Starting phenix.real_space_refine
on Thu Jul  2 19:20:41 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8bwo_16292/07_2026/8bwo_16292.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8bwo_16292/07_2026/8bwo_16292.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8bwo_16292/07_2026/8bwo_16292.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8bwo_16292/07_2026/8bwo_16292.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/8bwo_16292/07_2026/8bwo_16292.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8bwo_16292/07_2026/8bwo_16292.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8bwo_16292/07_2026/8bwo_16292.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8bwo_16292/07_2026/8bwo_16292.map"
  }
  resolution = 3.2
  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=   0.054
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     Mg      2      5.21       5
     S      42      5.16       5
     C    6279      2.51       5
     N    1636      2.21       5
     O    1747      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 9712
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 9648
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1211, 9648
          Classifications: {'peptide': 1211}
          Link IDs: {'PTRANS': 36, 'TRANS': 1174}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 64
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 64
          Unusual residues: {' MG': 2, 'ATP': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
  Time building chain proxies: 2.12, per 1000 atoms: 0.22
  Number of scatterers: 9712
  At special positions: 0
  Unit cell: (75.712, 90.688, 148.928, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      42     16.00
     P       6     15.00
     Mg      2     11.99
     O    1747      8.00
     N    1636      7.00
     C    6279      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.96
  Conformation dependent library (CDL) restraints added in 298.9 milliseconds
  

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2288

  Finding SS restraints...
    Secondary structure from input PDB file:
      53 helices and 6 sheets defined
      70.0% alpha, 8.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 15
    Processing helix  chain 'A' and resid 17 through 23
    Processing helix  chain 'A' and resid 24 through 26
      No H-bonds generated for 'chain 'A' and resid 24 through 26'
    Processing helix  chain 'A' and resid 27 through 35
      removed outlier: 3.776A  pdb=" N   PHE A  31 " --> pdb=" O   LEU A  27 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   ILE A  33 " --> pdb=" O   PRO A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 48 through 51
    Processing helix  chain 'A' and resid 52 through 69
    Processing helix  chain 'A' and resid 79 through 120
      removed outlier: 5.630A  pdb=" N   LYS A  90 " --> pdb=" O   LYS A  86 " (cutoff:3.500A)
      removed outlier: 5.501A  pdb=" N   SER A  91 " --> pdb=" O   CYS A  87 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   VAL A  94 " --> pdb=" O   LYS A  90 " (cutoff:3.500A)
      removed outlier: 4.311A  pdb=" N   LEU A  95 " --> pdb=" O   SER A  91 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   PHE A  98 " --> pdb=" O   VAL A  94 " (cutoff:3.500A)
      Proline residue:  A 110  - end of helix
    Processing helix  chain 'A' and resid 133 through 150
      removed outlier: 4.104A  pdb=" N   TYR A 137 " --> pdb=" O   THR A 133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 181
      removed outlier: 4.015A  pdb=" N   LEU A 154 " --> pdb=" O   ILE A 150 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   ARG A 180 " --> pdb=" O   ARG A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 190 through 200
    Processing helix  chain 'A' and resid 203 through 212
      removed outlier: 4.084A  pdb=" N   GLN A 207 " --> pdb=" O   ASN A 203 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   THR A 209 " --> pdb=" O   PHE A 205 " (cutoff:3.500A)
      removed outlier: 4.545A  pdb=" N   VAL A 210 " --> pdb=" O   ASP A 206 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   PHE A 211 " --> pdb=" O   GLN A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 231
      Proline residue:  A 219  - end of helix
    Processing helix  chain 'A' and resid 236 through 290
      removed outlier: 3.884A  pdb=" N   GLY A 240 " --> pdb=" O   SER A 236 " (cutoff:3.500A)
      Proline residue:  A 249  - end of helix
      removed outlier: 3.667A  pdb=" N   GLY A 255 " --> pdb=" O   GLN A 251 " (cutoff:3.500A)
      removed outlier: 4.249A  pdb=" N   LYS A 256 " --> pdb=" O   SER A 252 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   LEU A 257 " --> pdb=" O   CYS A 253 " (cutoff:3.500A)
      removed outlier: 5.576A  pdb=" N   ARG A 284 " --> pdb=" O   ILE A 280 " (cutoff:3.500A)
      removed outlier: 6.024A  pdb=" N   ILE A 285 " --> pdb=" O   THR A 281 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 291 through 341
      removed outlier: 3.690A  pdb=" N   LYS A 309 " --> pdb=" O   LYS A 305 " (cutoff:3.500A)
      removed outlier: 4.807A  pdb=" N   SER A 328 " --> pdb=" O   PHE A 324 " (cutoff:3.500A)
      removed outlier: 4.877A  pdb=" N   LYS A 329 " --> pdb=" O   PHE A 325 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   TYR A 339 " --> pdb=" O   THR A 335 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 348 through 367
      removed outlier: 4.928A  pdb=" N   LEU A 363 " --> pdb=" O   GLY A 359 " (cutoff:3.500A)
      removed outlier: 5.613A  pdb=" N   THR A 364 " --> pdb=" O   ALA A 360 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 367 through 391
      removed outlier: 3.677A  pdb=" N   VAL A 381 " --> pdb=" O   SER A 377 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 450 through 459
    Processing helix  chain 'A' and resid 489 through 495
    Processing helix  chain 'A' and resid 500 through 511
    Processing helix  chain 'A' and resid 529 through 533
    Processing helix  chain 'A' and resid 536 through 552
      removed outlier: 3.664A  pdb=" N   ARG A 542 " --> pdb=" O   GLY A 538 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   ALA A 548 " --> pdb=" O   ASN A 544 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   ASP A 552 " --> pdb=" O   ALA A 548 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 566 through 577
    Processing helix  chain 'A' and resid 593 through 598
      removed outlier: 3.624A  pdb=" N   LEU A 597 " --> pdb=" O   GLN A 593 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   LYS A 598 " --> pdb=" O   LEU A 594 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 593 through 598'
    Processing helix  chain 'A' and resid 616 through 621
    Processing helix  chain 'A' and resid 697 through 709
    Processing helix  chain 'A' and resid 710 through 743
      removed outlier: 3.573A  pdb=" N   PHE A 714 " --> pdb=" O   HIS A 710 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   ASP A 732 " --> pdb=" O   TYR A 728 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 749 through 756
      removed outlier: 3.685A  pdb=" N   GLY A 753 " --> pdb=" O   ASN A 750 " (cutoff:3.500A)
      removed outlier: 6.654A  pdb=" N   ASN A 754 " --> pdb=" O   GLY A 751 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   VAL A 755 " --> pdb=" O   GLY A 752 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 760 through 807
    Processing helix  chain 'A' and resid 809 through 816
      removed outlier: 3.767A  pdb=" N   PHE A 813 " --> pdb=" O   PRO A 809 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 817 through 834
      removed outlier: 3.964A  pdb=" N   ARG A 824 " --> pdb=" O   ARG A 820 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   ASP A 828 " --> pdb=" O   ARG A 824 " (cutoff:3.500A)
      removed outlier: 4.668A  pdb=" N   ILE A 829 " --> pdb=" O   PHE A 825 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 834 through 860
      removed outlier: 3.872A  pdb=" N   LEU A 838 " --> pdb=" O   ASP A 834 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 861 through 863
      No H-bonds generated for 'chain 'A' and resid 861 through 863'
    Processing helix  chain 'A' and resid 864 through 910
      Proline residue:  A 870  - end of helix
      removed outlier: 3.549A  pdb=" N   ILE A 873 " --> pdb=" O   VAL A 869 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   THR A 885 " --> pdb=" O   TYR A 881 " (cutoff:3.500A)
      removed outlier: 4.456A  pdb=" N   ASP A 888 " --> pdb=" O   GLU A 884 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   SER A 898 " --> pdb=" O   SER A 894 " (cutoff:3.500A)
      Proline residue:  A 899  - end of helix
    Processing helix  chain 'A' and resid 910 through 918
    Processing helix  chain 'A' and resid 919 through 966
    Processing helix  chain 'A' and resid 967 through 975
      removed outlier: 6.236A  pdb=" N   ALA A 971 " --> pdb=" O   LEU A 968 " (cutoff:3.500A)
      removed outlier: 5.814A  pdb=" N   LYS A 972 " --> pdb=" O   ILE A 969 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 976 through 981
      removed outlier: 3.672A  pdb=" N   GLY A 980 " --> pdb=" O   ALA A 976 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 985 through 1007
      removed outlier: 4.724A  pdb=" N   GLY A 991 " --> pdb=" O   LEU A 987 " (cutoff:3.500A)
      removed outlier: 4.830A  pdb=" N   GLN A 994 " --> pdb=" O   MET A 990 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   GLU A1004 " --> pdb=" O   SER A1000 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1007 through 1018
      removed outlier: 3.698A  pdb=" N   TYR A1016 " --> pdb=" O   ARG A1012 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1080 through 1089
      removed outlier: 4.003A  pdb=" N   ILE A1085 " --> pdb=" O   LYS A1081 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   SER A1086 " --> pdb=" O   SER A1082 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1106 through 1108
      No H-bonds generated for 'chain 'A' and resid 1106 through 1108'
    Processing helix  chain 'A' and resid 1109 through 1116
      removed outlier: 4.073A  pdb=" N   LYS A1116 " --> pdb=" O   ASP A1112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1130 through 1136
    Processing helix  chain 'A' and resid 1142 through 1153
    Processing helix  chain 'A' and resid 1155 through 1162
      removed outlier: 3.573A  pdb=" N   ASP A1161 " --> pdb=" O   GLU A1157 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1164 through 1168
    Processing helix  chain 'A' and resid 1171 through 1175
    Processing helix  chain 'A' and resid 1178 through 1194
      removed outlier: 3.597A  pdb=" N   CYS A1186 " --> pdb=" O   ARG A1182 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   LYS A1194 " --> pdb=" O   ALA A1190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1208 through 1223
      removed outlier: 3.964A  pdb=" N   LEU A1214 " --> pdb=" O   ARG A1210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1234 through 1239
    Processing helix  chain 'A' and resid 1257 through 1263
    Processing helix  chain 'A' and resid 1267 through 1276
    Processing helix  chain 'A' and resid 1277 through 1293
    Processing sheet with id=AA1, first strand: chain 'A' and resid 428 through 431
      removed outlier: 5.761A  pdb=" N   GLN A 429 " --> pdb=" O   ALA A 417 " (cutoff:3.500A)
      removed outlier: 7.626A  pdb=" N   ALA A 417 " --> pdb=" O   GLN A 429 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 428 through 431
      removed outlier: 5.761A  pdb=" N   GLN A 429 " --> pdb=" O   ALA A 417 " (cutoff:3.500A)
      removed outlier: 7.626A  pdb=" N   ALA A 417 " --> pdb=" O   GLN A 429 " (cutoff:3.500A)
      removed outlier: 4.360A  pdb=" N   PHE A 415 " --> pdb=" O   HIS A 466 " (cutoff:3.500A)
      removed outlier: 6.660A  pdb=" N   HIS A 466 " --> pdb=" O   PHE A 415 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 475 through 478
      removed outlier: 6.497A  pdb=" N   GLU A 439 " --> pdb=" O   THR A 587 " (cutoff:3.500A)
      removed outlier: 7.860A  pdb=" N   LEU A 589 " --> pdb=" O   GLU A 439 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   LEU A 441 " --> pdb=" O   LEU A 589 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   GLN A 613 " --> pdb=" O   ILE A 605 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   LYS A 607 " --> pdb=" O   MET A 611 " (cutoff:3.500A)
      removed outlier: 5.325A  pdb=" N   MET A 611 " --> pdb=" O   LYS A 607 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 487 through 488
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1058 through 1065
      removed outlier: 5.708A  pdb=" N   LYS A1059 " --> pdb=" O   PHE A1048 " (cutoff:3.500A)
      removed outlier: 7.131A  pdb=" N   PHE A1048 " --> pdb=" O   LYS A1059 " (cutoff:3.500A)
      removed outlier: 7.614A  pdb=" N   ALA A1063 " --> pdb=" O   ASP A1044 " (cutoff:3.500A)
      removed outlier: 5.531A  pdb=" N   ASP A1044 " --> pdb=" O   ALA A1063 " (cutoff:3.500A)
      removed outlier: 7.300A  pdb=" N   ILE A1065 " --> pdb=" O   ILE A1042 " (cutoff:3.500A)
      removed outlier: 5.549A  pdb=" N   ILE A1042 " --> pdb=" O   ILE A1065 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1117 through 1120
      removed outlier: 7.283A  pdb=" N   LEU A1198 " --> pdb=" O   LEU A1229 " (cutoff:3.500A)
      removed outlier: 7.719A  pdb=" N   ILE A1231 " --> pdb=" O   LEU A1198 " (cutoff:3.500A)
      removed outlier: 6.228A  pdb=" N   ILE A1200 " --> pdb=" O   ILE A1231 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   LYS A1070 " --> pdb=" O   LYS A1243 " (cutoff:3.500A)
      removed outlier: 7.775A  pdb=" N   MET A1245 " --> pdb=" O   LYS A1070 " (cutoff:3.500A)
      removed outlier: 6.390A  pdb=" N   GLY A1072 " --> pdb=" O   MET A1245 " (cutoff:3.500A)
      removed outlier: 7.658A  pdb=" N   LEU A1247 " --> pdb=" O   GLY A1072 " (cutoff:3.500A)
      removed outlier: 6.285A  pdb=" N   VAL A1074 " --> pdb=" O   LEU A1247 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   ASP A1256 " --> pdb=" O   ILE A1244 " (cutoff:3.500A)

    617 hydrogen bonds defined for protein.
    1794 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.61

  Time building geometry restraints manager: 1.21 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3058
        1.34 -     1.46: 1356
        1.46 -     1.57: 5430
        1.57 -     1.69: 4
        1.69 -     1.81: 68
  Bond restraints: 9916
  Sorted by residual:
  bond pdb=" C5' ATP A1401 "
       pdb=" O5' ATP A1401 "
    ideal  model  delta    sigma   weight residual
    1.443  1.221  0.222 1.00e-02 1.00e+04 4.95e+02
  bond pdb=" C5' ATP A1402 "
       pdb=" O5' ATP A1402 "
    ideal  model  delta    sigma   weight residual
    1.443  1.221  0.222 1.00e-02 1.00e+04 4.92e+02
  bond pdb=" C4' ATP A1401 "
       pdb=" O4' ATP A1401 "
    ideal  model  delta    sigma   weight residual
    1.444  1.397  0.047 1.10e-02 8.26e+03 1.80e+01
  bond pdb=" C1' ATP A1402 "
       pdb=" O4' ATP A1402 "
    ideal  model  delta    sigma   weight residual
    1.416  1.364  0.052 1.30e-02 5.92e+03 1.59e+01
  bond pdb=" C4' ATP A1402 "
       pdb=" O4' ATP A1402 "
    ideal  model  delta    sigma   weight residual
    1.444  1.401  0.043 1.10e-02 8.26e+03 1.54e+01
  ... (remaining 9911 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     7.43: 13428
        7.43 -    14.85: 13
       14.85 -    22.27: 1
       22.27 -    29.70: 4
       29.70 -    37.12: 4
  Bond angle restraints: 13450
  Sorted by residual:
  angle pdb=" C5' ATP A1402 "
        pdb=" O5' ATP A1402 "
        pdb=" PA  ATP A1402 "
      ideal   model   delta    sigma   weight residual
     121.27  158.39  -37.12 1.00e+00 1.00e+00 1.38e+03
  angle pdb=" C5' ATP A1401 "
        pdb=" O5' ATP A1401 "
        pdb=" PA  ATP A1401 "
      ideal   model   delta    sigma   weight residual
     121.27  157.40  -36.13 1.00e+00 1.00e+00 1.31e+03
  angle pdb=" C3' ATP A1402 "
        pdb=" C4' ATP A1402 "
        pdb=" C5' ATP A1402 "
      ideal   model   delta    sigma   weight residual
     115.19   83.42   31.77 1.76e+00 3.23e-01 3.26e+02
  angle pdb=" C3' ATP A1401 "
        pdb=" C4' ATP A1401 "
        pdb=" C5' ATP A1401 "
      ideal   model   delta    sigma   weight residual
     115.19   85.14   30.05 1.76e+00 3.23e-01 2.92e+02
  angle pdb=" C4' ATP A1402 "
        pdb=" C5' ATP A1402 "
        pdb=" O5' ATP A1402 "
      ideal   model   delta    sigma   weight residual
     108.83  137.57  -28.74 2.33e+00 1.85e-01 1.52e+02
  ... (remaining 13445 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.80: 5442
       17.80 -    35.61: 361
       35.61 -    53.41: 58
       53.41 -    71.22: 16
       71.22 -    89.02: 10
  Dihedral angle restraints: 5887
    sinusoidal: 2356
      harmonic: 3531
  Sorted by residual:
  dihedral pdb=" CA  CYS A1226 "
           pdb=" C   CYS A1226 "
           pdb=" N   THR A1227 "
           pdb=" CA  THR A1227 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.93   28.07     0      5.00e+00 4.00e-02 3.15e+01
  dihedral pdb=" CA  MET A 409 "
           pdb=" C   MET A 409 "
           pdb=" N   VAL A 410 "
           pdb=" CA  VAL A 410 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.03   27.97     0      5.00e+00 4.00e-02 3.13e+01
  dihedral pdb=" CA  LEU A 513 "
           pdb=" C   LEU A 513 "
           pdb=" N   LYS A 514 "
           pdb=" CA  LYS A 514 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.37   25.63     0      5.00e+00 4.00e-02 2.63e+01
  ... (remaining 5884 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.090: 1472
       0.090 -    0.180: 83
       0.180 -    0.270: 4
       0.270 -    0.360: 1
       0.360 -    0.450: 2
  Chirality restraints: 1562
  Sorted by residual:
  chirality pdb=" C4' ATP A1402 "
            pdb=" C3' ATP A1402 "
            pdb=" C5' ATP A1402 "
            pdb=" O4' ATP A1402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.94    0.45 2.00e-01 2.50e+01 5.07e+00
  chirality pdb=" C4' ATP A1401 "
            pdb=" C3' ATP A1401 "
            pdb=" C5' ATP A1401 "
            pdb=" O4' ATP A1401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.94    0.45 2.00e-01 2.50e+01 5.06e+00
  chirality pdb=" C3' ATP A1402 "
            pdb=" C2' ATP A1402 "
            pdb=" C4' ATP A1402 "
            pdb=" O3' ATP A1402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.34   -0.29 2.00e-01 2.50e+01 2.14e+00
  ... (remaining 1559 not shown)

  Planarity restraints: 1660
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 157 "    0.002 2.00e-02 2.50e+03   1.72e-02 5.93e+00
        pdb=" CG  TYR A 157 "    0.001 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 157 "    0.022 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 157 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 157 "   -0.024 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 157 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 157 "   -0.024 2.00e-02 2.50e+03
        pdb=" OH  TYR A 157 "    0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A  37 "   -0.174 9.50e-02 1.11e+02   7.87e-02 4.98e+00
        pdb=" NE  ARG A  37 "    0.017 2.00e-02 2.50e+03
        pdb=" CZ  ARG A  37 "   -0.017 2.00e-02 2.50e+03
        pdb=" NH1 ARG A  37 "    0.008 2.00e-02 2.50e+03
        pdb=" NH2 ARG A  37 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 998 "   -0.170 9.50e-02 1.11e+02   7.67e-02 4.89e+00
        pdb=" NE  ARG A 998 "    0.017 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 998 "   -0.018 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 998 "    0.008 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 998 "    0.000 2.00e-02 2.50e+03
  ... (remaining 1657 not shown)

  Histogram of nonbonded interaction distances:
        1.90 -     2.50: 44
        2.50 -     3.10: 7428
        3.10 -     3.70: 14881
        3.70 -     4.30: 22729
        4.30 -     4.90: 37486
  Nonbonded interactions: 82568
  Sorted by model distance:
  nonbonded pdb=" O3G ATP A1402 "
            pdb="MG    MG A1403 "
     model   vdw
     1.900 2.170
  nonbonded pdb=" O1B ATP A1402 "
            pdb="MG    MG A1403 "
     model   vdw
     1.940 2.170
  nonbonded pdb=" OG  SER A1082 "
            pdb="MG    MG A1404 "
     model   vdw
     1.945 2.170
  nonbonded pdb=" OE1 GLN A1122 "
            pdb="MG    MG A1404 "
     model   vdw
     2.004 2.170
  nonbonded pdb=" OH  TYR A  92 "
            pdb=" O   THR A 209 "
     model   vdw
     2.251 3.040
  ... (remaining 82563 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.620
  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:          0.130
  Check model and map are aligned:         0.040
  Set scattering table:                    0.020
  Process input model:                     10.050
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7861
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   0.222   9916  Z= 0.392
  Angle     :  1.109  37.125  13450  Z= 0.718
  Chirality :  0.050   0.450   1562
  Planarity :  0.008   0.079   1660
  Dihedral  : 13.352  89.020   3599
  Min Nonbonded Distance : 1.900

Molprobity Statistics.
  All-atom Clashscore : 2.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  :  2.47 %
    Favored  : 97.06 %
  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: -1.54 (0.22), residues: 1203
  helix: -1.22 (0.16), residues: 761
  sheet: -0.58 (0.59), residues: 68
  loop : -0.16 (0.34), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.021   0.004   ARG A 782 
 TYR   0.026   0.005   TYR A 157 
 PHE   0.020   0.002   PHE A 948 
 TRP   0.027   0.002   TRP A 711 
 HIS   0.004   0.001   HIS A 172 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00527 /  0.39 ( 9916)
  covalent geometry    : angle       1.10948 /  0.72 (13450)
  hydrogen bonds       : bond        0.19516 / 12.48 (  615)
  hydrogen bonds       : angle       7.76780 /  5.63 ( 1794)

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 224
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.7466 (pt0) cc_final: 0.6664 (pm20)
REVERT: A   76 GLN cc_start: 0.5073 (pt0) cc_final: 0.4846 (mt0)
REVERT: A  176 ARG cc_start: 0.7245 (ttm170) cc_final: 0.7028 (ttt-90)
REVERT: A  264 LYS cc_start: 0.7508 (mttp) cc_final: 0.7197 (mttp)
REVERT: A  293 LYS cc_start: 0.7341 (mttt) cc_final: 0.7083 (mmmt)
REVERT: A  413 GLN cc_start: 0.7676 (tt0) cc_final: 0.7243 (tp40)
REVERT: A  509 LYS cc_start: 0.8138 (ttmt) cc_final: 0.7650 (tttp)
REVERT: A  571 ARG cc_start: 0.7027 (ttt180) cc_final: 0.6808 (tmm160)
REVERT: A  695 LYS cc_start: 0.7108 (ptpt) cc_final: 0.6088 (tptt)
REVERT: A  706 ARG cc_start: 0.7723 (mmm-85) cc_final: 0.6696 (tpt90)
REVERT: A  715 ILE cc_start: 0.8179 (mm) cc_final: 0.7977 (mp)
REVERT: A  835 LEU cc_start: 0.8349 (tp) cc_final: 0.8111 (tt)
REVERT: A  925 GLU cc_start: 0.7874 (tt0) cc_final: 0.7594 (tt0)
REVERT: A 1020 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7303 (pm20)
REVERT: A 1021 LYS cc_start: 0.8391 (mtpt) cc_final: 0.7960 (mmtm)
REVERT: A 1077 THR cc_start: 0.8683 (p) cc_final: 0.8479 (p)
REVERT: A 1152 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7748 (mt-10)
REVERT: A 1169 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7614 (mm-30)
REVERT: A 1201 ASP cc_start: 0.8160 (t0) cc_final: 0.7841 (t0)
REVERT: A 1210 ARG cc_start: 0.7879 (mtp85) cc_final: 0.7353 (mtt90)
  outliers start: 5
  outliers final: 1
  residues processed: 226
  average time/residue: 0.1237
  time to fit residues: 36.9257
Evaluate side-chains
  142 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 141
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  233 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 108 optimal weight:    0.0570
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    0.8980
   chunk 113 optimal weight:    0.9980
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.1980
   chunk 117 optimal weight:    1.9990
   overall best weight:    0.4498

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 153 HIS
A 703 ASN
** A 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1047 ASN
A1225 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.152949 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.125563 restraints weight = 12033.316|
|-----------------------------------------------------------------------------|
r_work (start): 0.3421 rms_B_bonded: 2.18
r_work: 0.3288 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3149 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3149
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8525
moved from start:          0.2270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9916  Z= 0.142
  Angle     :  0.597   7.766  13450  Z= 0.318
  Chirality :  0.042   0.164   1562
  Planarity :  0.004   0.050   1660
  Dihedral  :  5.886  70.536   1311
  Min Nonbonded Distance : 1.943

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  :  6.65 %
    Favored  : 91.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.43 (0.24), residues: 1203
  helix:  0.55 (0.18), residues: 773
  sheet: -0.65 (0.58), residues: 68
  loop :  0.22 (0.34), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 951 
 TYR   0.013   0.001   TYR A 768 
 PHE   0.017   0.001   PHE A 336 
 TRP   0.021   0.001   TRP A 763 
 HIS   0.004   0.001   HIS A 213 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00305 /  0.14 ( 9916)
  covalent geometry    : angle       0.59707 /  0.32 (13450)
  hydrogen bonds       : bond        0.05085 /  3.25 (  615)
  hydrogen bonds       : angle       4.93199 /  3.70 ( 1794)

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 177
  time to evaluate  : 0.277 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.7927 (pt0) cc_final: 0.7371 (pm20)
REVERT: A   77 LYS cc_start: 0.8231 (pptt) cc_final: 0.7944 (mmmt)
REVERT: A   89 TRP cc_start: 0.8609 (p-90) cc_final: 0.8385 (p-90)
REVERT: A  226 THR cc_start: 0.8935 (t) cc_final: 0.8572 (p)
REVERT: A  264 LYS cc_start: 0.8627 (mttp) cc_final: 0.8403 (mttt)
REVERT: A  326 SER cc_start: 0.9002 (p) cc_final: 0.8796 (p)
REVERT: A  413 GLN cc_start: 0.8374 (tt0) cc_final: 0.7890 (tp40)
REVERT: A  481 GLN cc_start: 0.8612 (mm-40) cc_final: 0.8308 (mm-40)
REVERT: A  509 LYS cc_start: 0.8811 (ttmt) cc_final: 0.8411 (tttp)
REVERT: A  544 ASN cc_start: 0.8575 (t0) cc_final: 0.8360 (t0)
REVERT: A  571 ARG cc_start: 0.7917 (ttt180) cc_final: 0.7467 (tmm160)
REVERT: A  607 LYS cc_start: 0.7051 (mttt) cc_final: 0.6797 (pptt)
REVERT: A  692 SER cc_start: 0.7756 (t) cc_final: 0.7419 (m)
REVERT: A  695 LYS cc_start: 0.7600 (ptpt) cc_final: 0.6682 (tttp)
REVERT: A  706 ARG cc_start: 0.8067 (mmm-85) cc_final: 0.6962 (tpt90)
REVERT: A  744 MET cc_start: 0.5023 (OUTLIER) cc_final: 0.4134 (pp-130)
REVERT: A  925 GLU cc_start: 0.8773 (tt0) cc_final: 0.8426 (mt-10)
REVERT: A 1020 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7751 (pm20)
REVERT: A 1021 LYS cc_start: 0.8488 (mtpt) cc_final: 0.8286 (mmtm)
REVERT: A 1066 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8327 (mtmm)
REVERT: A 1140 GLU cc_start: 0.8502 (tt0) cc_final: 0.8238 (mt-10)
REVERT: A 1169 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7563 (mm-30)
REVERT: A 1176 ASN cc_start: 0.8245 (t0) cc_final: 0.7874 (t0)
REVERT: A 1210 ARG cc_start: 0.8404 (mtp85) cc_final: 0.7750 (mtt90)
REVERT: A 1274 GLN cc_start: 0.8467 (mm-40) cc_final: 0.7926 (tt0)
  outliers start: 16
  outliers final: 8
  residues processed: 185
  average time/residue: 0.1166
  time to fit residues: 28.8670
Evaluate side-chains
  158 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 148
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 ASP
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  346 ILE
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  744 MET
Chi-restraints excluded: chain A residue  805 ILE
Chi-restraints excluded: chain A residue  906 SER
Chi-restraints excluded: chain A residue  993 PHE
Chi-restraints excluded: chain A residue 1066 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 13 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 100 optimal weight:    0.1980
   chunk 24 optimal weight:    1.9990
   chunk 120 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 68 optimal weight:    1.9990
   chunk 47 optimal weight:    0.8980
   chunk 110 optimal weight:    0.5980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A1216 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.151464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.124419 restraints weight = 12019.376|
|-----------------------------------------------------------------------------|
r_work (start): 0.3421 rms_B_bonded: 1.99
r_work: 0.3290 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3153 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8543
moved from start:          0.2819

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9916  Z= 0.142
  Angle     :  0.548   7.093  13450  Z= 0.290
  Chirality :  0.041   0.151   1562
  Planarity :  0.004   0.037   1660
  Dihedral  :  5.526  75.590   1311
  Min Nonbonded Distance : 1.901

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 10.16 %
    Favored  : 88.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.87 (0.24), residues: 1203
  helix:  0.95 (0.18), residues: 772
  sheet: -1.07 (0.55), residues: 75
  loop :  0.41 (0.35), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 384 
 TYR   0.009   0.001   TYR A1259 
 PHE   0.017   0.002   PHE A 698 
 TRP   0.019   0.001   TRP A 763 
 HIS   0.004   0.001   HIS A 152 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00321 /  0.14 ( 9916)
  covalent geometry    : angle       0.54807 /  0.29 (13450)
  hydrogen bonds       : bond        0.04638 /  2.96 (  615)
  hydrogen bonds       : angle       4.62792 /  3.48 ( 1794)

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 161
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.7995 (pt0) cc_final: 0.7381 (pm20)
REVERT: A   77 LYS cc_start: 0.8214 (pptt) cc_final: 0.7992 (mmmt)
REVERT: A   89 TRP cc_start: 0.8630 (p-90) cc_final: 0.8393 (p-90)
REVERT: A  176 ARG cc_start: 0.8194 (ttm170) cc_final: 0.7942 (ttt180)
REVERT: A  264 LYS cc_start: 0.8626 (mttp) cc_final: 0.8402 (mttt)
REVERT: A  276 MET cc_start: 0.8937 (tpp) cc_final: 0.8476 (mmm)
REVERT: A  312 ARG cc_start: 0.8202 (mtm-85) cc_final: 0.7998 (mtt-85)
REVERT: A  413 GLN cc_start: 0.8407 (tt0) cc_final: 0.7928 (tp40)
REVERT: A  481 GLN cc_start: 0.8676 (mm-40) cc_final: 0.8389 (mm-40)
REVERT: A  509 LYS cc_start: 0.8867 (ttmt) cc_final: 0.8477 (tttm)
REVERT: A  571 ARG cc_start: 0.7933 (ttt180) cc_final: 0.7491 (tmm160)
REVERT: A  695 LYS cc_start: 0.7659 (ptpt) cc_final: 0.6686 (tttp)
REVERT: A  706 ARG cc_start: 0.8005 (mmm-85) cc_final: 0.7753 (mmm-85)
REVERT: A  744 MET cc_start: 0.5217 (OUTLIER) cc_final: 0.4244 (pp-130)
REVERT: A  925 GLU cc_start: 0.8779 (tt0) cc_final: 0.8436 (mt-10)
REVERT: A 1020 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7793 (pm20)
REVERT: A 1021 LYS cc_start: 0.8524 (mtpt) cc_final: 0.8293 (mmtm)
REVERT: A 1140 GLU cc_start: 0.8435 (tt0) cc_final: 0.8193 (mt-10)
REVERT: A 1169 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7628 (mm-30)
REVERT: A 1176 ASN cc_start: 0.8371 (t0) cc_final: 0.8017 (t0)
REVERT: A 1210 ARG cc_start: 0.8431 (mtp85) cc_final: 0.7815 (mtt90)
REVERT: A 1253 LYS cc_start: 0.8599 (ptmt) cc_final: 0.8311 (ptmm)
REVERT: A 1274 GLN cc_start: 0.8448 (mm-40) cc_final: 0.7872 (tt0)
  outliers start: 17
  outliers final: 9
  residues processed: 173
  average time/residue: 0.1098
  time to fit residues: 25.9939
Evaluate side-chains
  154 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 144
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 CYS
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain A residue  346 ILE
Chi-restraints excluded: chain A residue  351 VAL
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  486 SER
Chi-restraints excluded: chain A residue  744 MET
Chi-restraints excluded: chain A residue 1061 LEU
Chi-restraints excluded: chain A residue 1108 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 54 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9980
   chunk 116 optimal weight:    2.9990
   chunk 64 optimal weight:    1.9990
   chunk 77 optimal weight:    6.9990
   chunk 37 optimal weight:    0.6980
   chunk 34 optimal weight:    0.1980
   chunk 66 optimal weight:    7.9990
   chunk 35 optimal weight:    0.9990
   chunk 83 optimal weight:    0.7980
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 544 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.150877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.124490 restraints weight = 12114.083|
|-----------------------------------------------------------------------------|
r_work (start): 0.3380 rms_B_bonded: 1.91
r_work: 0.3242 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3104 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3104
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8541
moved from start:          0.3091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9916  Z= 0.151
  Angle     :  0.551   6.843  13450  Z= 0.288
  Chirality :  0.041   0.154   1562
  Planarity :  0.004   0.038   1660
  Dihedral  :  5.413  79.315   1311
  Min Nonbonded Distance : 1.904

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 11.49 %
    Favored  : 86.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.97 (0.24), residues: 1203
  helix:  1.05 (0.18), residues: 773
  sheet: -1.05 (0.56), residues: 75
  loop :  0.39 (0.35), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 384 
 TYR   0.014   0.001   TYR A1259 
 PHE   0.018   0.002   PHE A 698 
 TRP   0.018   0.001   TRP A 763 
 HIS   0.004   0.001   HIS A 152 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00350 /  0.15 ( 9916)
  covalent geometry    : angle       0.55091 /  0.29 (13450)
  hydrogen bonds       : bond        0.04482 /  2.87 (  615)
  hydrogen bonds       : angle       4.56399 /  3.43 ( 1794)

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 151
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.7992 (pt0) cc_final: 0.7356 (pm20)
REVERT: A   58 GLU cc_start: 0.8252 (tt0) cc_final: 0.8043 (tt0)
REVERT: A   77 LYS cc_start: 0.8167 (pptt) cc_final: 0.7931 (mmmt)
REVERT: A   89 TRP cc_start: 0.8637 (p-90) cc_final: 0.8403 (p-90)
REVERT: A  176 ARG cc_start: 0.8179 (ttm170) cc_final: 0.7912 (ttt180)
REVERT: A  226 THR cc_start: 0.8902 (t) cc_final: 0.8689 (m)
REVERT: A  264 LYS cc_start: 0.8602 (mttp) cc_final: 0.8363 (mttt)
REVERT: A  338 THR cc_start: 0.8436 (OUTLIER) cc_final: 0.7951 (p)
REVERT: A  413 GLN cc_start: 0.8439 (tt0) cc_final: 0.7902 (tp40)
REVERT: A  509 LYS cc_start: 0.8860 (ttmt) cc_final: 0.8454 (tttm)
REVERT: A  571 ARG cc_start: 0.7954 (ttt180) cc_final: 0.7454 (tmm160)
REVERT: A  695 LYS cc_start: 0.7595 (ptpt) cc_final: 0.6556 (tttp)
REVERT: A  744 MET cc_start: 0.5066 (OUTLIER) cc_final: 0.4088 (pp-130)
REVERT: A  925 GLU cc_start: 0.8792 (tt0) cc_final: 0.8447 (mt-10)
REVERT: A 1020 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7791 (pm20)
REVERT: A 1021 LYS cc_start: 0.8537 (mtpt) cc_final: 0.8269 (mmtm)
REVERT: A 1140 GLU cc_start: 0.8427 (tt0) cc_final: 0.8211 (mt-10)
REVERT: A 1169 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7629 (mm-30)
REVERT: A 1176 ASN cc_start: 0.8370 (t0) cc_final: 0.8011 (t0)
REVERT: A 1210 ARG cc_start: 0.8424 (mtp85) cc_final: 0.7599 (mpt180)
REVERT: A 1274 GLN cc_start: 0.8478 (mm-40) cc_final: 0.7916 (tt0)
  outliers start: 21
  outliers final: 15
  residues processed: 161
  average time/residue: 0.1042
  time to fit residues: 23.1892
Evaluate side-chains
  162 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 145
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 ASP
Chi-restraints excluded: chain A residue  161 CYS
Chi-restraints excluded: chain A residue  338 THR
Chi-restraints excluded: chain A residue  346 ILE
Chi-restraints excluded: chain A residue  351 VAL
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  486 SER
Chi-restraints excluded: chain A residue  744 MET
Chi-restraints excluded: chain A residue  805 ILE
Chi-restraints excluded: chain A residue  854 VAL
Chi-restraints excluded: chain A residue  906 SER
Chi-restraints excluded: chain A residue 1061 LEU
Chi-restraints excluded: chain A residue 1108 ILE
Chi-restraints excluded: chain A residue 1125 VAL
Chi-restraints excluded: chain A residue 1130 THR
Chi-restraints excluded: chain A residue 1187 LEU
Chi-restraints excluded: chain A residue 1238 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   chunk 69 optimal weight:    4.9990
   chunk 63 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 95 optimal weight:    2.9990
   chunk 11 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 57 optimal weight:    0.1980
   chunk 56 optimal weight:    2.9990
   chunk 99 optimal weight:    0.5980
   overall best weight:    0.9384

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.149754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.123698 restraints weight = 12038.947|
|-----------------------------------------------------------------------------|
r_work (start): 0.3404 rms_B_bonded: 1.89
r_work: 0.3260 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3122 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3122
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8595
moved from start:          0.3229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9916  Z= 0.173
  Angle     :  0.565   7.475  13450  Z= 0.296
  Chirality :  0.041   0.151   1562
  Planarity :  0.004   0.039   1660
  Dihedral  :  5.404  82.608   1309
  Min Nonbonded Distance : 1.889

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 12.92 %
    Favored  : 85.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.87 (0.24), residues: 1203
  helix:  1.03 (0.18), residues: 773
  sheet: -1.03 (0.57), residues: 70
  loop :  0.17 (0.34), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 384 
 TYR   0.018   0.001   TYR A 737 
 PHE   0.018   0.002   PHE A 698 
 TRP   0.018   0.001   TRP A 230 
 HIS   0.005   0.001   HIS A 152 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00411 /  0.17 ( 9916)
  covalent geometry    : angle       0.56519 /  0.30 (13450)
  hydrogen bonds       : bond        0.04606 /  2.94 (  615)
  hydrogen bonds       : angle       4.59876 /  3.46 ( 1794)

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 150
  time to evaluate  : 0.219 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8089 (pt0) cc_final: 0.7507 (pm20)
REVERT: A   77 LYS cc_start: 0.8194 (pptt) cc_final: 0.7974 (mmmt)
REVERT: A   89 TRP cc_start: 0.8668 (p-90) cc_final: 0.8447 (p-90)
REVERT: A  226 THR cc_start: 0.8968 (t) cc_final: 0.8744 (m)
REVERT: A  264 LYS cc_start: 0.8644 (mttp) cc_final: 0.8411 (mttt)
REVERT: A  276 MET cc_start: 0.8937 (tpp) cc_final: 0.8482 (mmm)
REVERT: A  338 THR cc_start: 0.8586 (OUTLIER) cc_final: 0.8089 (p)
REVERT: A  413 GLN cc_start: 0.8466 (tt0) cc_final: 0.7956 (tp40)
REVERT: A  509 LYS cc_start: 0.8900 (ttmt) cc_final: 0.8501 (tttp)
REVERT: A  571 ARG cc_start: 0.7953 (ttt180) cc_final: 0.7468 (tmm160)
REVERT: A  607 LYS cc_start: 0.7751 (pptt) cc_final: 0.7542 (pptt)
REVERT: A  695 LYS cc_start: 0.7670 (ptpt) cc_final: 0.6632 (tttp)
REVERT: A  715 ILE cc_start: 0.8240 (mp) cc_final: 0.7932 (tp)
REVERT: A  744 MET cc_start: 0.5212 (OUTLIER) cc_final: 0.4252 (pp-130)
REVERT: A 1020 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7854 (pm20)
REVERT: A 1021 LYS cc_start: 0.8632 (mtpt) cc_final: 0.8366 (mmtm)
REVERT: A 1176 ASN cc_start: 0.8467 (t0) cc_final: 0.8129 (t0)
REVERT: A 1195 ASN cc_start: 0.8248 (m-40) cc_final: 0.7667 (m-40)
REVERT: A 1210 ARG cc_start: 0.8436 (mtp85) cc_final: 0.7667 (mpt180)
REVERT: A 1259 TYR cc_start: 0.8183 (t80) cc_final: 0.7922 (t80)
REVERT: A 1274 GLN cc_start: 0.8486 (mm-40) cc_final: 0.7935 (tt0)
  outliers start: 22
  outliers final: 17
  residues processed: 161
  average time/residue: 0.0943
  time to fit residues: 21.1619
Evaluate side-chains
  160 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 141
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  161 CYS
Chi-restraints excluded: chain A residue  338 THR
Chi-restraints excluded: chain A residue  351 VAL
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  486 SER
Chi-restraints excluded: chain A residue  744 MET
Chi-restraints excluded: chain A residue  773 VAL
Chi-restraints excluded: chain A residue  805 ILE
Chi-restraints excluded: chain A residue  835 LEU
Chi-restraints excluded: chain A residue  854 VAL
Chi-restraints excluded: chain A residue  906 SER
Chi-restraints excluded: chain A residue 1061 LEU
Chi-restraints excluded: chain A residue 1108 ILE
Chi-restraints excluded: chain A residue 1125 VAL
Chi-restraints excluded: chain A residue 1130 THR
Chi-restraints excluded: chain A residue 1187 LEU
Chi-restraints excluded: chain A residue 1238 ILE
Chi-restraints excluded: chain A residue 1253 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 82 optimal weight:    0.6980
   chunk 83 optimal weight:    0.5980
   chunk 17 optimal weight:    2.9990
   chunk 94 optimal weight:    0.0010
   chunk 36 optimal weight:    1.9990
   chunk 113 optimal weight:    0.5980
   chunk 41 optimal weight:    0.9990
   chunk 90 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 66 optimal weight:    9.9990
   chunk 34 optimal weight:    1.9990
   overall best weight:    0.5788

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.151175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.122844 restraints weight = 12041.597|
|-----------------------------------------------------------------------------|
r_work (start): 0.3414 rms_B_bonded: 2.21
r_work: 0.3280 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3140 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8564
moved from start:          0.3449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9916  Z= 0.134
  Angle     :  0.524   6.936  13450  Z= 0.275
  Chirality :  0.040   0.149   1562
  Planarity :  0.003   0.039   1660
  Dihedral  :  5.272  89.289   1309
  Min Nonbonded Distance : 1.950

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 14.43 %
    Favored  : 83.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.09 (0.24), residues: 1203
  helix:  1.23 (0.19), residues: 771
  sheet: -0.95 (0.57), residues: 70
  loop :  0.18 (0.33), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 384 
 TYR   0.016   0.001   TYR A 737 
 PHE   0.019   0.001   PHE A 352 
 TRP   0.018   0.001   TRP A 230 
 HIS   0.003   0.001   HIS A 152 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00302 /  0.13 ( 9916)
  covalent geometry    : angle       0.52429 /  0.28 (13450)
  hydrogen bonds       : bond        0.04266 /  2.73 (  615)
  hydrogen bonds       : angle       4.43461 /  3.35 ( 1794)

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 149
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8101 (pt0) cc_final: 0.7479 (pm20)
REVERT: A   77 LYS cc_start: 0.8175 (pptt) cc_final: 0.7940 (mmmt)
REVERT: A   89 TRP cc_start: 0.8648 (p-90) cc_final: 0.8430 (p-90)
REVERT: A  226 THR cc_start: 0.8919 (t) cc_final: 0.8711 (m)
REVERT: A  264 LYS cc_start: 0.8636 (mttp) cc_final: 0.8405 (mttt)
REVERT: A  276 MET cc_start: 0.8935 (tpp) cc_final: 0.8494 (mmm)
REVERT: A  338 THR cc_start: 0.8406 (OUTLIER) cc_final: 0.8004 (p)
REVERT: A  384 ARG cc_start: 0.8087 (mtm110) cc_final: 0.7820 (mtm-85)
REVERT: A  413 GLN cc_start: 0.8444 (tt0) cc_final: 0.7928 (tp40)
REVERT: A  509 LYS cc_start: 0.8914 (ttmt) cc_final: 0.8522 (tttp)
REVERT: A  571 ARG cc_start: 0.7956 (ttt180) cc_final: 0.7436 (tmm160)
REVERT: A  744 MET cc_start: 0.5163 (OUTLIER) cc_final: 0.4145 (pp-130)
REVERT: A  845 GLN cc_start: 0.7615 (pt0) cc_final: 0.7373 (mt0)
REVERT: A 1020 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7835 (pm20)
REVERT: A 1021 LYS cc_start: 0.8648 (mtpt) cc_final: 0.8342 (mmtm)
REVERT: A 1176 ASN cc_start: 0.8427 (t0) cc_final: 0.8101 (t0)
REVERT: A 1195 ASN cc_start: 0.8103 (m-40) cc_final: 0.7558 (m-40)
REVERT: A 1210 ARG cc_start: 0.8434 (mtp85) cc_final: 0.7644 (mpt180)
REVERT: A 1274 GLN cc_start: 0.8481 (mm-40) cc_final: 0.7951 (tt0)
  outliers start: 18
  outliers final: 16
  residues processed: 158
  average time/residue: 0.1036
  time to fit residues: 22.8754
Evaluate side-chains
  154 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 136
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  161 CYS
Chi-restraints excluded: chain A residue  338 THR
Chi-restraints excluded: chain A residue  346 ILE
Chi-restraints excluded: chain A residue  351 VAL
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  486 SER
Chi-restraints excluded: chain A residue  744 MET
Chi-restraints excluded: chain A residue  805 ILE
Chi-restraints excluded: chain A residue  835 LEU
Chi-restraints excluded: chain A residue  906 SER
Chi-restraints excluded: chain A residue 1061 LEU
Chi-restraints excluded: chain A residue 1108 ILE
Chi-restraints excluded: chain A residue 1111 HIS
Chi-restraints excluded: chain A residue 1125 VAL
Chi-restraints excluded: chain A residue 1130 THR
Chi-restraints excluded: chain A residue 1238 ILE
Chi-restraints excluded: chain A residue 1253 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 51 optimal weight:    0.8980
   chunk 15 optimal weight:    0.5980
   chunk 94 optimal weight:    0.1980
   chunk 98 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 81 optimal weight:    2.9990
   chunk 73 optimal weight:    0.0570
   chunk 78 optimal weight:    0.0370
   chunk 49 optimal weight:    0.9980
   chunk 59 optimal weight:    0.9990
   chunk 113 optimal weight:    0.9990
   overall best weight:    0.3576

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A1196 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.153216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.124888 restraints weight = 12110.174|
|-----------------------------------------------------------------------------|
r_work (start): 0.3438 rms_B_bonded: 2.23
r_work: 0.3303 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3162 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8535
moved from start:          0.3662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9916  Z= 0.118
  Angle     :  0.521   6.923  13450  Z= 0.274
  Chirality :  0.039   0.162   1562
  Planarity :  0.003   0.039   1660
  Dihedral  :  5.057  85.877   1309
  Min Nonbonded Distance : 1.984

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 15.19 %
    Favored  : 83.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.29 (0.24), residues: 1203
  helix:  1.41 (0.19), residues: 771
  sheet: -0.75 (0.60), residues: 70
  loop :  0.17 (0.33), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 706 
 TYR   0.015   0.001   TYR A 737 
 PHE   0.018   0.001   PHE A 698 
 TRP   0.017   0.001   TRP A 763 
 HIS   0.002   0.001   HIS A 710 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00257 /  0.12 ( 9916)
  covalent geometry    : angle       0.52120 /  0.27 (13450)
  hydrogen bonds       : bond        0.04042 /  2.60 (  615)
  hydrogen bonds       : angle       4.31004 /  3.24 ( 1794)

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 149
  time to evaluate  : 0.434 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8081 (pt0) cc_final: 0.7463 (pm20)
REVERT: A   77 LYS cc_start: 0.8143 (pptt) cc_final: 0.7921 (mmmt)
REVERT: A   89 TRP cc_start: 0.8628 (p-90) cc_final: 0.8413 (p-90)
REVERT: A  226 THR cc_start: 0.8917 (t) cc_final: 0.8674 (m)
REVERT: A  264 LYS cc_start: 0.8628 (mttp) cc_final: 0.8374 (mttt)
REVERT: A  276 MET cc_start: 0.8927 (tpp) cc_final: 0.8513 (mmm)
REVERT: A  407 LYS cc_start: 0.7450 (mtpt) cc_final: 0.7210 (mtmm)
REVERT: A  413 GLN cc_start: 0.8443 (tt0) cc_final: 0.8041 (tp40)
REVERT: A  571 ARG cc_start: 0.7944 (ttt180) cc_final: 0.7431 (tmm160)
REVERT: A  744 MET cc_start: 0.5124 (OUTLIER) cc_final: 0.4117 (pp-130)
REVERT: A 1011 GLU cc_start: 0.8032 (tm-30) cc_final: 0.7732 (tm-30)
REVERT: A 1020 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7781 (pm20)
REVERT: A 1021 LYS cc_start: 0.8588 (mtpt) cc_final: 0.8308 (mmtm)
REVERT: A 1176 ASN cc_start: 0.8414 (t0) cc_final: 0.8077 (t0)
REVERT: A 1195 ASN cc_start: 0.7881 (m-40) cc_final: 0.7302 (m-40)
REVERT: A 1210 ARG cc_start: 0.8419 (mtp85) cc_final: 0.7571 (mpt180)
REVERT: A 1259 TYR cc_start: 0.8013 (t80) cc_final: 0.7704 (t80)
REVERT: A 1263 GLN cc_start: 0.7699 (pt0) cc_final: 0.7041 (pp30)
REVERT: A 1274 GLN cc_start: 0.8414 (mm-40) cc_final: 0.7901 (tt0)
  outliers start: 16
  outliers final: 13
  residues processed: 157
  average time/residue: 0.1075
  time to fit residues: 23.4117
Evaluate side-chains
  154 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 140
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  161 CYS
Chi-restraints excluded: chain A residue  346 ILE
Chi-restraints excluded: chain A residue  351 VAL
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  744 MET
Chi-restraints excluded: chain A residue  805 ILE
Chi-restraints excluded: chain A residue  835 LEU
Chi-restraints excluded: chain A residue  906 SER
Chi-restraints excluded: chain A residue 1061 LEU
Chi-restraints excluded: chain A residue 1111 HIS
Chi-restraints excluded: chain A residue 1125 VAL
Chi-restraints excluded: chain A residue 1238 ILE
Chi-restraints excluded: chain A residue 1253 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 93 optimal weight:    0.8980
   chunk 5 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 75 optimal weight:    0.8980
   chunk 13 optimal weight:    1.9990
   chunk 111 optimal weight:    0.8980
   chunk 46 optimal weight:    0.8980
   chunk 2 optimal weight:    0.7980
   chunk 33 optimal weight:    0.8980
   chunk 115 optimal weight:    3.9990
   chunk 30 optimal weight:    0.6980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 109 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.149784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.121859 restraints weight = 12206.772|
|-----------------------------------------------------------------------------|
r_work (start): 0.3402 rms_B_bonded: 2.12
r_work: 0.3263 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3123 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8579
moved from start:          0.3654

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   9916  Z= 0.156
  Angle     :  0.541   6.952  13450  Z= 0.283
  Chirality :  0.040   0.149   1562
  Planarity :  0.004   0.040   1660
  Dihedral  :  5.103  87.628   1309
  Min Nonbonded Distance : 1.925

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 15.19 %
    Favored  : 83.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.14 (0.24), residues: 1203
  helix:  1.29 (0.18), residues: 771
  sheet: -0.74 (0.61), residues: 65
  loop :  0.07 (0.33), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 384 
 TYR   0.015   0.001   TYR A 737 
 PHE   0.020   0.002   PHE A 352 
 TRP   0.014   0.001   TRP A 763 
 HIS   0.004   0.001   HIS A 710 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00368 /  0.16 ( 9916)
  covalent geometry    : angle       0.54140 /  0.28 (13450)
  hydrogen bonds       : bond        0.04329 /  2.77 (  615)
  hydrogen bonds       : angle       4.38381 /  3.29 ( 1794)

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 138
  time to evaluate  : 0.426 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8115 (pt0) cc_final: 0.7512 (pm20)
REVERT: A   77 LYS cc_start: 0.8158 (pptt) cc_final: 0.7934 (mmmt)
REVERT: A   89 TRP cc_start: 0.8662 (p-90) cc_final: 0.8434 (p-90)
REVERT: A  226 THR cc_start: 0.8933 (t) cc_final: 0.8697 (m)
REVERT: A  264 LYS cc_start: 0.8633 (mttp) cc_final: 0.8400 (mttt)
REVERT: A  276 MET cc_start: 0.8926 (tpp) cc_final: 0.8517 (mmm)
REVERT: A  338 THR cc_start: 0.8477 (OUTLIER) cc_final: 0.8022 (p)
REVERT: A  413 GLN cc_start: 0.8387 (tt0) cc_final: 0.8000 (tp40)
REVERT: A  571 ARG cc_start: 0.7955 (ttt180) cc_final: 0.7417 (tmm160)
REVERT: A  744 MET cc_start: 0.5017 (OUTLIER) cc_final: 0.4046 (pp-130)
REVERT: A 1020 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7781 (pm20)
REVERT: A 1021 LYS cc_start: 0.8661 (mtpt) cc_final: 0.8361 (mmtm)
REVERT: A 1176 ASN cc_start: 0.8473 (t0) cc_final: 0.8135 (t0)
REVERT: A 1195 ASN cc_start: 0.8136 (m-40) cc_final: 0.7547 (m-40)
REVERT: A 1210 ARG cc_start: 0.8430 (mtp85) cc_final: 0.7621 (mpt180)
REVERT: A 1263 GLN cc_start: 0.7652 (pt0) cc_final: 0.6990 (pp30)
REVERT: A 1274 GLN cc_start: 0.8454 (mm-40) cc_final: 0.7926 (tt0)
  outliers start: 19
  outliers final: 13
  residues processed: 149
  average time/residue: 0.1075
  time to fit residues: 22.5637
Evaluate side-chains
  148 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 133
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  161 CYS
Chi-restraints excluded: chain A residue  338 THR
Chi-restraints excluded: chain A residue  351 VAL
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  744 MET
Chi-restraints excluded: chain A residue  805 ILE
Chi-restraints excluded: chain A residue  835 LEU
Chi-restraints excluded: chain A residue  906 SER
Chi-restraints excluded: chain A residue 1061 LEU
Chi-restraints excluded: chain A residue 1111 HIS
Chi-restraints excluded: chain A residue 1125 VAL
Chi-restraints excluded: chain A residue 1130 THR
Chi-restraints excluded: chain A residue 1238 ILE
Chi-restraints excluded: chain A residue 1253 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 116 optimal weight:    2.9990
   chunk 81 optimal weight:    0.7980
   chunk 89 optimal weight:    4.9990
   chunk 117 optimal weight:    0.6980
   chunk 103 optimal weight:    0.8980
   chunk 44 optimal weight:    2.9990
   chunk 98 optimal weight:    0.9990
   chunk 9 optimal weight:    3.9990
   chunk 67 optimal weight:    9.9990
   chunk 35 optimal weight:    0.9990
   chunk 73 optimal weight:    1.9990
   overall best weight:    0.8784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A1151 GLN
A1196 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.148618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.120255 restraints weight = 12201.329|
|-----------------------------------------------------------------------------|
r_work (start): 0.3369 rms_B_bonded: 2.19
r_work: 0.3232 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3092 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3092
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8590
moved from start:          0.3682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9916  Z= 0.168
  Angle     :  0.562   8.542  13450  Z= 0.293
  Chirality :  0.041   0.176   1562
  Planarity :  0.004   0.054   1660
  Dihedral  :  5.128  89.047   1309
  Min Nonbonded Distance : 1.916

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 15.19 %
    Favored  : 82.91 %
  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:  1.07 (0.24), residues: 1203
  helix:  1.27 (0.18), residues: 765
  sheet: -0.77 (0.61), residues: 65
  loop : -0.01 (0.33), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 384 
 TYR   0.016   0.001   TYR A 737 
 PHE   0.019   0.002   PHE A 352 
 TRP   0.013   0.001   TRP A 763 
 HIS   0.004   0.001   HIS A 710 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00399 /  0.17 ( 9916)
  covalent geometry    : angle       0.56188 /  0.29 (13450)
  hydrogen bonds       : bond        0.04427 /  2.83 (  615)
  hydrogen bonds       : angle       4.43101 /  3.33 ( 1794)

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 137
  time to evaluate  : 0.370 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8118 (pt0) cc_final: 0.7508 (pm20)
REVERT: A   77 LYS cc_start: 0.8179 (pptt) cc_final: 0.7923 (mmmt)
REVERT: A   89 TRP cc_start: 0.8652 (p-90) cc_final: 0.8432 (p-90)
REVERT: A  226 THR cc_start: 0.8936 (t) cc_final: 0.8680 (m)
REVERT: A  264 LYS cc_start: 0.8655 (mttp) cc_final: 0.8428 (mttt)
REVERT: A  276 MET cc_start: 0.8922 (tpp) cc_final: 0.8520 (mmm)
REVERT: A  338 THR cc_start: 0.8475 (OUTLIER) cc_final: 0.8003 (p)
REVERT: A  413 GLN cc_start: 0.8398 (tt0) cc_final: 0.7983 (tp40)
REVERT: A  744 MET cc_start: 0.4948 (OUTLIER) cc_final: 0.3958 (pp-130)
REVERT: A  931 GLN cc_start: 0.8373 (mm-40) cc_final: 0.7996 (mt0)
REVERT: A 1016 TYR cc_start: 0.8539 (m-10) cc_final: 0.8321 (m-10)
REVERT: A 1020 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7753 (pm20)
REVERT: A 1021 LYS cc_start: 0.8683 (mtpt) cc_final: 0.8341 (mmtm)
REVERT: A 1176 ASN cc_start: 0.8477 (t0) cc_final: 0.8153 (t0)
REVERT: A 1195 ASN cc_start: 0.8200 (m-40) cc_final: 0.7607 (m-40)
REVERT: A 1210 ARG cc_start: 0.8455 (mtp85) cc_final: 0.7619 (mpt180)
REVERT: A 1259 TYR cc_start: 0.8076 (t80) cc_final: 0.7821 (t80)
REVERT: A 1274 GLN cc_start: 0.8470 (mm-40) cc_final: 0.7927 (tt0)
  outliers start: 20
  outliers final: 16
  residues processed: 148
  average time/residue: 0.1109
  time to fit residues: 22.8284
Evaluate side-chains
  151 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 133
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  161 CYS
Chi-restraints excluded: chain A residue  338 THR
Chi-restraints excluded: chain A residue  351 VAL
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  744 MET
Chi-restraints excluded: chain A residue  773 VAL
Chi-restraints excluded: chain A residue  805 ILE
Chi-restraints excluded: chain A residue  835 LEU
Chi-restraints excluded: chain A residue  906 SER
Chi-restraints excluded: chain A residue 1061 LEU
Chi-restraints excluded: chain A residue 1111 HIS
Chi-restraints excluded: chain A residue 1125 VAL
Chi-restraints excluded: chain A residue 1130 THR
Chi-restraints excluded: chain A residue 1151 GLN
Chi-restraints excluded: chain A residue 1187 LEU
Chi-restraints excluded: chain A residue 1238 ILE
Chi-restraints excluded: chain A residue 1253 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 45 optimal weight:    3.9990
   chunk 57 optimal weight:    2.9990
   chunk 27 optimal weight:    0.5980
   chunk 94 optimal weight:    3.9990
   chunk 115 optimal weight:    0.3980
   chunk 109 optimal weight:    0.9990
   chunk 79 optimal weight:    0.9990
   chunk 59 optimal weight:    0.7980
   chunk 100 optimal weight:    0.9980
   chunk 120 optimal weight:    0.9990
   chunk 73 optimal weight:    0.0770
   overall best weight:    0.5738

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 849 GLN
A1151 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.151356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.123467 restraints weight = 12119.503|
|-----------------------------------------------------------------------------|
r_work (start): 0.3393 rms_B_bonded: 2.19
r_work: 0.3256 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3113 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3113
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8563
moved from start:          0.3786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9916  Z= 0.136
  Angle     :  0.539   8.233  13450  Z= 0.282
  Chirality :  0.040   0.177   1562
  Planarity :  0.004   0.063   1660
  Dihedral  :  4.987  83.711   1309
  Min Nonbonded Distance : 1.942

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 15.48 %
    Favored  : 82.91 %
  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:  1.18 (0.24), residues: 1203
  helix:  1.36 (0.19), residues: 766
  sheet: -0.71 (0.61), residues: 65
  loop :  0.01 (0.33), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 384 
 TYR   0.015   0.001   TYR A 737 
 PHE   0.021   0.001   PHE A 352 
 TRP   0.014   0.001   TRP A 763 
 HIS   0.004   0.001   HIS A 710 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00312 /  0.14 ( 9916)
  covalent geometry    : angle       0.53896 /  0.28 (13450)
  hydrogen bonds       : bond        0.04227 /  2.71 (  615)
  hydrogen bonds       : angle       4.35722 /  3.28 ( 1794)

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 135
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8091 (pt0) cc_final: 0.7450 (pm20)
REVERT: A   77 LYS cc_start: 0.8179 (pptt) cc_final: 0.7924 (mmmt)
REVERT: A   89 TRP cc_start: 0.8652 (p-90) cc_final: 0.8425 (p-90)
REVERT: A  103 GLU cc_start: 0.7172 (mm-30) cc_final: 0.6950 (mm-30)
REVERT: A  226 THR cc_start: 0.8913 (t) cc_final: 0.8649 (m)
REVERT: A  264 LYS cc_start: 0.8629 (mttp) cc_final: 0.8408 (mttt)
REVERT: A  276 MET cc_start: 0.8884 (tpp) cc_final: 0.8478 (mmm)
REVERT: A  338 THR cc_start: 0.8391 (OUTLIER) cc_final: 0.7965 (p)
REVERT: A  384 ARG cc_start: 0.8090 (mtm110) cc_final: 0.7813 (mtm-85)
REVERT: A  413 GLN cc_start: 0.8426 (tt0) cc_final: 0.7997 (tp40)
REVERT: A  744 MET cc_start: 0.4928 (OUTLIER) cc_final: 0.3948 (pp-130)
REVERT: A  931 GLN cc_start: 0.8341 (mm-40) cc_final: 0.8007 (mt0)
REVERT: A 1011 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7747 (tm-30)
REVERT: A 1016 TYR cc_start: 0.8543 (m-10) cc_final: 0.8330 (m-10)
REVERT: A 1020 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7742 (pm20)
REVERT: A 1021 LYS cc_start: 0.8688 (mtpt) cc_final: 0.8314 (mmtm)
REVERT: A 1176 ASN cc_start: 0.8453 (t0) cc_final: 0.8127 (t0)
REVERT: A 1195 ASN cc_start: 0.8094 (m-40) cc_final: 0.7487 (m-40)
REVERT: A 1210 ARG cc_start: 0.8429 (mtp85) cc_final: 0.7576 (mpt180)
REVERT: A 1259 TYR cc_start: 0.8064 (t80) cc_final: 0.7765 (t80)
REVERT: A 1263 GLN cc_start: 0.7609 (pt0) cc_final: 0.7001 (pp30)
REVERT: A 1274 GLN cc_start: 0.8436 (mm-40) cc_final: 0.7894 (tt0)
  outliers start: 17
  outliers final: 14
  residues processed: 144
  average time/residue: 0.1089
  time to fit residues: 21.8705
Evaluate side-chains
  149 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 133
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  161 CYS
Chi-restraints excluded: chain A residue  338 THR
Chi-restraints excluded: chain A residue  351 VAL
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  744 MET
Chi-restraints excluded: chain A residue  805 ILE
Chi-restraints excluded: chain A residue  835 LEU
Chi-restraints excluded: chain A residue  906 SER
Chi-restraints excluded: chain A residue 1111 HIS
Chi-restraints excluded: chain A residue 1125 VAL
Chi-restraints excluded: chain A residue 1130 THR
Chi-restraints excluded: chain A residue 1151 GLN
Chi-restraints excluded: chain A residue 1187 LEU
Chi-restraints excluded: chain A residue 1238 ILE
Chi-restraints excluded: chain A residue 1253 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 95 optimal weight:    0.6980
   chunk 86 optimal weight:    0.6980
   chunk 54 optimal weight:    2.9990
   chunk 96 optimal weight:    0.0000
   chunk 41 optimal weight:    0.9980
   chunk 119 optimal weight:    0.9980
   chunk 29 optimal weight:    0.8980
   chunk 45 optimal weight:    2.9990
   chunk 52 optimal weight:    0.5980
   chunk 63 optimal weight:    0.6980
   chunk 59 optimal weight:    0.9990
   overall best weight:    0.5384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A1151 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.150669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.123140 restraints weight = 12171.659|
|-----------------------------------------------------------------------------|
r_work (start): 0.3379 rms_B_bonded: 2.16
r_work: 0.3237 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3093 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3093
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8564
moved from start:          0.3828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9916  Z= 0.133
  Angle     :  0.533   7.957  13450  Z= 0.278
  Chirality :  0.040   0.172   1562
  Planarity :  0.004   0.068   1660
  Dihedral  :  4.938  81.938   1309
  Min Nonbonded Distance : 1.945

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 15.67 %
    Favored  : 82.81 %
  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:  1.21 (0.24), residues: 1203
  helix:  1.39 (0.19), residues: 766
  sheet: -0.64 (0.62), residues: 65
  loop : -0.01 (0.33), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 384 
 TYR   0.019   0.001   TYR A 737 
 PHE   0.018   0.001   PHE A 352 
 TRP   0.014   0.001   TRP A 763 
 HIS   0.004   0.001   HIS A 710 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00304 /  0.13 ( 9916)
  covalent geometry    : angle       0.53344 /  0.28 (13450)
  hydrogen bonds       : bond        0.04182 /  2.68 (  615)
  hydrogen bonds       : angle       4.33576 /  3.26 ( 1794)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2634.85 seconds
wall clock time: 45 minutes 58.72 seconds (2758.72 seconds total)