Starting phenix.real_space_refine
on Sun Jun  8 20:01:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8bwo_16292/06_2025/8bwo_16292.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8bwo_16292/06_2025/8bwo_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8bwo_16292/06_2025/8bwo_16292.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8bwo_16292/06_2025/8bwo_16292.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8bwo_16292/06_2025/8bwo_16292.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8bwo_16292/06_2025/8bwo_16292.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 6.48, per 1000 atoms: 0.67
  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: 2.48
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 1.07
  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: 3.56

  Time building geometry restraints manager: 2.94 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 -    17.98: 5481
       17.98 -    35.96: 371
       35.96 -    53.95: 66
       53.95 -    71.93: 19
       71.93 -    89.91: 12
  Dihedral angle restraints: 5949
    sinusoidal: 2418
      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 5946 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:             3.120
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.400
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     26.090
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.810
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7452
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  : 13.918  89.908   3661
  Min Nonbonded Distance : 1.900

Molprobity Statistics.
  All-atom Clashscore : 2.44
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.027   0.002   TRP A 711 
 HIS   0.004   0.001   HIS A 172 
 PHE   0.020   0.002   PHE A 948 
 TYR   0.026   0.005   TYR A 157 
 ARG   0.021   0.004   ARG A 782 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.19516 (  615)
  hydrogen bonds       : angle       7.76780 ( 1794)
  covalent geometry    : bond        0.00527 ( 9916)
  covalent geometry    : angle       1.10948 (13450)

*********************** 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  : 1.050 
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: 0.8392 (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: 0.7820 (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: 0.2969
  time to fit residues: 87.2783
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  : 1.050 
-------------------------------------------------------------------------------
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 102 optimal weight:    2.9990
   chunk 91 optimal weight:    3.9990
   chunk 50 optimal weight:    0.3980
   chunk 31 optimal weight:    1.9990
   chunk 61 optimal weight:    4.9990
   chunk 48 optimal weight:    1.9990
   chunk 94 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9980
   chunk 57 optimal weight:    4.9990
   chunk 70 optimal weight:    0.9980
   chunk 109 optimal weight:    0.5980
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
A 153 HIS
A 183 ASN
A 703 ASN
A1047 ASN
A1225 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.149046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.121226 restraints weight = 12022.716|
|-----------------------------------------------------------------------------|
r_work (start): 0.3367 rms_B_bonded: 2.18
r_work: 0.3235 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3095 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.3095
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8280
moved from start:          0.2235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   9916  Z= 0.192
  Angle     :  0.641   7.822  13450  Z= 0.341
  Chirality :  0.044   0.154   1562
  Planarity :  0.004   0.054   1660
  Dihedral  :  8.519  74.875   1373
  Min Nonbonded Distance : 1.876

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  :  7.31 %
    Favored  : 90.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.15 (0.23), residues: 1203
  helix:  0.35 (0.18), residues: 772
  sheet: -0.79 (0.59), residues: 68
  loop :  0.07 (0.34), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 763 
 HIS   0.005   0.001   HIS A 153 
 PHE   0.016   0.002   PHE A 336 
 TYR   0.013   0.002   TYR A 737 
 ARG   0.005   0.001   ARG A1193 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05362 (  615)
  hydrogen bonds       : angle       5.04975 ( 1794)
  covalent geometry    : bond        0.00453 ( 9916)
  covalent geometry    : angle       0.64142 (13450)

*********************** 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
  194 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 175
  time to evaluate  : 1.044 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.7990 (pt0) cc_final: 0.7368 (pm20)
REVERT: A   76 GLN cc_start: 0.5614 (pt0) cc_final: 0.5123 (mt0)
REVERT: A   77 LYS cc_start: 0.8230 (pptt) cc_final: 0.7951 (mmmt)
REVERT: A   89 TRP cc_start: 0.8652 (p-90) cc_final: 0.8412 (p-90)
REVERT: A  165 ARG cc_start: 0.8333 (mtt90) cc_final: 0.7948 (mtm180)
REVERT: A  176 ARG cc_start: 0.8255 (ttm170) cc_final: 0.8017 (ttt180)
REVERT: A  264 LYS cc_start: 0.8638 (mttp) cc_final: 0.8397 (mttt)
REVERT: A  312 ARG cc_start: 0.8226 (mtm-85) cc_final: 0.8026 (mtt180)
REVERT: A  413 GLN cc_start: 0.8364 (tt0) cc_final: 0.7877 (tp40)
REVERT: A  509 LYS cc_start: 0.8836 (ttmt) cc_final: 0.8428 (tttp)
REVERT: A  571 ARG cc_start: 0.7985 (ttt180) cc_final: 0.7515 (tmm160)
REVERT: A  607 LYS cc_start: 0.7203 (mttt) cc_final: 0.6922 (pptt)
REVERT: A  611 MET cc_start: 0.8747 (ttp) cc_final: 0.8500 (ttp)
REVERT: A  695 LYS cc_start: 0.7607 (ptpt) cc_final: 0.6649 (tttp)
REVERT: A  706 ARG cc_start: 0.8129 (mmm-85) cc_final: 0.6961 (tpt90)
REVERT: A  744 MET cc_start: 0.5141 (OUTLIER) cc_final: 0.4193 (pp-130)
REVERT: A  800 LYS cc_start: 0.7827 (mtmt) cc_final: 0.7570 (mmtp)
REVERT: A 1020 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7752 (pm20)
REVERT: A 1021 LYS cc_start: 0.8533 (mtpt) cc_final: 0.8294 (mmtm)
REVERT: A 1066 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8311 (mtmm)
REVERT: A 1140 GLU cc_start: 0.8481 (tt0) cc_final: 0.8196 (mt-10)
REVERT: A 1169 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7572 (mm-30)
REVERT: A 1176 ASN cc_start: 0.8318 (t0) cc_final: 0.7977 (t0)
REVERT: A 1210 ARG cc_start: 0.8433 (mtp85) cc_final: 0.7771 (mtt90)
REVERT: A 1274 GLN cc_start: 0.8515 (mm-40) cc_final: 0.7944 (tt0)
  outliers start: 19
  outliers final: 10
  residues processed: 184
  average time/residue: 0.2604
  time to fit residues: 64.1345
Evaluate side-chains
  163 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 151
  time to evaluate  : 1.038 
-------------------------------------------------------------------------------
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  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  906 SER
Chi-restraints excluded: chain A residue  993 PHE
Chi-restraints excluded: chain A residue 1066 LYS
Chi-restraints excluded: chain A residue 1108 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 41 optimal weight:    0.6980
   chunk 73 optimal weight:    0.7980
   chunk 43 optimal weight:    0.7980
   chunk 57 optimal weight:    0.5980
   chunk 36 optimal weight:    0.5980
   chunk 87 optimal weight:    0.9980
   chunk 4 optimal weight:    0.8980
   chunk 3 optimal weight:    0.0980
   chunk 60 optimal weight:    7.9990
   chunk 26 optimal weight:    0.9980
   chunk 79 optimal weight:    0.8980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A1216 GLN

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 = 0.150949 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.123269 restraints weight = 12103.038|
|-----------------------------------------------------------------------------|
r_work (start): 0.3406 rms_B_bonded: 2.21
r_work: 0.3276 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3139 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8235
moved from start:          0.2803

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9916  Z= 0.136
  Angle     :  0.543   7.159  13450  Z= 0.287
  Chirality :  0.041   0.149   1562
  Planarity :  0.004   0.036   1660
  Dihedral  :  7.961  76.610   1373
  Min Nonbonded Distance : 1.942

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 10.54 %
    Favored  : 87.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.80 (0.24), residues: 1203
  helix:  0.90 (0.18), residues: 773
  sheet: -1.09 (0.56), residues: 75
  loop :  0.38 (0.35), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 763 
 HIS   0.003   0.001   HIS A 152 
 PHE   0.017   0.001   PHE A 698 
 TYR   0.010   0.001   TYR A 737 
 ARG   0.003   0.000   ARG A 998 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04604 (  615)
  hydrogen bonds       : angle       4.64600 ( 1794)
  covalent geometry    : bond        0.00297 ( 9916)
  covalent geometry    : angle       0.54255 (13450)

*********************** 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
  186 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 166
  time to evaluate  : 1.088 
Fit side-chains
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.7915 (pt0) cc_final: 0.7337 (pm20)
REVERT: A   76 GLN cc_start: 0.5493 (pt0) cc_final: 0.5153 (mt0)
REVERT: A   77 LYS cc_start: 0.8244 (pptt) cc_final: 0.7990 (mmmt)
REVERT: A   89 TRP cc_start: 0.8656 (p-90) cc_final: 0.8402 (p-90)
REVERT: A  176 ARG cc_start: 0.8217 (ttm170) cc_final: 0.7941 (ttt180)
REVERT: A  264 LYS cc_start: 0.8607 (mttp) cc_final: 0.8369 (mttt)
REVERT: A  276 MET cc_start: 0.8940 (tpp) cc_final: 0.8493 (mmm)
REVERT: A  312 ARG cc_start: 0.8203 (mtm-85) cc_final: 0.7998 (mtt-85)
REVERT: A  413 GLN cc_start: 0.8404 (tt0) cc_final: 0.7894 (tp40)
REVERT: A  481 GLN cc_start: 0.8669 (mm-40) cc_final: 0.8418 (mm-40)
REVERT: A  509 LYS cc_start: 0.8854 (ttmt) cc_final: 0.8454 (tttm)
REVERT: A  571 ARG cc_start: 0.8001 (ttt180) cc_final: 0.7485 (tmm160)
REVERT: A  607 LYS cc_start: 0.7180 (mttt) cc_final: 0.6961 (pptt)
REVERT: A  611 MET cc_start: 0.8628 (ttp) cc_final: 0.8379 (ttp)
REVERT: A  695 LYS cc_start: 0.7648 (ptpt) cc_final: 0.6668 (tttp)
REVERT: A  706 ARG cc_start: 0.7994 (mmm-85) cc_final: 0.7750 (mmm-85)
REVERT: A  744 MET cc_start: 0.5202 (OUTLIER) cc_final: 0.4228 (pp-130)
REVERT: A  800 LYS cc_start: 0.7767 (mtmt) cc_final: 0.7516 (mmtm)
REVERT: A 1020 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7777 (pm20)
REVERT: A 1021 LYS cc_start: 0.8556 (mtpt) cc_final: 0.8275 (mmtm)
REVERT: A 1140 GLU cc_start: 0.8482 (tt0) cc_final: 0.8240 (mt-10)
REVERT: A 1169 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7640 (mm-30)
REVERT: A 1176 ASN cc_start: 0.8365 (t0) cc_final: 0.8027 (t0)
REVERT: A 1194 LYS cc_start: 0.7379 (mtmm) cc_final: 0.7128 (ptpt)
REVERT: A 1210 ARG cc_start: 0.8447 (mtp85) cc_final: 0.7792 (mtt90)
REVERT: A 1253 LYS cc_start: 0.8591 (ptmt) cc_final: 0.8292 (ptmm)
REVERT: A 1274 GLN cc_start: 0.8515 (mm-40) cc_final: 0.7893 (tt0)
  outliers start: 20
  outliers final: 10
  residues processed: 179
  average time/residue: 0.3237
  time to fit residues: 78.8211
Evaluate side-chains
  160 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 149
  time to evaluate  : 1.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
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  805 ILE
Chi-restraints excluded: chain A residue 1011 GLU
Chi-restraints excluded: chain A residue 1061 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 86 optimal weight:    0.9980
   chunk 4 optimal weight:    0.8980
   chunk 82 optimal weight:    0.9990
   chunk 61 optimal weight:    4.9990
   chunk 90 optimal weight:    7.9990
   chunk 113 optimal weight:    0.9980
   chunk 100 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 38 optimal weight:    9.9990
   overall best weight:    0.9780

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

Flipped N/Q/H residues before XYZ refinement:
A 183 ASN
A 544 ASN
A 602 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.148274 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.120349 restraints weight = 12073.322|
|-----------------------------------------------------------------------------|
r_work (start): 0.3368 rms_B_bonded: 2.18
r_work: 0.3231 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3092 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.3092
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8295
moved from start:          0.3012

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9916  Z= 0.181
  Angle     :  0.576   6.773  13450  Z= 0.302
  Chirality :  0.042   0.154   1562
  Planarity :  0.004   0.039   1660
  Dihedral  :  7.876  79.109   1373
  Min Nonbonded Distance : 1.858

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 12.16 %
    Favored  : 85.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.80 (0.24), residues: 1203
  helix:  0.93 (0.18), residues: 773
  sheet: -0.86 (0.57), residues: 70
  loop :  0.22 (0.34), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 763 
 HIS   0.005   0.001   HIS A 152 
 PHE   0.018   0.002   PHE A 698 
 TYR   0.013   0.002   TYR A1259 
 ARG   0.005   0.000   ARG A 384 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04724 (  615)
  hydrogen bonds       : angle       4.66039 ( 1794)
  covalent geometry    : bond        0.00430 ( 9916)
  covalent geometry    : angle       0.57616 (13450)

*********************** 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
  181 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 156
  time to evaluate  : 1.250 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.7960 (pt0) cc_final: 0.7323 (pm20)
REVERT: A   76 GLN cc_start: 0.5589 (pt0) cc_final: 0.5230 (mt0)
REVERT: A   77 LYS cc_start: 0.8187 (pptt) cc_final: 0.7926 (mmmt)
REVERT: A   89 TRP cc_start: 0.8683 (p-90) cc_final: 0.8456 (p-90)
REVERT: A  226 THR cc_start: 0.8945 (t) cc_final: 0.8734 (m)
REVERT: A  232 GLU cc_start: 0.7683 (tp30) cc_final: 0.7444 (tm-30)
REVERT: A  264 LYS cc_start: 0.8631 (mttp) cc_final: 0.8399 (mttt)
REVERT: A  413 GLN cc_start: 0.8439 (tt0) cc_final: 0.8016 (tp40)
REVERT: A  509 LYS cc_start: 0.8893 (ttmt) cc_final: 0.8478 (tttp)
REVERT: A  571 ARG cc_start: 0.8015 (ttt180) cc_final: 0.7478 (tmm160)
REVERT: A  695 LYS cc_start: 0.7619 (ptpt) cc_final: 0.6571 (tttp)
REVERT: A  744 MET cc_start: 0.5186 (OUTLIER) cc_final: 0.4143 (pp-130)
REVERT: A  800 LYS cc_start: 0.7837 (mtmt) cc_final: 0.7545 (mmtm)
REVERT: A 1020 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7787 (pm20)
REVERT: A 1021 LYS cc_start: 0.8608 (mtpt) cc_final: 0.8302 (mmtm)
REVERT: A 1140 GLU cc_start: 0.8413 (tt0) cc_final: 0.8204 (mt-10)
REVERT: A 1176 ASN cc_start: 0.8437 (t0) cc_final: 0.8125 (t0)
REVERT: A 1194 LYS cc_start: 0.7657 (mtmm) cc_final: 0.7341 (ptpt)
REVERT: A 1210 ARG cc_start: 0.8479 (mtp85) cc_final: 0.7628 (mpt180)
REVERT: A 1272 MET cc_start: 0.7581 (mtp) cc_final: 0.7263 (mtt)
REVERT: A 1274 GLN cc_start: 0.8518 (mm-40) cc_final: 0.7940 (tt0)
  outliers start: 25
  outliers final: 20
  residues processed: 168
  average time/residue: 0.2619
  time to fit residues: 59.6965
Evaluate side-chains
  169 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 148
  time to evaluate  : 1.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 ASP
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  285 ILE
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  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 1011 GLU
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 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 57 optimal weight:    0.0270
   chunk 92 optimal weight:    0.5980
   chunk 24 optimal weight:    1.9990
   chunk 76 optimal weight:    0.9990
   chunk 1 optimal weight:    0.6980
   chunk 16 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9980
   chunk 84 optimal weight:    0.0980
   chunk 3 optimal weight:    0.7980
   chunk 19 optimal weight:    0.7980
   overall best weight:    0.4438

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

Flipped N/Q/H residues before XYZ refinement:
A 183 ASN
A1196 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.151760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.123537 restraints weight = 11961.468|
|-----------------------------------------------------------------------------|
r_work (start): 0.3436 rms_B_bonded: 2.21
r_work: 0.3301 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3160 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3160
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8228
moved from start:          0.3366

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9916  Z= 0.121
  Angle     :  0.514   6.838  13450  Z= 0.272
  Chirality :  0.039   0.147   1562
  Planarity :  0.003   0.039   1660
  Dihedral  :  7.548  83.014   1373
  Min Nonbonded Distance : 1.973

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 13.58 %
    Favored  : 84.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.12 (0.24), residues: 1203
  helix:  1.23 (0.19), residues: 769
  sheet: -0.68 (0.59), residues: 70
  loop :  0.21 (0.34), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 763 
 HIS   0.003   0.001   HIS A 153 
 PHE   0.018   0.001   PHE A 698 
 TYR   0.014   0.001   TYR A1259 
 ARG   0.005   0.000   ARG A 384 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04177 (  615)
  hydrogen bonds       : angle       4.43274 ( 1794)
  covalent geometry    : bond        0.00262 ( 9916)
  covalent geometry    : angle       0.51401 (13450)

*********************** 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
  186 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 164
  time to evaluate  : 1.167 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.7817 (pt0) cc_final: 0.7274 (pm20)
REVERT: A   76 GLN cc_start: 0.5587 (pt0) cc_final: 0.5267 (mt0)
REVERT: A   77 LYS cc_start: 0.8242 (pptt) cc_final: 0.7973 (mmmt)
REVERT: A   89 TRP cc_start: 0.8646 (p-90) cc_final: 0.8430 (p-90)
REVERT: A  226 THR cc_start: 0.8922 (t) cc_final: 0.8680 (m)
REVERT: A  264 LYS cc_start: 0.8612 (mttp) cc_final: 0.8358 (mttt)
REVERT: A  276 MET cc_start: 0.8906 (tpp) cc_final: 0.8654 (mmm)
REVERT: A  338 THR cc_start: 0.8346 (OUTLIER) cc_final: 0.7970 (p)
REVERT: A  413 GLN cc_start: 0.8443 (tt0) cc_final: 0.7906 (tp40)
REVERT: A  509 LYS cc_start: 0.8887 (ttmt) cc_final: 0.8476 (tttp)
REVERT: A  571 ARG cc_start: 0.7983 (ttt180) cc_final: 0.7447 (tmm160)
REVERT: A  715 ILE cc_start: 0.8217 (mp) cc_final: 0.7887 (tp)
REVERT: A  744 MET cc_start: 0.5069 (OUTLIER) cc_final: 0.4100 (pp-130)
REVERT: A  800 LYS cc_start: 0.7741 (mtmt) cc_final: 0.7535 (mmtm)
REVERT: A  845 GLN cc_start: 0.7542 (pt0) cc_final: 0.7337 (mt0)
REVERT: A  931 GLN cc_start: 0.8307 (mm-40) cc_final: 0.7896 (mt0)
REVERT: A 1020 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7771 (pm20)
REVERT: A 1021 LYS cc_start: 0.8588 (mtpt) cc_final: 0.8291 (mmtm)
REVERT: A 1140 GLU cc_start: 0.8445 (tt0) cc_final: 0.8133 (mt-10)
REVERT: A 1176 ASN cc_start: 0.8346 (t0) cc_final: 0.8055 (t0)
REVERT: A 1195 ASN cc_start: 0.8339 (m-40) cc_final: 0.7788 (m-40)
REVERT: A 1210 ARG cc_start: 0.8446 (mtp85) cc_final: 0.7608 (mpt180)
REVERT: A 1259 TYR cc_start: 0.8150 (t80) cc_final: 0.7872 (t80)
REVERT: A 1274 GLN cc_start: 0.8448 (mm-40) cc_final: 0.7868 (tt0)
  outliers start: 22
  outliers final: 13
  residues processed: 175
  average time/residue: 0.2764
  time to fit residues: 66.2170
Evaluate side-chains
  157 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 142
  time to evaluate  : 1.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  416 THR
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 1011 GLU
Chi-restraints excluded: chain A residue 1061 LEU
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 59 optimal weight:    7.9990
   chunk 3 optimal weight:    0.2980
   chunk 38 optimal weight:    0.0870
   chunk 87 optimal weight:    0.8980
   chunk 37 optimal weight:    0.5980
   chunk 74 optimal weight:    0.5980
   chunk 8 optimal weight:    0.9990
   chunk 71 optimal weight:    0.6980
   chunk 31 optimal weight:    1.9990
   chunk 113 optimal weight:    0.9980
   chunk 79 optimal weight:    1.9990
   overall best weight:    0.4558

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

Flipped N/Q/H residues before XYZ refinement:
A 183 ASN

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 = 0.151329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.124832 restraints weight = 11948.728|
|-----------------------------------------------------------------------------|
r_work (start): 0.3385 rms_B_bonded: 1.98
r_work: 0.3252 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3111 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8217
moved from start:          0.3538

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= 0.128
  Angle     :  0.534   8.136  13450  Z= 0.281
  Chirality :  0.040   0.176   1562
  Planarity :  0.003   0.039   1660
  Dihedral  :  7.505  87.085   1371
  Min Nonbonded Distance : 1.933

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 15.00 %
    Favored  : 83.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.24 (0.24), residues: 1203
  helix:  1.34 (0.18), residues: 770
  sheet: -0.64 (0.60), residues: 70
  loop :  0.21 (0.34), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 763 
 HIS   0.002   0.001   HIS A 934 
 PHE   0.020   0.001   PHE A 352 
 TYR   0.011   0.001   TYR A1270 
 ARG   0.006   0.000   ARG A 384 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04172 (  615)
  hydrogen bonds       : angle       4.36153 ( 1794)
  covalent geometry    : bond        0.00284 ( 9916)
  covalent geometry    : angle       0.53373 (13450)

*********************** 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: 16
    poor density    : 151
  time to evaluate  : 1.108 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.7942 (pt0) cc_final: 0.7342 (pm20)
REVERT: A   76 GLN cc_start: 0.5579 (pt0) cc_final: 0.5278 (mt0)
REVERT: A   77 LYS cc_start: 0.8212 (pptt) cc_final: 0.7968 (mmmt)
REVERT: A   89 TRP cc_start: 0.8640 (p-90) cc_final: 0.8422 (p-90)
REVERT: A  226 THR cc_start: 0.8887 (t) cc_final: 0.8679 (m)
REVERT: A  264 LYS cc_start: 0.8601 (mttp) cc_final: 0.8353 (mttt)
REVERT: A  276 MET cc_start: 0.8888 (tpp) cc_final: 0.8483 (mmm)
REVERT: A  338 THR cc_start: 0.8339 (OUTLIER) cc_final: 0.7947 (p)
REVERT: A  384 ARG cc_start: 0.8047 (mtm110) cc_final: 0.7772 (mtm-85)
REVERT: A  413 GLN cc_start: 0.8408 (tt0) cc_final: 0.7863 (tp40)
REVERT: A  571 ARG cc_start: 0.7906 (ttt180) cc_final: 0.7423 (tmm160)
REVERT: A  744 MET cc_start: 0.5024 (OUTLIER) cc_final: 0.4036 (pp-130)
REVERT: A  800 LYS cc_start: 0.7742 (mtmt) cc_final: 0.7482 (mmtm)
REVERT: A 1020 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7741 (pm20)
REVERT: A 1021 LYS cc_start: 0.8628 (mtpt) cc_final: 0.8311 (mmtm)
REVERT: A 1176 ASN cc_start: 0.8365 (t0) cc_final: 0.8069 (t0)
REVERT: A 1195 ASN cc_start: 0.8140 (m-40) cc_final: 0.7539 (m-40)
REVERT: A 1210 ARG cc_start: 0.8398 (mtp85) cc_final: 0.7588 (mpt180)
REVERT: A 1263 GLN cc_start: 0.7662 (pt0) cc_final: 0.7034 (pp30)
REVERT: A 1274 GLN cc_start: 0.8505 (mm-40) cc_final: 0.7985 (tt0)
  outliers start: 16
  outliers final: 11
  residues processed: 160
  average time/residue: 0.2564
  time to fit residues: 56.5904
Evaluate side-chains
  154 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 141
  time to evaluate  : 1.015 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  338 THR
Chi-restraints excluded: chain A residue  416 THR
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 1011 GLU
Chi-restraints excluded: chain A residue 1061 LEU
Chi-restraints excluded: chain A residue 1104 LEU
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 118 optimal weight:    3.9990
   chunk 117 optimal weight:    0.4980
   chunk 42 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 81 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   chunk 115 optimal weight:    3.9990
   chunk 64 optimal weight:    0.8980
   chunk 17 optimal weight:    5.9990
   chunk 110 optimal weight:    0.9980
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
A 109 GLN
A 183 ASN
A1151 GLN
A1196 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.147917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.120928 restraints weight = 12162.213|
|-----------------------------------------------------------------------------|
r_work (start): 0.3336 rms_B_bonded: 2.02
r_work: 0.3205 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3066 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8287
moved from start:          0.3496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057   9916  Z= 0.193
  Angle     :  0.580   8.534  13450  Z= 0.305
  Chirality :  0.042   0.149   1562
  Planarity :  0.004   0.041   1660
  Dihedral  :  7.776  88.312   1371
  Min Nonbonded Distance : 1.863

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 15.10 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.00 (0.24), residues: 1203
  helix:  1.13 (0.18), residues: 770
  sheet: -0.71 (0.59), residues: 70
  loop :  0.18 (0.33), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 230 
 HIS   0.005   0.001   HIS A 152 
 PHE   0.019   0.002   PHE A 698 
 TYR   0.013   0.001   TYR A 737 
 ARG   0.005   0.000   ARG A 706 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04621 (  615)
  hydrogen bonds       : angle       4.54569 ( 1794)
  covalent geometry    : bond        0.00464 ( 9916)
  covalent geometry    : angle       0.58002 (13450)

*********************** 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
  161 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 141
  time to evaluate  : 1.075 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8032 (pt0) cc_final: 0.7414 (pm20)
REVERT: A   76 GLN cc_start: 0.5694 (pt0) cc_final: 0.5260 (mt0)
REVERT: A   77 LYS cc_start: 0.8185 (pptt) cc_final: 0.7920 (mmmt)
REVERT: A   89 TRP cc_start: 0.8655 (p-90) cc_final: 0.8439 (p-90)
REVERT: A  264 LYS cc_start: 0.8661 (mttp) cc_final: 0.8429 (mttt)
REVERT: A  276 MET cc_start: 0.8897 (tpp) cc_final: 0.8515 (mmm)
REVERT: A  338 THR cc_start: 0.8496 (OUTLIER) cc_final: 0.7984 (p)
REVERT: A  413 GLN cc_start: 0.8387 (tt0) cc_final: 0.7869 (tp40)
REVERT: A  571 ARG cc_start: 0.7971 (ttt180) cc_final: 0.7422 (tmm160)
REVERT: A  715 ILE cc_start: 0.8256 (mp) cc_final: 0.8036 (tp)
REVERT: A  744 MET cc_start: 0.4959 (OUTLIER) cc_final: 0.3999 (pp-130)
REVERT: A  800 LYS cc_start: 0.7818 (mtmt) cc_final: 0.7509 (mmtm)
REVERT: A 1020 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7753 (pm20)
REVERT: A 1021 LYS cc_start: 0.8705 (mtpt) cc_final: 0.8372 (mmtm)
REVERT: A 1176 ASN cc_start: 0.8421 (t0) cc_final: 0.8097 (t0)
REVERT: A 1195 ASN cc_start: 0.8381 (m-40) cc_final: 0.7789 (m-40)
REVERT: A 1210 ARG cc_start: 0.8446 (mtp85) cc_final: 0.7610 (mpt180)
REVERT: A 1274 GLN cc_start: 0.8510 (mm-40) cc_final: 0.7947 (tt0)
  outliers start: 20
  outliers final: 14
  residues processed: 153
  average time/residue: 0.2472
  time to fit residues: 51.7622
Evaluate side-chains
  151 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 135
  time to evaluate  : 1.060 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  116 ILE
Chi-restraints excluded: chain A residue  338 THR
Chi-restraints excluded: chain A residue  351 VAL
Chi-restraints excluded: chain A residue  416 THR
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 1011 GLU
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 4 optimal weight:    2.9990
   chunk 75 optimal weight:    0.7980
   chunk 21 optimal weight:    0.7980
   chunk 89 optimal weight:    9.9990
   chunk 48 optimal weight:    0.5980
   chunk 45 optimal weight:    2.9990
   chunk 70 optimal weight:    0.5980
   chunk 66 optimal weight:    6.9990
   chunk 96 optimal weight:    0.0970
   chunk 8 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   overall best weight:    0.5778

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

Flipped N/Q/H residues before XYZ refinement:
A 183 ASN
A 849 GLN
A1151 GLN
A1196 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.149023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.120685 restraints weight = 12267.803|
|-----------------------------------------------------------------------------|
r_work (start): 0.3373 rms_B_bonded: 2.25
r_work: 0.3242 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3099 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8253
moved from start:          0.3666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9916  Z= 0.135
  Angle     :  0.527   7.978  13450  Z= 0.278
  Chirality :  0.040   0.147   1562
  Planarity :  0.003   0.041   1660
  Dihedral  :  7.604  79.056   1371
  Min Nonbonded Distance : 1.962

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 15.29 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.19 (0.24), residues: 1203
  helix:  1.29 (0.18), residues: 771
  sheet: -0.65 (0.61), residues: 70
  loop :  0.20 (0.34), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 230 
 HIS   0.003   0.001   HIS A 934 
 PHE   0.017   0.001   PHE A 698 
 TYR   0.012   0.001   TYR A1259 
 ARG   0.007   0.000   ARG A 384 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04218 (  615)
  hydrogen bonds       : angle       4.40129 ( 1794)
  covalent geometry    : bond        0.00307 ( 9916)
  covalent geometry    : angle       0.52676 (13450)

*********************** 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
  159 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 141
  time to evaluate  : 1.046 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8047 (pt0) cc_final: 0.7465 (pm20)
REVERT: A   76 GLN cc_start: 0.5596 (pt0) cc_final: 0.5205 (mt0)
REVERT: A   77 LYS cc_start: 0.8166 (pptt) cc_final: 0.7887 (mmmt)
REVERT: A   89 TRP cc_start: 0.8653 (p-90) cc_final: 0.8426 (p-90)
REVERT: A  264 LYS cc_start: 0.8619 (mttp) cc_final: 0.8376 (mttt)
REVERT: A  276 MET cc_start: 0.8899 (tpp) cc_final: 0.8509 (mmm)
REVERT: A  338 THR cc_start: 0.8374 (OUTLIER) cc_final: 0.7963 (p)
REVERT: A  384 ARG cc_start: 0.8086 (mtm110) cc_final: 0.7810 (mtm-85)
REVERT: A  413 GLN cc_start: 0.8388 (tt0) cc_final: 0.7967 (tp40)
REVERT: A  571 ARG cc_start: 0.7986 (ttt180) cc_final: 0.7407 (tmm160)
REVERT: A  715 ILE cc_start: 0.8181 (mp) cc_final: 0.7933 (tp)
REVERT: A  744 MET cc_start: 0.4849 (OUTLIER) cc_final: 0.3896 (pp-130)
REVERT: A  800 LYS cc_start: 0.7803 (mtmt) cc_final: 0.7512 (mmtm)
REVERT: A 1016 TYR cc_start: 0.8553 (m-10) cc_final: 0.8325 (m-10)
REVERT: A 1020 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7751 (pm20)
REVERT: A 1021 LYS cc_start: 0.8690 (mtpt) cc_final: 0.8347 (mmtm)
REVERT: A 1176 ASN cc_start: 0.8403 (t0) cc_final: 0.8096 (t0)
REVERT: A 1195 ASN cc_start: 0.8183 (m-40) cc_final: 0.7588 (m-40)
REVERT: A 1210 ARG cc_start: 0.8452 (mtp85) cc_final: 0.7597 (mpt180)
REVERT: A 1259 TYR cc_start: 0.8117 (t80) cc_final: 0.7857 (t80)
REVERT: A 1274 GLN cc_start: 0.8457 (mm-40) cc_final: 0.7916 (tt0)
  outliers start: 18
  outliers final: 14
  residues processed: 152
  average time/residue: 0.2426
  time to fit residues: 50.4645
Evaluate side-chains
  154 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 138
  time to evaluate  : 1.034 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  116 ILE
Chi-restraints excluded: chain A residue  338 THR
Chi-restraints excluded: chain A residue  351 VAL
Chi-restraints excluded: chain A residue  416 THR
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 1011 GLU
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 1187 LEU
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 72 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 24 optimal weight:    1.9990
   chunk 94 optimal weight:    0.6980
   chunk 42 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   chunk 100 optimal weight:    0.5980
   chunk 98 optimal weight:    1.9990
   chunk 50 optimal weight:    0.6980
   chunk 55 optimal weight:    1.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 183 ASN
A1151 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.149014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.120514 restraints weight = 12274.832|
|-----------------------------------------------------------------------------|
r_work (start): 0.3355 rms_B_bonded: 2.21
r_work: 0.3223 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3081 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3081
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8274
moved from start:          0.3690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9916  Z= 0.154
  Angle     :  0.544   8.260  13450  Z= 0.286
  Chirality :  0.040   0.160   1562
  Planarity :  0.003   0.041   1660
  Dihedral  :  7.412  81.473   1371
  Min Nonbonded Distance : 1.934

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 15.57 %
    Favored  : 82.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.15 (0.24), residues: 1203
  helix:  1.30 (0.19), residues: 765
  sheet: -0.61 (0.62), residues: 65
  loop :  0.08 (0.33), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A 230 
 HIS   0.003   0.001   HIS A 934 
 PHE   0.019   0.001   PHE A 698 
 TYR   0.018   0.001   TYR A 737 
 ARG   0.007   0.000   ARG A 384 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04340 (  615)
  hydrogen bonds       : angle       4.43117 ( 1794)
  covalent geometry    : bond        0.00360 ( 9916)
  covalent geometry    : angle       0.54412 (13450)

*********************** 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
  156 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 137
  time to evaluate  : 1.148 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8074 (pt0) cc_final: 0.7460 (pm20)
REVERT: A   76 GLN cc_start: 0.5616 (pt0) cc_final: 0.5187 (mt0)
REVERT: A   77 LYS cc_start: 0.8179 (pptt) cc_final: 0.7907 (mmmt)
REVERT: A   89 TRP cc_start: 0.8655 (p-90) cc_final: 0.8433 (p-90)
REVERT: A  264 LYS cc_start: 0.8644 (mttp) cc_final: 0.8421 (mttt)
REVERT: A  276 MET cc_start: 0.8901 (tpp) cc_final: 0.8514 (mmm)
REVERT: A  338 THR cc_start: 0.8449 (OUTLIER) cc_final: 0.7985 (p)
REVERT: A  384 ARG cc_start: 0.8098 (mtm110) cc_final: 0.7825 (mtm-85)
REVERT: A  413 GLN cc_start: 0.8400 (tt0) cc_final: 0.7969 (tp40)
REVERT: A  571 ARG cc_start: 0.8002 (ttt180) cc_final: 0.7432 (tmm160)
REVERT: A  715 ILE cc_start: 0.8131 (mp) cc_final: 0.7879 (tp)
REVERT: A  744 MET cc_start: 0.4876 (OUTLIER) cc_final: 0.3909 (pp-130)
REVERT: A  800 LYS cc_start: 0.7811 (mtmt) cc_final: 0.7511 (mmtm)
REVERT: A 1016 TYR cc_start: 0.8574 (m-10) cc_final: 0.8342 (m-10)
REVERT: A 1020 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7723 (pm20)
REVERT: A 1021 LYS cc_start: 0.8690 (mtpt) cc_final: 0.8333 (mmtm)
REVERT: A 1176 ASN cc_start: 0.8424 (t0) cc_final: 0.8120 (t0)
REVERT: A 1195 ASN cc_start: 0.8234 (m-40) cc_final: 0.7572 (m110)
REVERT: A 1210 ARG cc_start: 0.8450 (mtp85) cc_final: 0.7593 (mpt180)
REVERT: A 1274 GLN cc_start: 0.8456 (mm-40) cc_final: 0.7890 (tt0)
  outliers start: 19
  outliers final: 16
  residues processed: 150
  average time/residue: 0.2711
  time to fit residues: 55.6812
Evaluate side-chains
  150 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 132
  time to evaluate  : 1.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  116 ILE
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  338 THR
Chi-restraints excluded: chain A residue  351 VAL
Chi-restraints excluded: chain A residue  416 THR
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 1011 GLU
Chi-restraints excluded: chain A residue 1046 VAL
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 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 37 optimal weight:    0.3980
   chunk 112 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 109 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9980
   chunk 85 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9990
   chunk 102 optimal weight:    0.9990
   chunk 104 optimal weight:    0.9990
   chunk 66 optimal weight:    0.9980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 183 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.147926 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.120684 restraints weight = 12107.056|
|-----------------------------------------------------------------------------|
r_work (start): 0.3373 rms_B_bonded: 2.09
r_work: 0.3237 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3094 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3094
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8274
moved from start:          0.3713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9916  Z= 0.165
  Angle     :  0.561   9.122  13450  Z= 0.294
  Chirality :  0.041   0.155   1562
  Planarity :  0.003   0.041   1660
  Dihedral  :  7.270  68.584   1371
  Min Nonbonded Distance : 1.911

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 15.67 %
    Favored  : 82.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.10 (0.24), residues: 1203
  helix:  1.26 (0.18), residues: 765
  sheet: -0.59 (0.62), residues: 65
  loop :  0.04 (0.33), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 230 
 HIS   0.004   0.001   HIS A 934 
 PHE   0.018   0.001   PHE A 698 
 TYR   0.019   0.001   TYR A 737 
 ARG   0.006   0.000   ARG A 384 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04394 (  615)
  hydrogen bonds       : angle       4.46028 ( 1794)
  covalent geometry    : bond        0.00389 ( 9916)
  covalent geometry    : angle       0.56081 (13450)

********************** 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
  153 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 134
  time to evaluate  : 1.122 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8080 (pt0) cc_final: 0.7456 (pm20)
REVERT: A   76 GLN cc_start: 0.5648 (pt0) cc_final: 0.5215 (mt0)
REVERT: A   77 LYS cc_start: 0.8159 (pptt) cc_final: 0.7892 (mmmt)
REVERT: A   89 TRP cc_start: 0.8650 (p-90) cc_final: 0.8423 (p-90)
REVERT: A  264 LYS cc_start: 0.8638 (mttp) cc_final: 0.8416 (mttt)
REVERT: A  276 MET cc_start: 0.8896 (tpp) cc_final: 0.8509 (mmm)
REVERT: A  338 THR cc_start: 0.8470 (OUTLIER) cc_final: 0.7982 (p)
REVERT: A  384 ARG cc_start: 0.8084 (mtm110) cc_final: 0.7814 (mtm-85)
REVERT: A  413 GLN cc_start: 0.8396 (tt0) cc_final: 0.7967 (tp40)
REVERT: A  715 ILE cc_start: 0.8144 (mp) cc_final: 0.7888 (tp)
REVERT: A  744 MET cc_start: 0.4910 (OUTLIER) cc_final: 0.3932 (pp-130)
REVERT: A  800 LYS cc_start: 0.7804 (mtmt) cc_final: 0.7494 (mmtm)
REVERT: A 1016 TYR cc_start: 0.8584 (m-10) cc_final: 0.8354 (m-10)
REVERT: A 1020 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7736 (pm20)
REVERT: A 1021 LYS cc_start: 0.8703 (mtpt) cc_final: 0.8299 (mmtm)
REVERT: A 1176 ASN cc_start: 0.8379 (t0) cc_final: 0.8080 (t0)
REVERT: A 1195 ASN cc_start: 0.8237 (m-40) cc_final: 0.7586 (m110)
REVERT: A 1210 ARG cc_start: 0.8449 (mtp85) cc_final: 0.7592 (mpt180)
REVERT: A 1259 TYR cc_start: 0.8091 (t80) cc_final: 0.7843 (t80)
REVERT: A 1274 GLN cc_start: 0.8463 (mm-40) cc_final: 0.7909 (tt0)
  outliers start: 19
  outliers final: 17
  residues processed: 147
  average time/residue: 0.3201
  time to fit residues: 65.7520
Evaluate side-chains
  151 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 132
  time to evaluate  : 1.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  116 ILE
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  338 THR
Chi-restraints excluded: chain A residue  351 VAL
Chi-restraints excluded: chain A residue  416 THR
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 1011 GLU
Chi-restraints excluded: chain A residue 1046 VAL
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 1187 LEU
Chi-restraints excluded: chain A residue 1238 ILE
Chi-restraints excluded: chain A residue 1247 LEU
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 49 optimal weight:    0.5980
   chunk 50 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 116 optimal weight:    1.9990
   chunk 2 optimal weight:    0.0980
   chunk 52 optimal weight:    0.6980
   chunk 64 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9980
   chunk 57 optimal weight:    1.9990
   chunk 94 optimal weight:    0.1980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
A1151 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 = 0.151452 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.125540 restraints weight = 11982.408|
|-----------------------------------------------------------------------------|
r_work (start): 0.3412 rms_B_bonded: 1.92
r_work: 0.3281 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3144 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8236
moved from start:          0.3846

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= 0.132
  Angle     :  0.530   7.939  13450  Z= 0.280
  Chirality :  0.040   0.154   1562
  Planarity :  0.003   0.041   1660
  Dihedral  :  6.976  59.246   1371
  Min Nonbonded Distance : 1.923

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 15.95 %
    Favored  : 82.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.26 (0.24), residues: 1203
  helix:  1.40 (0.19), residues: 765
  sheet: -0.52 (0.63), residues: 65
  loop :  0.07 (0.33), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 230 
 HIS   0.003   0.001   HIS A 153 
 PHE   0.019   0.001   PHE A 698 
 TYR   0.017   0.001   TYR A 737 
 ARG   0.006   0.000   ARG A 384 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04142 (  615)
  hydrogen bonds       : angle       4.35538 ( 1794)
  covalent geometry    : bond        0.00297 ( 9916)
  covalent geometry    : angle       0.52994 (13450)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5989.97 seconds
wall clock time: 105 minutes 48.69 seconds (6348.69 seconds total)