
  outliers start: 48
  outliers final: 38
  residues processed: 161
  average time/residue: 0.0763
  time to fit residues: 20.0480
Evaluate side-chains
  152 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 111
  time to evaluate  : 0.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   99 GLU
Chi-restraints excluded: chain B residue  132 GLU
Chi-restraints excluded: chain A residue  761 LEU
Chi-restraints excluded: chain A residue 1008 VAL
Chi-restraints excluded: chain A residue 1080 VAL
Chi-restraints excluded: chain A residue 1174 SER
Chi-restraints excluded: chain A residue 1177 ILE
Chi-restraints excluded: chain A residue 1198 LEU
Chi-restraints excluded: chain A residue 1299 LEU
Chi-restraints excluded: chain A residue 1339 ILE
Chi-restraints excluded: chain A residue 1410 THR
Chi-restraints excluded: chain A residue 1428 VAL
Chi-restraints excluded: chain A residue 1449 LEU
Chi-restraints excluded: chain A residue 1733 TYR
Chi-restraints excluded: chain A residue 1762 PHE
Chi-restraints excluded: chain A residue 1765 ILE
Chi-restraints excluded: chain A residue 1767 VAL
Chi-restraints excluded: chain A residue 1784 ILE
Chi-restraints excluded: chain A residue 1810 LYS
Chi-restraints excluded: chain A residue 1924 LEU
Chi-restraints excluded: chain A residue 1949 LEU
Chi-restraints excluded: chain A residue 1958 LEU
Chi-restraints excluded: chain A residue 1967 THR
Chi-restraints excluded: chain A residue 1982 LEU
Chi-restraints excluded: chain A residue 1986 HIS
Chi-restraints excluded: chain A residue 2015 ILE
Chi-restraints excluded: chain A residue 2018 TYR
Chi-restraints excluded: chain A residue 2035 THR
Chi-restraints excluded: chain A residue 2088 ILE
Chi-restraints excluded: chain A residue 2096 VAL
Chi-restraints excluded: chain A residue 2216 VAL
Chi-restraints excluded: chain A residue 2301 MET
Chi-restraints excluded: chain A residue 2323 ILE
Chi-restraints excluded: chain A residue 2356 THR
Chi-restraints excluded: chain A residue 2370 SER
Chi-restraints excluded: chain A residue 2375 VAL
Chi-restraints excluded: chain A residue 2387 ILE
Chi-restraints excluded: chain A residue 2396 VAL
Chi-restraints excluded: chain A residue 2416 THR
Chi-restraints excluded: chain A residue 2426 TRP
Chi-restraints excluded: chain A residue 2457 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 39 optimal weight:    2.9990
   chunk 94 optimal weight:    1.9990
   chunk 146 optimal weight:    6.9990
   chunk 16 optimal weight:    1.9990
   chunk 41 optimal weight:    0.0170
   chunk 121 optimal weight:    0.0050
   chunk 98 optimal weight:    0.5980
   chunk 89 optimal weight:    7.9990
   chunk 59 optimal weight:    1.9990
   chunk 61 optimal weight:    0.0670
   chunk 147 optimal weight:    0.7980
   overall best weight:    0.2970

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

Flipped N/Q/H residues before XYZ refinement:
** A1929 HIS ** 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 = 0.4003 r_free = 0.4003 target = 0.115609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.096295 restraints weight = 35541.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.096909 restraints weight = 23244.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.097799 restraints weight = 21061.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.098074 restraints weight = 15970.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.098224 restraints weight = 15768.453|
|-----------------------------------------------------------------------------|
r_work (final): 0.3680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7451
moved from start:          0.2354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  11791  Z= 0.101
  Angle     :  0.652  15.656  16102  Z= 0.305
  Chirality :  0.044   0.305   2007
  Planarity :  0.004   0.056   2012
  Dihedral  :  6.114 144.214   1666
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 10.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.75 %
    Favored  : 92.25 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 24.25 %
    Favored  : 71.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -1.40 (0.22), residues: 1522
  helix:  0.71 (0.24), residues: 524
  sheet: -1.76 (0.36), residues: 208
  loop : -1.88 (0.23), residues: 790

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A2514 
 TYR   0.014   0.001   TYR A1092 
 PHE   0.020   0.001   PHE A 676 
 TRP   0.012   0.001   TRP A2426 
 HIS   0.007   0.001   HIS A1926 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 (11790)
  covalent geometry    : angle       0.65228 (16102)
  hydrogen bonds       : bond        0.02694 (  407)
  hydrogen bonds       : angle       4.69123 ( 1107)
  Misc. bond           : bond        0.00160 (    1)

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

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

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 121
  time to evaluate  : 0.476 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   66 GLU cc_start: 0.8759 (mm-30) cc_final: 0.8215 (mm-30)
REVERT: B   95 LEU cc_start: 0.9028 (pt) cc_final: 0.8755 (tp)
REVERT: A  761 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7775 (mm)
REVERT: A 1419 TYR cc_start: 0.7275 (m-10) cc_final: 0.6752 (m-10)
  outliers start: 43
  outliers final: 33
  residues processed: 159
  average time/residue: 0.0835
  time to fit residues: 21.2111
Evaluate side-chains
  146 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 112
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   99 GLU
Chi-restraints excluded: chain A residue  761 LEU
Chi-restraints excluded: chain A residue 1008 VAL
Chi-restraints excluded: chain A residue 1080 VAL
Chi-restraints excluded: chain A residue 1174 SER
Chi-restraints excluded: chain A residue 1177 ILE
Chi-restraints excluded: chain A residue 1185 PHE
Chi-restraints excluded: chain A residue 1299 LEU
Chi-restraints excluded: chain A residue 1339 ILE
Chi-restraints excluded: chain A residue 1410 THR
Chi-restraints excluded: chain A residue 1428 VAL
Chi-restraints excluded: chain A residue 1449 LEU
Chi-restraints excluded: chain A residue 1733 TYR
Chi-restraints excluded: chain A residue 1762 PHE
Chi-restraints excluded: chain A residue 1765 ILE
Chi-restraints excluded: chain A residue 1767 VAL
Chi-restraints excluded: chain A residue 1784 ILE
Chi-restraints excluded: chain A residue 1810 LYS
Chi-restraints excluded: chain A residue 1949 LEU
Chi-restraints excluded: chain A residue 1967 THR
Chi-restraints excluded: chain A residue 1982 LEU
Chi-restraints excluded: chain A residue 1986 HIS
Chi-restraints excluded: chain A residue 2018 TYR
Chi-restraints excluded: chain A residue 2035 THR
Chi-restraints excluded: chain A residue 2096 VAL
Chi-restraints excluded: chain A residue 2216 VAL
Chi-restraints excluded: chain A residue 2301 MET
Chi-restraints excluded: chain A residue 2303 LEU
Chi-restraints excluded: chain A residue 2323 ILE
Chi-restraints excluded: chain A residue 2356 THR
Chi-restraints excluded: chain A residue 2370 SER
Chi-restraints excluded: chain A residue 2375 VAL
Chi-restraints excluded: chain A residue 2416 THR
Chi-restraints excluded: chain A residue 2457 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 104 optimal weight:    4.9990
   chunk 48 optimal weight:    0.6980
   chunk 155 optimal weight:    4.9990
   chunk 52 optimal weight:    1.9990
   chunk 84 optimal weight:    4.9990
   chunk 24 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9990
   chunk 113 optimal weight:    1.9990
   chunk 112 optimal weight:    0.0980
   chunk 142 optimal weight:    4.9990
   chunk 31 optimal weight:    8.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
** A1929 HIS ** 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 = 0.3982 r_free = 0.3982 target = 0.114201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.095175 restraints weight = 35956.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.095611 restraints weight = 26685.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.096236 restraints weight = 25999.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.096791 restraints weight = 17960.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.097208 restraints weight = 16428.341|
|-----------------------------------------------------------------------------|
r_work (final): 0.3663
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7479
moved from start:          0.2488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  11791  Z= 0.131
  Angle     :  0.693  15.442  16102  Z= 0.326
  Chirality :  0.045   0.276   2007
  Planarity :  0.004   0.055   2012
  Dihedral  :  6.184 144.317   1666
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 12.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.28 %
    Favored  : 91.72 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 25.04 %
    Favored  : 71.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: 1522
  helix:  0.74 (0.24), residues: 518
  sheet: -1.72 (0.36), residues: 208
  loop : -1.90 (0.23), residues: 796

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1501 
 TYR   0.014   0.001   TYR A1733 
 PHE   0.021   0.001   PHE A 676 
 TRP   0.021   0.001   TRP A2426 
 HIS   0.008   0.001   HIS A1926 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 (11790)
  covalent geometry    : angle       0.69344 (16102)
  hydrogen bonds       : bond        0.02873 (  407)
  hydrogen bonds       : angle       4.86914 ( 1107)
  Misc. bond           : bond        0.00162 (    1)

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

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

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 116
  time to evaluate  : 0.483 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   66 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8175 (mm-30)
REVERT: B   95 LEU cc_start: 0.9028 (pt) cc_final: 0.8698 (tp)
REVERT: A  761 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7795 (mm)
REVERT: A 1014 GLU cc_start: 0.6643 (tm-30) cc_final: 0.6430 (tm-30)
REVERT: A 1419 TYR cc_start: 0.7352 (m-10) cc_final: 0.6844 (m-10)
  outliers start: 37
  outliers final: 34
  residues processed: 148
  average time/residue: 0.0774
  time to fit residues: 18.6251
Evaluate side-chains
  149 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 114
  time to evaluate  : 0.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   99 GLU
Chi-restraints excluded: chain A residue  761 LEU
Chi-restraints excluded: chain A residue 1008 VAL
Chi-restraints excluded: chain A residue 1080 VAL
Chi-restraints excluded: chain A residue 1174 SER
Chi-restraints excluded: chain A residue 1177 ILE
Chi-restraints excluded: chain A residue 1185 PHE
Chi-restraints excluded: chain A residue 1299 LEU
Chi-restraints excluded: chain A residue 1339 ILE
Chi-restraints excluded: chain A residue 1410 THR
Chi-restraints excluded: chain A residue 1428 VAL
Chi-restraints excluded: chain A residue 1449 LEU
Chi-restraints excluded: chain A residue 1733 TYR
Chi-restraints excluded: chain A residue 1762 PHE
Chi-restraints excluded: chain A residue 1765 ILE
Chi-restraints excluded: chain A residue 1767 VAL
Chi-restraints excluded: chain A residue 1784 ILE
Chi-restraints excluded: chain A residue 1810 LYS
Chi-restraints excluded: chain A residue 1924 LEU
Chi-restraints excluded: chain A residue 1949 LEU
Chi-restraints excluded: chain A residue 1958 LEU
Chi-restraints excluded: chain A residue 1967 THR
Chi-restraints excluded: chain A residue 1982 LEU
Chi-restraints excluded: chain A residue 1986 HIS
Chi-restraints excluded: chain A residue 2018 TYR
Chi-restraints excluded: chain A residue 2035 THR
Chi-restraints excluded: chain A residue 2096 VAL
Chi-restraints excluded: chain A residue 2216 VAL
Chi-restraints excluded: chain A residue 2301 MET
Chi-restraints excluded: chain A residue 2303 LEU
Chi-restraints excluded: chain A residue 2323 ILE
Chi-restraints excluded: chain A residue 2356 THR
Chi-restraints excluded: chain A residue 2370 SER
Chi-restraints excluded: chain A residue 2416 THR
Chi-restraints excluded: chain A residue 2457 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 29 optimal weight:    0.8980
   chunk 135 optimal weight:    1.9990
   chunk 101 optimal weight:    1.9990
   chunk 106 optimal weight:    2.9990
   chunk 80 optimal weight:    8.9990
   chunk 109 optimal weight:    0.2980
   chunk 128 optimal weight:   10.0000
   chunk 91 optimal weight:    4.9990
   chunk 99 optimal weight:    0.4980
   chunk 32 optimal weight:    2.9990
   chunk 75 optimal weight:    3.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1929 HIS ** 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 = 0.3963 r_free = 0.3963 target = 0.113077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.094007 restraints weight = 36180.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.094310 restraints weight = 27834.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.094953 restraints weight = 27659.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.095469 restraints weight = 19050.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.095727 restraints weight = 17578.460|
|-----------------------------------------------------------------------------|
r_work (final): 0.3637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7520
moved from start:          0.2582

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  11791  Z= 0.147
  Angle     :  0.699  15.193  16102  Z= 0.330
  Chirality :  0.045   0.244   2007
  Planarity :  0.004   0.055   2012
  Dihedral  :  6.293 144.302   1666
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 13.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.54 %
    Favored  : 91.46 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 25.31 %
    Favored  : 71.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: 1522
  helix:  0.69 (0.23), residues: 521
  sheet: -1.76 (0.36), residues: 209
  loop : -1.92 (0.23), residues: 792

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A2514 
 TYR   0.016   0.002   TYR A1733 
 PHE   0.021   0.001   PHE A 676 
 TRP   0.024   0.002   TRP A2426 
 HIS   0.008   0.001   HIS A1926 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 (11790)
  covalent geometry    : angle       0.69924 (16102)
  hydrogen bonds       : bond        0.02930 (  407)
  hydrogen bonds       : angle       4.93825 ( 1107)
  Misc. bond           : bond        0.00165 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1731.45 seconds
wall clock time: 30 minutes 48.28 seconds (1848.28 seconds total)