Starting phenix.real_space_refine
on Mon Jul 28 00:13:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7y1j_33563/07_2025/7y1j_33563.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7y1j_33563/07_2025/7y1j_33563.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7y1j_33563/07_2025/7y1j_33563.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7y1j_33563/07_2025/7y1j_33563.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7y1j_33563/07_2025/7y1j_33563.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7y1j_33563/07_2025/7y1j_33563.cif"
  }
  resolution = 3.0
  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=   0.001 sd=   0.138
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      51      5.16       5
     C    6129      2.51       5
     N    1573      2.21       5
     O    1726      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 9487
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 9390
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1204, 9390
          Classifications: {'peptide': 1204}
          Incomplete info: {'truncation_to_alanine': 26}
          Link IDs: {'PTRANS': 35, 'TRANS': 1168}
          Chain breaks: 6
          Unresolved non-hydrogen bonds: 103
          Unresolved non-hydrogen angles: 122
          Unresolved non-hydrogen dihedrals: 86
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 6, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 61
    Chain: "A"
      Number of atoms: 97
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 97
          Unusual residues: {' MG': 2, 'ATP': 2, 'BJX': 1}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
  Time building chain proxies: 6.06, per 1000 atoms: 0.64
  Number of scatterers: 9487
  At special positions: 0
  Unit cell: (70.5324, 102.939, 133.44, 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      51     16.00
     P       6     15.00
     Mg      2     11.99
     O    1726      8.00
     N    1573      7.00
     C    6129      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: 2.36
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2270

  Finding SS restraints...
    Secondary structure from input PDB file:
      51 helices and 5 sheets defined
      72.8% alpha, 8.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.02
  Creating SS restraints...
    Processing helix  chain 'A' and resid 216 through 227
    Processing helix  chain 'A' and resid 228 through 230
      No H-bonds generated for 'chain 'A' and resid 228 through 230'
    Processing helix  chain 'A' and resid 231 through 241
      removed outlier: 3.525A  pdb=" N   ALA A 238 " --> pdb=" O   LEU A 234 " (cutoff:3.500A)
      removed outlier: 4.180A  pdb=" N   HIS A 239 " --> pdb=" O   ILE A 235 " (cutoff:3.500A)
      removed outlier: 4.148A  pdb=" N   ARG A 240 " --> pdb=" O   ILE A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 255
    Processing helix  chain 'A' and resid 256 through 274
      removed outlier: 3.521A  pdb=" N   LYS A 274 " --> pdb=" O   GLU A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 293
    Processing helix  chain 'A' and resid 294 through 312
      removed outlier: 3.528A  pdb=" N   PHE A 312 " --> pdb=" O   ASP A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 324
    Processing helix  chain 'A' and resid 343 through 346
    Processing helix  chain 'A' and resid 347 through 395
    Processing helix  chain 'A' and resid 405 through 416
    Processing helix  chain 'A' and resid 416 through 450
      Proline residue:  A 429  - end of helix
      removed outlier: 3.993A  pdb=" N   TRP A 432 " --> pdb=" O   CYS A 428 " (cutoff:3.500A)
      Proline residue:  A 435  - end of helix
    Processing helix  chain 'A' and resid 451 through 462
      removed outlier: 3.929A  pdb=" N   VAL A 455 " --> pdb=" O   SER A 451 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   GLY A 456 " --> pdb=" O   SER A 452 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 462 through 497
      removed outlier: 3.575A  pdb=" N   ILE A 466 " --> pdb=" O   LEU A 462 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 506
    Processing helix  chain 'A' and resid 507 through 558
      removed outlier: 3.653A  pdb=" N   THR A 518 " --> pdb=" O   SER A 514 " (cutoff:3.500A)
      Proline residue:  A 544  - end of helix
    Processing helix  chain 'A' and resid 564 through 607
      removed outlier: 4.243A  pdb=" N   THR A 580 " --> pdb=" O   HIS A 576 " (cutoff:3.500A)
      Proline residue:  A 581  - end of helix
      removed outlier: 4.677A  pdb=" N   SER A 586 " --> pdb=" O   LEU A 582 " (cutoff:3.500A)
      removed outlier: 4.579A  pdb=" N   THR A 587 " --> pdb=" O   PHE A 583 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 706 through 715
    Processing helix  chain 'A' and resid 761 through 768
    Processing helix  chain 'A' and resid 773 through 784
    Processing helix  chain 'A' and resid 786 through 792
      removed outlier: 3.730A  pdb=" N   LEU A 792 " --> pdb=" O   PRO A 788 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 795 through 799
      removed outlier: 3.720A  pdb=" N   GLN A 798 " --> pdb=" O   PHE A 795 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 809 through 824
      removed outlier: 3.544A  pdb=" N   GLN A 824 " --> pdb=" O   ARG A 820 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 839 through 850
    Processing helix  chain 'A' and resid 853 through 858
      removed outlier: 3.535A  pdb=" N   ASP A 858 " --> pdb=" O   PHE A 854 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 868 through 875
      removed outlier: 3.927A  pdb=" N   THR A 873 " --> pdb=" O   GLN A 870 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 891 through 899
    Processing helix  chain 'A' and resid 899 through 921
      removed outlier: 4.070A  pdb=" N   LYS A 919 " --> pdb=" O   GLN A 915 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   ASP A 920 " --> pdb=" O   GLU A 916 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 924 through 937
      removed outlier: 3.535A  pdb=" N   LEU A 928 " --> pdb=" O   ASP A 924 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   MET A 937 " --> pdb=" O   LEU A 933 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 967 through 971
      removed outlier: 3.508A  pdb=" N   THR A 971 " --> pdb=" O   MET A 967 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 967 through 971'
    Processing helix  chain 'A' and resid 974 through 984
    Processing helix  chain 'A' and resid 986 through 1016
    Processing helix  chain 'A' and resid 1028 through 1074
      removed outlier: 3.604A  pdb=" N   GLU A1054 " --> pdb=" O   SER A1050 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   ASN A1070 " --> pdb=" O   HIS A1066 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1076 through 1083
      removed outlier: 3.813A  pdb=" N   PHE A1080 " --> pdb=" O   PRO A1076 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1084 through 1102
      removed outlier: 3.584A  pdb=" N   ILE A1088 " --> pdb=" O   PRO A1084 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   ASP A1095 " --> pdb=" O   ARG A1091 " (cutoff:3.500A)
      removed outlier: 4.513A  pdb=" N   THR A1096 " --> pdb=" O   PHE A1092 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1102 through 1128
    Processing helix  chain 'A' and resid 1130 through 1176
      removed outlier: 3.835A  pdb=" N   ALA A1134 " --> pdb=" O   VAL A1130 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ALA A1136 " --> pdb=" O   LEU A1132 " (cutoff:3.500A)
      Proline residue:  A1137  - end of helix
      removed outlier: 3.640A  pdb=" N   PHE A1149 " --> pdb=" O   ILE A1145 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   LYS A1154 " --> pdb=" O   ARG A1150 " (cutoff:3.500A)
      Proline residue:  A1166  - end of helix
    Processing helix  chain 'A' and resid 1177 through 1185
    Processing helix  chain 'A' and resid 1186 through 1237
    Processing helix  chain 'A' and resid 1240 through 1283
      removed outlier: 3.885A  pdb=" N   THR A1255 " --> pdb=" O   ALA A1251 " (cutoff:3.500A)
      removed outlier: 4.397A  pdb=" N   ASN A1256 " --> pdb=" O   LEU A1252 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   TYR A1257 " --> pdb=" O   THR A1253 " (cutoff:3.500A)
      removed outlier: 4.513A  pdb=" N   ASN A1259 " --> pdb=" O   THR A1255 " (cutoff:3.500A)
      removed outlier: 4.237A  pdb=" N   TRP A1260 " --> pdb=" O   ASN A1256 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   VAL A1262 " --> pdb=" O   LEU A1258 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   ALA A1274 " --> pdb=" O   VAL A1270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1348 through 1356
      removed outlier: 3.659A  pdb=" N   PHE A1356 " --> pdb=" O   SER A1352 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1377 through 1384
      removed outlier: 3.511A  pdb=" N   ARG A1384 " --> pdb=" O   THR A1380 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1399 through 1404
    Processing helix  chain 'A' and resid 1410 through 1421
    Processing helix  chain 'A' and resid 1423 through 1430
    Processing helix  chain 'A' and resid 1432 through 1435
      removed outlier: 3.628A  pdb=" N   ASP A1435 " --> pdb=" O   GLY A1432 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1432 through 1435'
    Processing helix  chain 'A' and resid 1446 through 1462
      removed outlier: 3.609A  pdb=" N   LYS A1462 " --> pdb=" O   ALA A1458 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1476 through 1491
    Processing helix  chain 'A' and resid 1502 through 1507
      removed outlier: 3.541A  pdb=" N   MET A1507 " --> pdb=" O   SER A1504 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1525 through 1532
      removed outlier: 3.593A  pdb=" N   HIS A1532 " --> pdb=" O   ASN A1528 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1535 through 1542
    Processing sheet with id=AA1, first strand: chain 'A' and resid 682 through 692
      removed outlier: 5.085A  pdb=" N   SER A 685 " --> pdb=" O   PHE A 675 " (cutoff:3.500A)
      removed outlier: 7.099A  pdb=" N   PHE A 675 " --> pdb=" O   SER A 685 " (cutoff:3.500A)
      removed outlier: 7.488A  pdb=" N   ILE A 689 " --> pdb=" O   THR A 671 " (cutoff:3.500A)
      removed outlier: 5.357A  pdb=" N   THR A 671 " --> pdb=" O   ILE A 689 " (cutoff:3.500A)
      removed outlier: 7.333A  pdb=" N   ILE A 691 " --> pdb=" O   LYS A 669 " (cutoff:3.500A)
      removed outlier: 5.824A  pdb=" N   LYS A 669 " --> pdb=" O   ILE A 691 " (cutoff:3.500A)
      removed outlier: 4.446A  pdb=" N   GLY A 673 " --> pdb=" O   GLU A 722 " (cutoff:3.500A)
      removed outlier: 6.246A  pdb=" N   GLU A 722 " --> pdb=" O   GLY A 673 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   PHE A 675 " --> pdb=" O   THR A 720 " (cutoff:3.500A)
      removed outlier: 6.716A  pdb=" N   THR A 720 " --> pdb=" O   PHE A 675 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 748 through 751
      removed outlier: 6.513A  pdb=" N   VAL A 829 " --> pdb=" O   VAL A 863 " (cutoff:3.500A)
      removed outlier: 7.665A  pdb=" N   VAL A 865 " --> pdb=" O   VAL A 829 " (cutoff:3.500A)
      removed outlier: 6.635A  pdb=" N   LEU A 831 " --> pdb=" O   VAL A 865 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   THR A 697 " --> pdb=" O   LEU A 864 " (cutoff:3.500A)
      removed outlier: 6.399A  pdb=" N   LEU A 696 " --> pdb=" O   TRP A 877 " (cutoff:3.500A)
      removed outlier: 7.830A  pdb=" N   ILE A 879 " --> pdb=" O   LEU A 696 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   MET A 698 " --> pdb=" O   ILE A 879 " (cutoff:3.500A)
      removed outlier: 7.460A  pdb=" N   MET A 881 " --> pdb=" O   MET A 698 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   VAL A 700 " --> pdb=" O   MET A 881 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   ARG A 888 " --> pdb=" O   ALA A 880 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1325 through 1332
      removed outlier: 6.734A  pdb=" N   LYS A1326 " --> pdb=" O   CYS A1314 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   CYS A1314 " --> pdb=" O   LYS A1326 " (cutoff:3.500A)
      removed outlier: 5.109A  pdb=" N   VAL A1328 " --> pdb=" O   ASP A1312 " (cutoff:3.500A)
      removed outlier: 4.250A  pdb=" N   LEU A1313 " --> pdb=" O   ASP A1363 " (cutoff:3.500A)
      removed outlier: 6.722A  pdb=" N   ASP A1363 " --> pdb=" O   LEU A1313 " (cutoff:3.500A)
      removed outlier: 7.206A  pdb=" N   VAL A1315 " --> pdb=" O   ILE A1361 " (cutoff:3.500A)
      removed outlier: 7.079A  pdb=" N   ILE A1361 " --> pdb=" O   VAL A1315 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1386 through 1388
      removed outlier: 6.618A  pdb=" N   SER A1386 " --> pdb=" O   ILE A1467 " (cutoff:3.500A)
      removed outlier: 7.837A  pdb=" N   ASP A1469 " --> pdb=" O   SER A1386 " (cutoff:3.500A)
      removed outlier: 6.795A  pdb=" N   ILE A1388 " --> pdb=" O   ASP A1469 " (cutoff:3.500A)
      removed outlier: 6.435A  pdb=" N   LEU A1466 " --> pdb=" O   VAL A1497 " (cutoff:3.500A)
      removed outlier: 7.611A  pdb=" N   ILE A1499 " --> pdb=" O   LEU A1466 " (cutoff:3.500A)
      removed outlier: 6.862A  pdb=" N   MET A1468 " --> pdb=" O   ILE A1499 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   VAL A1338 " --> pdb=" O   THR A1498 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   GLU A1522 " --> pdb=" O   VAL A1514 " (cutoff:3.500A)
      removed outlier: 6.729A  pdb=" N   SER A1516 " --> pdb=" O   LEU A1520 " (cutoff:3.500A)
      removed outlier: 5.281A  pdb=" N   LEU A1520 " --> pdb=" O   SER A1516 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1397 through 1398

    648 hydrogen bonds defined for protein.
    1908 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: 3.61

  Time building geometry restraints manager: 2.84 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1499
        1.31 -     1.43: 2484
        1.43 -     1.56: 5599
        1.56 -     1.68: 10
        1.68 -     1.81: 83
  Bond restraints: 9675
  Sorted by residual:
  bond pdb=" C16 BJX A1605 "
       pdb=" N1  BJX A1605 "
    ideal  model  delta    sigma   weight residual
    1.344  1.446 -0.102 2.00e-02 2.50e+03 2.63e+01
  bond pdb=" C21 BJX A1605 "
       pdb=" O1  BJX A1605 "
    ideal  model  delta    sigma   weight residual
    1.347  1.397 -0.050 2.00e-02 2.50e+03 6.17e+00
  bond pdb=" O   BJX A1605 "
       pdb=" C16 BJX A1605 "
    ideal  model  delta    sigma   weight residual
    1.221  1.181  0.040 2.00e-02 2.50e+03 3.99e+00
  bond pdb=" N   BJX A1605 "
       pdb=" C6  BJX A1605 "
    ideal  model  delta    sigma   weight residual
    1.412  1.450 -0.038 2.00e-02 2.50e+03 3.70e+00
  bond pdb=" C17 BJX A1605 "
       pdb=" C18 BJX A1605 "
    ideal  model  delta    sigma   weight residual
    1.498  1.523 -0.025 2.00e-02 2.50e+03 1.62e+00
  ... (remaining 9670 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.39: 12877
        1.39 -     2.77: 203
        2.77 -     4.16: 45
        4.16 -     5.55: 16
        5.55 -     6.93: 5
  Bond angle restraints: 13146
  Sorted by residual:
  angle pdb=" N   GLY A1177 "
        pdb=" CA  GLY A1177 "
        pdb=" C   GLY A1177 "
      ideal   model   delta    sigma   weight residual
     115.63  110.45    5.18 1.49e+00 4.50e-01 1.21e+01
  angle pdb=" CA  GLY A1177 "
        pdb=" C   GLY A1177 "
        pdb=" N   LEU A1178 "
      ideal   model   delta    sigma   weight residual
     118.64  115.13    3.51 1.24e+00 6.50e-01 8.01e+00
  angle pdb=" CA  GLY A1177 "
        pdb=" C   GLY A1177 "
        pdb=" O   GLY A1177 "
      ideal   model   delta    sigma   weight residual
     118.95  121.53   -2.58 1.00e+00 1.00e+00 6.65e+00
  angle pdb=" O2  BJX A1605 "
        pdb=" C24 BJX A1605 "
        pdb=" O3  BJX A1605 "
      ideal   model   delta    sigma   weight residual
     126.98  120.05    6.93 3.00e+00 1.11e-01 5.34e+00
  angle pdb=" C1  BJX A1605 "
        pdb=" N   BJX A1605 "
        pdb=" C6  BJX A1605 "
      ideal   model   delta    sigma   weight residual
     117.04  110.14    6.90 3.00e+00 1.11e-01 5.29e+00
  ... (remaining 13141 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.97: 5681
       31.97 -    63.95: 103
       63.95 -    95.92: 8
       95.92 -   127.89: 0
      127.89 -   159.86: 1
  Dihedral angle restraints: 5793
    sinusoidal: 2289
      harmonic: 3504
  Sorted by residual:
  dihedral pdb=" O   BJX A1605 "
           pdb=" C16 BJX A1605 "
           pdb=" C17 BJX A1605 "
           pdb=" C18 BJX A1605 "
      ideal   model   delta sinusoidal    sigma   weight residual
      10.31 -149.55  159.86     1      3.00e+01 1.11e-03 2.07e+01
  dihedral pdb=" CA  LEU A 448 "
           pdb=" C   LEU A 448 "
           pdb=" N   LEU A 449 "
           pdb=" CA  LEU A 449 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.06  -15.94     0      5.00e+00 4.00e-02 1.02e+01
  dihedral pdb=" N   GLN A 870 "
           pdb=" CA  GLN A 870 "
           pdb=" CB  GLN A 870 "
           pdb=" CG  GLN A 870 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00    0.10   59.90     3      1.50e+01 4.44e-03 9.48e+00
  ... (remaining 5790 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 1133
       0.037 -    0.074: 312
       0.074 -    0.111: 94
       0.111 -    0.148: 19
       0.148 -    0.185: 2
  Chirality restraints: 1560
  Sorted by residual:
  chirality pdb=" C5  BJX A1605 "
            pdb=" C7  BJX A1605 "
            pdb=" C8  BJX A1605 "
            pdb=" N1  BJX A1605 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.62   -0.19 2.00e-01 2.50e+01 8.59e-01
  chirality pdb=" CA  CYS A 428 "
            pdb=" N   CYS A 428 "
            pdb=" C   CYS A 428 "
            pdb=" CB  CYS A 428 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.13e-01
  chirality pdb=" CA  ILE A1361 "
            pdb=" N   ILE A1361 "
            pdb=" C   ILE A1361 "
            pdb=" CB  ILE A1361 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.33e-01
  ... (remaining 1557 not shown)

  Planarity restraints: 1613
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A1103 "    0.023 5.00e-02 4.00e+02   3.44e-02 1.89e+00
        pdb=" N   PRO A1104 "   -0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO A1104 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A1104 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A1526 "   -0.023 5.00e-02 4.00e+02   3.41e-02 1.86e+00
        pdb=" N   PRO A1527 "    0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO A1527 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A1527 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A1143 "    0.007 2.00e-02 2.50e+03   1.36e-02 1.84e+00
        pdb=" C   TYR A1143 "   -0.023 2.00e-02 2.50e+03
        pdb=" O   TYR A1143 "    0.009 2.00e-02 2.50e+03
        pdb=" N   PHE A1144 "    0.008 2.00e-02 2.50e+03
  ... (remaining 1610 not shown)

  Histogram of nonbonded interaction distances:
        1.97 -     2.56: 62
        2.56 -     3.14: 7773
        3.14 -     3.73: 15412
        3.73 -     4.31: 21524
        4.31 -     4.90: 36631
  Nonbonded interactions: 81402
  Sorted by model distance:
  nonbonded pdb=" OG  SER A1349 "
            pdb="MG    MG A1603 "
     model   vdw
     1.971 2.170
  nonbonded pdb=" OG  SER A 708 "
            pdb="MG    MG A1604 "
     model   vdw
     1.972 2.170
  nonbonded pdb=" OE1 GLN A 753 "
            pdb="MG    MG A1604 "
     model   vdw
     1.978 2.170
  nonbonded pdb=" O1G ATP A1601 "
            pdb="MG    MG A1604 "
     model   vdw
     2.166 2.170
  nonbonded pdb=" O2B ATP A1601 "
            pdb="MG    MG A1604 "
     model   vdw
     2.168 2.170
  ... (remaining 81397 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.130
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.400
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     25.490
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.050
  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:13.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   43.690
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.102   9675  Z= 0.171
  Angle     :  0.509   6.932  13146  Z= 0.273
  Chirality :  0.039   0.185   1560
  Planarity :  0.004   0.034   1613
  Dihedral  : 12.137 159.862   3523
  Min Nonbonded Distance : 1.971

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.84 %
    Favored  : 99.16 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  :  3.35 %
    Favored  : 95.96 %
  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:  2.20 (0.24), residues: 1190
  helix:  2.04 (0.18), residues: 808
  sheet:  0.57 (0.65), residues: 65
  loop :  0.23 (0.34), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A1214 
 HIS   0.005   0.001   HIS A1001 
 PHE   0.013   0.001   PHE A 569 
 TYR   0.013   0.001   TYR A 228 
 ARG   0.003   0.000   ARG A1457 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10953 (  648)
  hydrogen bonds       : angle       5.17416 ( 1908)
  covalent geometry    : bond        0.00378 ( 9675)
  covalent geometry    : angle       0.50918 (13146)

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 193
  time to evaluate  : 1.109 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  225 LYS cc_start: 0.7879 (mttm) cc_final: 0.7640 (mmtt)
REVERT: A  235 ILE cc_start: 0.8337 (OUTLIER) cc_final: 0.7990 (mp)
REVERT: A  375 GLU cc_start: 0.7437 (tt0) cc_final: 0.7150 (tt0)
REVERT: A  472 THR cc_start: 0.8678 (m) cc_final: 0.8477 (p)
REVERT: A  514 SER cc_start: 0.8568 (t) cc_final: 0.8222 (p)
REVERT: A  525 SER cc_start: 0.8045 (t) cc_final: 0.7718 (m)
REVERT: A  527 LYS cc_start: 0.7871 (ttpt) cc_final: 0.7371 (tttt)
REVERT: A  607 LEU cc_start: 0.8151 (mp) cc_final: 0.7497 (pp)
REVERT: A  782 ASP cc_start: 0.7396 (m-30) cc_final: 0.7158 (m-30)
REVERT: A  797 ASP cc_start: 0.8117 (m-30) cc_final: 0.7755 (m-30)
REVERT: A  853 LYS cc_start: 0.8435 (tttt) cc_final: 0.7970 (tttm)
REVERT: A  976 LYS cc_start: 0.8079 (mttt) cc_final: 0.7622 (mmpt)
REVERT: A 1004 ILE cc_start: 0.8367 (mt) cc_final: 0.8162 (mm)
REVERT: A 1055 TRP cc_start: 0.7288 (t60) cc_final: 0.6644 (t-100)
REVERT: A 1100 ASP cc_start: 0.7924 (m-30) cc_final: 0.7665 (m-30)
REVERT: A 1185 ARG cc_start: 0.7894 (mtp85) cc_final: 0.7587 (mtt-85)
REVERT: A 1282 LEU cc_start: 0.7993 (mt) cc_final: 0.7774 (mt)
REVERT: A 1307 GLU cc_start: 0.7419 (mt-10) cc_final: 0.7039 (mt-10)
REVERT: A 1312 ASP cc_start: 0.7486 (t70) cc_final: 0.6581 (t70)
REVERT: A 1360 ASP cc_start: 0.7650 (t0) cc_final: 0.7113 (m-30)
REVERT: A 1422 GLN cc_start: 0.8366 (mm-40) cc_final: 0.8125 (mm-40)
REVERT: A 1468 MET cc_start: 0.8954 (mtm) cc_final: 0.8720 (mtp)
  outliers start: 7
  outliers final: 4
  residues processed: 199
  average time/residue: 1.1416
  time to fit residues: 244.7027
Evaluate side-chains
  148 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 143
  time to evaluate  : 1.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  235 ILE
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  282 THR
Chi-restraints excluded: chain A residue  870 GLN
Chi-restraints excluded: chain A residue 1281 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 101 optimal weight:    2.9990
   chunk 90 optimal weight:    4.9990
   chunk 50 optimal weight:    0.5980
   chunk 31 optimal weight:    0.5980
   chunk 61 optimal weight:    0.8980
   chunk 48 optimal weight:    1.9990
   chunk 94 optimal weight:    3.9990
   chunk 36 optimal weight:    0.8980
   chunk 57 optimal weight:    4.9990
   chunk 70 optimal weight:    0.8980
   chunk 108 optimal weight:    5.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 221 ASN
A 271 GLN
A 420 GLN
A 478 GLN
A 540 ASN
** A 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1066 HIS
A1319 ASN
A1425 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.143251 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.110746 restraints weight = 10210.131|
|-----------------------------------------------------------------------------|
r_work (start): 0.3087 rms_B_bonded: 1.52
r_work: 0.2950 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.2807 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.2807
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8375
moved from start:          0.1126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   9675  Z= 0.143
  Angle     :  0.486   6.581  13146  Z= 0.253
  Chirality :  0.039   0.165   1560
  Planarity :  0.004   0.042   1613
  Dihedral  : 10.593 165.452   1382
  Min Nonbonded Distance : 1.945

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  :  8.87 %
    Favored  : 87.88 %
  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:  2.57 (0.24), residues: 1190
  helix:  2.32 (0.18), residues: 814
  sheet:  0.44 (0.65), residues: 65
  loop :  0.38 (0.34), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A1214 
 HIS   0.004   0.001   HIS A1001 
 PHE   0.013   0.001   PHE A 569 
 TYR   0.013   0.001   TYR A 228 
 ARG   0.007   0.001   ARG A1413 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05052 (  648)
  hydrogen bonds       : angle       4.13911 ( 1908)
  covalent geometry    : bond        0.00315 ( 9675)
  covalent geometry    : angle       0.48614 (13146)

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 153
  time to evaluate  : 1.142 
Fit side-chains
REVERT: A  225 LYS cc_start: 0.8629 (mttm) cc_final: 0.8137 (mmtt)
REVERT: A  235 ILE cc_start: 0.9023 (OUTLIER) cc_final: 0.8451 (mp)
REVERT: A  241 LYS cc_start: 0.8215 (pttm) cc_final: 0.7342 (tttp)
REVERT: A  375 GLU cc_start: 0.8268 (tt0) cc_final: 0.8068 (tt0)
REVERT: A  514 SER cc_start: 0.8982 (t) cc_final: 0.8654 (p)
REVERT: A  525 SER cc_start: 0.8633 (t) cc_final: 0.8222 (m)
REVERT: A  527 LYS cc_start: 0.8326 (ttpt) cc_final: 0.7818 (tttt)
REVERT: A  672 ASN cc_start: 0.8591 (OUTLIER) cc_final: 0.7983 (t160)
REVERT: A  782 ASP cc_start: 0.8027 (m-30) cc_final: 0.7815 (m-30)
REVERT: A  797 ASP cc_start: 0.8559 (m-30) cc_final: 0.8281 (m-30)
REVERT: A  833 ASP cc_start: 0.8223 (OUTLIER) cc_final: 0.7982 (m-30)
REVERT: A  853 LYS cc_start: 0.8878 (tttt) cc_final: 0.8290 (ttpt)
REVERT: A  907 LYS cc_start: 0.8633 (mtpt) cc_final: 0.8397 (ttpt)
REVERT: A  973 MET cc_start: 0.8282 (OUTLIER) cc_final: 0.7611 (tpt)
REVERT: A  976 LYS cc_start: 0.8424 (mttt) cc_final: 0.7644 (mptt)
REVERT: A 1055 TRP cc_start: 0.7931 (t60) cc_final: 0.7173 (t-100)
REVERT: A 1100 ASP cc_start: 0.8318 (m-30) cc_final: 0.8058 (m-30)
REVERT: A 1169 CYS cc_start: 0.8601 (m) cc_final: 0.8255 (t)
REVERT: A 1185 ARG cc_start: 0.8583 (mtp85) cc_final: 0.8220 (mtt-85)
REVERT: A 1277 LYS cc_start: 0.7979 (mttm) cc_final: 0.7591 (mttt)
REVERT: A 1282 LEU cc_start: 0.7806 (mt) cc_final: 0.7604 (mt)
REVERT: A 1307 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7555 (mt-10)
REVERT: A 1312 ASP cc_start: 0.7888 (t70) cc_final: 0.6997 (t70)
REVERT: A 1360 ASP cc_start: 0.7825 (t0) cc_final: 0.7298 (m-30)
REVERT: A 1422 GLN cc_start: 0.8582 (mm-40) cc_final: 0.8357 (mm-40)
REVERT: A 1463 SER cc_start: 0.7988 (t) cc_final: 0.7726 (p)
REVERT: A 1494 ARG cc_start: 0.8061 (mtt-85) cc_final: 0.7854 (mtt90)
  outliers start: 33
  outliers final: 8
  residues processed: 172
  average time/residue: 1.1617
  time to fit residues: 215.8422
Evaluate side-chains
  154 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 142
  time to evaluate  : 1.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  235 ILE
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  282 THR
Chi-restraints excluded: chain A residue  672 ASN
Chi-restraints excluded: chain A residue  833 ASP
Chi-restraints excluded: chain A residue  870 GLN
Chi-restraints excluded: chain A residue  973 MET
Chi-restraints excluded: chain A residue 1073 ILE
Chi-restraints excluded: chain A residue 1089 LEU
Chi-restraints excluded: chain A residue 1135 LEU
Chi-restraints excluded: chain A residue 1281 PHE
Chi-restraints excluded: chain A residue 1318 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 56 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   chunk 105 optimal weight:    0.7980
   chunk 88 optimal weight:    2.9990
   chunk 46 optimal weight:    3.9990
   chunk 101 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 76 optimal weight:    3.9990
   chunk 5 optimal weight:    0.4980
   chunk 24 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
A 478 GLN
A 540 ASN
A1319 ASN
A1402 ASN
A1425 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.137920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.106754 restraints weight = 10341.928|
|-----------------------------------------------------------------------------|
r_work (start): 0.3047 rms_B_bonded: 1.54
r_work: 0.2870 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.2723 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.2723
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8396
moved from start:          0.1367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9675  Z= 0.176
  Angle     :  0.502   6.575  13146  Z= 0.261
  Chirality :  0.040   0.170   1560
  Planarity :  0.004   0.041   1613
  Dihedral  : 10.443 165.605   1382
  Min Nonbonded Distance : 1.894

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 11.33 %
    Favored  : 85.71 %
  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:  2.42 (0.24), residues: 1190
  helix:  2.23 (0.18), residues: 815
  sheet:  0.33 (0.64), residues: 65
  loop :  0.29 (0.34), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A1214 
 HIS   0.005   0.001   HIS A1001 
 PHE   0.021   0.002   PHE A 552 
 TYR   0.018   0.001   TYR A 532 
 ARG   0.004   0.000   ARG A1413 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05164 (  648)
  hydrogen bonds       : angle       4.09252 ( 1908)
  covalent geometry    : bond        0.00410 ( 9675)
  covalent geometry    : angle       0.50226 (13146)

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 141
  time to evaluate  : 1.016 
Fit side-chains
REVERT: A  225 LYS cc_start: 0.8603 (mttm) cc_final: 0.8134 (mmtt)
REVERT: A  235 ILE cc_start: 0.9058 (OUTLIER) cc_final: 0.8450 (mp)
REVERT: A  241 LYS cc_start: 0.8149 (pttm) cc_final: 0.7310 (tttm)
REVERT: A  514 SER cc_start: 0.8974 (t) cc_final: 0.8615 (p)
REVERT: A  525 SER cc_start: 0.8640 (t) cc_final: 0.8210 (m)
REVERT: A  527 LYS cc_start: 0.8330 (ttpt) cc_final: 0.7817 (tttt)
REVERT: A  782 ASP cc_start: 0.7975 (m-30) cc_final: 0.7758 (m-30)
REVERT: A  797 ASP cc_start: 0.8607 (m-30) cc_final: 0.8349 (m-30)
REVERT: A  833 ASP cc_start: 0.8303 (OUTLIER) cc_final: 0.8055 (m-30)
REVERT: A  853 LYS cc_start: 0.8897 (tttt) cc_final: 0.8307 (ttpt)
REVERT: A  907 LYS cc_start: 0.8650 (mtpt) cc_final: 0.8367 (ttpt)
REVERT: A  973 MET cc_start: 0.8294 (OUTLIER) cc_final: 0.7641 (tpt)
REVERT: A  976 LYS cc_start: 0.8476 (mttt) cc_final: 0.7680 (mptt)
REVERT: A 1055 TRP cc_start: 0.7947 (t60) cc_final: 0.7172 (t-100)
REVERT: A 1100 ASP cc_start: 0.8393 (m-30) cc_final: 0.8109 (m-30)
REVERT: A 1169 CYS cc_start: 0.8620 (m) cc_final: 0.8259 (t)
REVERT: A 1185 ARG cc_start: 0.8594 (mtp85) cc_final: 0.8228 (mtt-85)
REVERT: A 1307 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7666 (mt-10)
REVERT: A 1360 ASP cc_start: 0.7972 (t0) cc_final: 0.7328 (m-30)
REVERT: A 1422 GLN cc_start: 0.8561 (mm-40) cc_final: 0.8301 (mm-40)
REVERT: A 1468 MET cc_start: 0.9162 (mtm) cc_final: 0.8948 (mtp)
  outliers start: 30
  outliers final: 15
  residues processed: 155
  average time/residue: 1.4978
  time to fit residues: 249.4150
Evaluate side-chains
  153 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 135
  time to evaluate  : 1.817 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  235 ILE
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  282 THR
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  485 SER
Chi-restraints excluded: chain A residue  771 SER
Chi-restraints excluded: chain A residue  781 THR
Chi-restraints excluded: chain A residue  833 ASP
Chi-restraints excluded: chain A residue  840 ILE
Chi-restraints excluded: chain A residue  870 GLN
Chi-restraints excluded: chain A residue  898 LYS
Chi-restraints excluded: chain A residue  973 MET
Chi-restraints excluded: chain A residue 1005 VAL
Chi-restraints excluded: chain A residue 1073 ILE
Chi-restraints excluded: chain A residue 1089 LEU
Chi-restraints excluded: chain A residue 1135 LEU
Chi-restraints excluded: chain A residue 1281 PHE
Chi-restraints excluded: chain A residue 1318 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 81 optimal weight:    0.9980
   chunk 73 optimal weight:    0.9990
   chunk 70 optimal weight:    1.9990
   chunk 26 optimal weight:    0.7980
   chunk 97 optimal weight:    4.9990
   chunk 32 optimal weight:    0.6980
   chunk 101 optimal weight:    0.3980
   chunk 25 optimal weight:    0.9990
   chunk 88 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9980
   chunk 107 optimal weight:    0.0370
   overall best weight:    0.5858

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

Flipped N/Q/H residues before XYZ refinement:
A 478 GLN
A 540 ASN
A1157 GLN
A1319 ASN
A1425 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.142046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.108449 restraints weight = 10189.418|
|-----------------------------------------------------------------------------|
r_work (start): 0.3059 rms_B_bonded: 1.62
r_work: 0.2916 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.2767 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.2767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8321
moved from start:          0.1549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9675  Z= 0.123
  Angle     :  0.454   6.604  13146  Z= 0.238
  Chirality :  0.038   0.161   1560
  Planarity :  0.003   0.036   1613
  Dihedral  :  9.947 163.787   1382
  Min Nonbonded Distance : 1.964

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 11.63 %
    Favored  : 85.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.63 (0.24), residues: 1190
  helix:  2.42 (0.18), residues: 817
  sheet:  0.53 (0.68), residues: 60
  loop :  0.23 (0.34), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A1214 
 HIS   0.003   0.000   HIS A1001 
 PHE   0.018   0.001   PHE A 552 
 TYR   0.014   0.001   TYR A 532 
 ARG   0.007   0.000   ARG A1494 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04591 (  648)
  hydrogen bonds       : angle       3.91988 ( 1908)
  covalent geometry    : bond        0.00262 ( 9675)
  covalent geometry    : angle       0.45388 (13146)

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 146
  time to evaluate  : 1.442 
Fit side-chains
REVERT: A  225 LYS cc_start: 0.8466 (mttm) cc_final: 0.7998 (mmtt)
REVERT: A  235 ILE cc_start: 0.9020 (OUTLIER) cc_final: 0.8429 (mp)
REVERT: A  241 LYS cc_start: 0.8040 (pttm) cc_final: 0.7209 (tttm)
REVERT: A  514 SER cc_start: 0.8969 (t) cc_final: 0.8655 (p)
REVERT: A  520 MET cc_start: 0.8119 (OUTLIER) cc_final: 0.7913 (mpm)
REVERT: A  525 SER cc_start: 0.8639 (t) cc_final: 0.8241 (m)
REVERT: A  527 LYS cc_start: 0.8262 (ttpt) cc_final: 0.7714 (tttt)
REVERT: A  764 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7615 (mt-10)
REVERT: A  778 LYS cc_start: 0.8383 (tptt) cc_final: 0.8092 (tmtm)
REVERT: A  782 ASP cc_start: 0.8007 (m-30) cc_final: 0.7762 (m-30)
REVERT: A  797 ASP cc_start: 0.8617 (m-30) cc_final: 0.8365 (m-30)
REVERT: A  853 LYS cc_start: 0.8881 (tttt) cc_final: 0.8357 (ttpt)
REVERT: A  896 GLN cc_start: 0.7870 (tt0) cc_final: 0.7452 (tt0)
REVERT: A  907 LYS cc_start: 0.8643 (mtpt) cc_final: 0.8357 (ttpt)
REVERT: A  973 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.7473 (tpt)
REVERT: A  976 LYS cc_start: 0.8431 (mttt) cc_final: 0.7617 (mptt)
REVERT: A 1055 TRP cc_start: 0.7841 (t60) cc_final: 0.7054 (t-100)
REVERT: A 1169 CYS cc_start: 0.8438 (m) cc_final: 0.8092 (t)
REVERT: A 1185 ARG cc_start: 0.8508 (mtp85) cc_final: 0.8145 (mtt-85)
REVERT: A 1277 LYS cc_start: 0.7929 (mttm) cc_final: 0.7601 (mttt)
REVERT: A 1307 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7568 (mt-10)
REVERT: A 1360 ASP cc_start: 0.7860 (t0) cc_final: 0.7216 (m-30)
REVERT: A 1420 ILE cc_start: 0.7916 (OUTLIER) cc_final: 0.7660 (mt)
REVERT: A 1422 GLN cc_start: 0.8537 (mm-40) cc_final: 0.8277 (mm-40)
REVERT: A 1425 ASN cc_start: 0.8070 (m-40) cc_final: 0.7389 (p0)
REVERT: A 1463 SER cc_start: 0.8120 (t) cc_final: 0.7699 (p)
REVERT: A 1468 MET cc_start: 0.9083 (mtm) cc_final: 0.8871 (mtp)
  outliers start: 30
  outliers final: 10
  residues processed: 163
  average time/residue: 1.2572
  time to fit residues: 220.0774
Evaluate side-chains
  154 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 139
  time to evaluate  : 1.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  235 ILE
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  485 SER
Chi-restraints excluded: chain A residue  520 MET
Chi-restraints excluded: chain A residue  764 GLU
Chi-restraints excluded: chain A residue  771 SER
Chi-restraints excluded: chain A residue  806 ILE
Chi-restraints excluded: chain A residue  840 ILE
Chi-restraints excluded: chain A residue  870 GLN
Chi-restraints excluded: chain A residue  973 MET
Chi-restraints excluded: chain A residue 1073 ILE
Chi-restraints excluded: chain A residue 1281 PHE
Chi-restraints excluded: chain A residue 1318 GLU
Chi-restraints excluded: chain A residue 1420 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 39 optimal weight:    3.9990
   chunk 62 optimal weight:    0.7980
   chunk 81 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   chunk 37 optimal weight:    0.8980
   chunk 7 optimal weight:    0.5980
   chunk 64 optimal weight:    1.9990
   chunk 97 optimal weight:    5.9990
   chunk 104 optimal weight:    3.9990
   chunk 65 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 478 GLN
A1157 GLN
A1279 ASN
A1319 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.141971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.109020 restraints weight = 10166.861|
|-----------------------------------------------------------------------------|
r_work (start): 0.3078 rms_B_bonded: 1.57
r_work: 0.2938 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.2791 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.2791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8353
moved from start:          0.1610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9675  Z= 0.140
  Angle     :  0.471   6.612  13146  Z= 0.246
  Chirality :  0.039   0.164   1560
  Planarity :  0.003   0.041   1613
  Dihedral  :  9.867 164.849   1381
  Min Nonbonded Distance : 1.923

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.01 %
    Favored  : 98.99 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 13.20 %
    Favored  : 84.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.61 (0.24), residues: 1190
  helix:  2.38 (0.18), residues: 818
  sheet:  0.26 (0.64), residues: 65
  loop :  0.33 (0.34), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A1214 
 HIS   0.004   0.000   HIS A1001 
 PHE   0.016   0.001   PHE A 552 
 TYR   0.016   0.001   TYR A 532 
 ARG   0.009   0.000   ARG A1494 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04700 (  648)
  hydrogen bonds       : angle       3.92618 ( 1908)
  covalent geometry    : bond        0.00316 ( 9675)
  covalent geometry    : angle       0.47093 (13146)

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 136
  time to evaluate  : 1.278 
Fit side-chains
REVERT: A  225 LYS cc_start: 0.8499 (mttm) cc_final: 0.8053 (mmtt)
REVERT: A  235 ILE cc_start: 0.9054 (OUTLIER) cc_final: 0.8453 (mp)
REVERT: A  241 LYS cc_start: 0.8076 (pttm) cc_final: 0.7307 (tttm)
REVERT: A  514 SER cc_start: 0.8982 (t) cc_final: 0.8682 (p)
REVERT: A  525 SER cc_start: 0.8622 (t) cc_final: 0.8204 (m)
REVERT: A  527 LYS cc_start: 0.8302 (ttpt) cc_final: 0.7769 (tttt)
REVERT: A  764 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7620 (mt-10)
REVERT: A  778 LYS cc_start: 0.8403 (tptt) cc_final: 0.8141 (tmtm)
REVERT: A  782 ASP cc_start: 0.8027 (m-30) cc_final: 0.7797 (m-30)
REVERT: A  797 ASP cc_start: 0.8607 (m-30) cc_final: 0.8344 (m-30)
REVERT: A  833 ASP cc_start: 0.8258 (OUTLIER) cc_final: 0.8017 (m-30)
REVERT: A  853 LYS cc_start: 0.8911 (tttt) cc_final: 0.8412 (ttpt)
REVERT: A  896 GLN cc_start: 0.7937 (tt0) cc_final: 0.7519 (tt0)
REVERT: A  907 LYS cc_start: 0.8638 (mtpt) cc_final: 0.8373 (ttpt)
REVERT: A  973 MET cc_start: 0.8274 (OUTLIER) cc_final: 0.7546 (tpt)
REVERT: A  976 LYS cc_start: 0.8457 (mttt) cc_final: 0.7654 (mptt)
REVERT: A 1055 TRP cc_start: 0.7893 (t60) cc_final: 0.7110 (t-100)
REVERT: A 1169 CYS cc_start: 0.8436 (m) cc_final: 0.8132 (t)
REVERT: A 1185 ARG cc_start: 0.8529 (mtp85) cc_final: 0.8165 (mtt-85)
REVERT: A 1277 LYS cc_start: 0.7935 (mttm) cc_final: 0.7605 (mttt)
REVERT: A 1307 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7605 (mt-10)
REVERT: A 1360 ASP cc_start: 0.7844 (t0) cc_final: 0.7281 (m-30)
REVERT: A 1425 ASN cc_start: 0.8032 (m-40) cc_final: 0.7411 (p0)
REVERT: A 1459 PHE cc_start: 0.8739 (t80) cc_final: 0.8433 (t80)
REVERT: A 1468 MET cc_start: 0.9111 (mtm) cc_final: 0.8896 (mtp)
  outliers start: 27
  outliers final: 11
  residues processed: 151
  average time/residue: 1.1887
  time to fit residues: 193.0353
Evaluate side-chains
  149 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 134
  time to evaluate  : 1.065 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  235 ILE
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  485 SER
Chi-restraints excluded: chain A residue  764 GLU
Chi-restraints excluded: chain A residue  833 ASP
Chi-restraints excluded: chain A residue  840 ILE
Chi-restraints excluded: chain A residue  973 MET
Chi-restraints excluded: chain A residue 1005 VAL
Chi-restraints excluded: chain A residue 1073 ILE
Chi-restraints excluded: chain A residue 1089 LEU
Chi-restraints excluded: chain A residue 1281 PHE
Chi-restraints excluded: chain A residue 1298 VAL
Chi-restraints excluded: chain A residue 1318 GLU
Chi-restraints excluded: chain A residue 1460 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 54 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   chunk 66 optimal weight:    0.8980
   chunk 82 optimal weight:    2.9990
   chunk 8 optimal weight:    0.6980
   chunk 57 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9980
   chunk 75 optimal weight:    3.9990
   chunk 35 optimal weight:    0.6980
   chunk 18 optimal weight:    0.7980
   chunk 19 optimal weight:    0.7980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 478 GLN
A1319 ASN
A1422 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.140843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.110750 restraints weight = 10228.874|
|-----------------------------------------------------------------------------|
r_work (start): 0.3116 rms_B_bonded: 1.46
r_work: 0.2933 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.2786 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.2786
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8422
moved from start:          0.1678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9675  Z= 0.137
  Angle     :  0.472   6.620  13146  Z= 0.246
  Chirality :  0.039   0.163   1560
  Planarity :  0.003   0.043   1613
  Dihedral  :  9.595 164.963   1378
  Min Nonbonded Distance : 1.929

Molprobity Statistics.
  All-atom Clashscore : 4.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 13.20 %
    Favored  : 84.04 %
  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:  2.61 (0.24), residues: 1190
  helix:  2.39 (0.18), residues: 818
  sheet:  0.49 (0.66), residues: 59
  loop :  0.26 (0.34), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A1214 
 HIS   0.004   0.000   HIS A1001 
 PHE   0.018   0.001   PHE A1445 
 TYR   0.017   0.001   TYR A 532 
 ARG   0.010   0.000   ARG A1494 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04673 (  648)
  hydrogen bonds       : angle       3.89654 ( 1908)
  covalent geometry    : bond        0.00308 ( 9675)
  covalent geometry    : angle       0.47159 (13146)

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 134
  time to evaluate  : 1.121 
Fit side-chains
REVERT: A  225 LYS cc_start: 0.8570 (mttm) cc_final: 0.8172 (mmtt)
REVERT: A  235 ILE cc_start: 0.9097 (OUTLIER) cc_final: 0.8505 (mp)
REVERT: A  241 LYS cc_start: 0.8105 (pttm) cc_final: 0.7374 (tttm)
REVERT: A  514 SER cc_start: 0.9044 (t) cc_final: 0.8776 (p)
REVERT: A  525 SER cc_start: 0.8676 (t) cc_final: 0.8242 (m)
REVERT: A  527 LYS cc_start: 0.8345 (ttpt) cc_final: 0.7861 (tttt)
REVERT: A  764 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7686 (mt-10)
REVERT: A  778 LYS cc_start: 0.8497 (tptt) cc_final: 0.8259 (tmtm)
REVERT: A  797 ASP cc_start: 0.8636 (m-30) cc_final: 0.8372 (m-30)
REVERT: A  833 ASP cc_start: 0.8270 (OUTLIER) cc_final: 0.8037 (m-30)
REVERT: A  853 LYS cc_start: 0.9000 (tttt) cc_final: 0.8550 (ttpt)
REVERT: A  907 LYS cc_start: 0.8706 (mtpt) cc_final: 0.8453 (ttpt)
REVERT: A  973 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.7576 (tpt)
REVERT: A  976 LYS cc_start: 0.8536 (mttt) cc_final: 0.7748 (mptt)
REVERT: A 1055 TRP cc_start: 0.7958 (t60) cc_final: 0.7219 (t-100)
REVERT: A 1091 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.7446 (mpt180)
REVERT: A 1169 CYS cc_start: 0.8476 (m) cc_final: 0.8226 (t)
REVERT: A 1185 ARG cc_start: 0.8569 (mtp85) cc_final: 0.8233 (mtt-85)
REVERT: A 1307 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7626 (mt-10)
REVERT: A 1360 ASP cc_start: 0.7993 (t0) cc_final: 0.7461 (m-30)
REVERT: A 1425 ASN cc_start: 0.8066 (m-40) cc_final: 0.7489 (p0)
  outliers start: 28
  outliers final: 11
  residues processed: 149
  average time/residue: 1.1607
  time to fit residues: 186.0174
Evaluate side-chains
  150 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 134
  time to evaluate  : 1.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  235 ILE
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  485 SER
Chi-restraints excluded: chain A residue  764 GLU
Chi-restraints excluded: chain A residue  771 SER
Chi-restraints excluded: chain A residue  833 ASP
Chi-restraints excluded: chain A residue  840 ILE
Chi-restraints excluded: chain A residue  973 MET
Chi-restraints excluded: chain A residue 1005 VAL
Chi-restraints excluded: chain A residue 1073 ILE
Chi-restraints excluded: chain A residue 1089 LEU
Chi-restraints excluded: chain A residue 1091 ARG
Chi-restraints excluded: chain A residue 1281 PHE
Chi-restraints excluded: chain A residue 1318 GLU
Chi-restraints excluded: chain A residue 1460 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 94 optimal weight:    0.6980
   chunk 37 optimal weight:    4.9990
   chunk 57 optimal weight:    3.9990
   chunk 100 optimal weight:    0.8980
   chunk 108 optimal weight:    3.9990
   chunk 41 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   chunk 112 optimal weight:    0.8980
   chunk 58 optimal weight:    0.9980
   chunk 33 optimal weight:    0.5980
   chunk 4 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 478 GLN
A 896 GLN
A1319 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.142161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.112143 restraints weight = 10312.707|
|-----------------------------------------------------------------------------|
r_work (start): 0.3091 rms_B_bonded: 1.46
r_work: 0.2906 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.2760 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.2760
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8435
moved from start:          0.1704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9675  Z= 0.140
  Angle     :  0.474   6.644  13146  Z= 0.247
  Chirality :  0.039   0.163   1560
  Planarity :  0.003   0.043   1613
  Dihedral  :  9.564 165.151   1378
  Min Nonbonded Distance : 1.927

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 13.60 %
    Favored  : 83.84 %
  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:  2.61 (0.24), residues: 1190
  helix:  2.37 (0.18), residues: 818
  sheet:  0.58 (0.66), residues: 59
  loop :  0.29 (0.34), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A1214 
 HIS   0.004   0.000   HIS A1001 
 PHE   0.019   0.001   PHE A1445 
 TYR   0.021   0.001   TYR A 532 
 ARG   0.010   0.000   ARG A1494 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04693 (  648)
  hydrogen bonds       : angle       3.89294 ( 1908)
  covalent geometry    : bond        0.00315 ( 9675)
  covalent geometry    : angle       0.47391 (13146)

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 138
  time to evaluate  : 1.255 
Fit side-chains
REVERT: A  225 LYS cc_start: 0.8588 (mttm) cc_final: 0.8198 (mmtt)
REVERT: A  235 ILE cc_start: 0.9097 (OUTLIER) cc_final: 0.8494 (mp)
REVERT: A  241 LYS cc_start: 0.8100 (pttm) cc_final: 0.7326 (tttm)
REVERT: A  514 SER cc_start: 0.9058 (t) cc_final: 0.8797 (p)
REVERT: A  525 SER cc_start: 0.8723 (t) cc_final: 0.8259 (m)
REVERT: A  527 LYS cc_start: 0.8376 (ttpt) cc_final: 0.7903 (tttt)
REVERT: A  764 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7697 (mt-10)
REVERT: A  797 ASP cc_start: 0.8626 (m-30) cc_final: 0.8364 (m-30)
REVERT: A  827 ASN cc_start: 0.8340 (t0) cc_final: 0.7906 (t0)
REVERT: A  833 ASP cc_start: 0.8276 (OUTLIER) cc_final: 0.8046 (m-30)
REVERT: A  853 LYS cc_start: 0.9004 (tttt) cc_final: 0.8559 (ttpt)
REVERT: A  896 GLN cc_start: 0.7892 (tt0) cc_final: 0.7562 (tt0)
REVERT: A  973 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.7651 (tpt)
REVERT: A  976 LYS cc_start: 0.8544 (mttt) cc_final: 0.7950 (mmpt)
REVERT: A 1055 TRP cc_start: 0.7995 (t60) cc_final: 0.7256 (t-100)
REVERT: A 1169 CYS cc_start: 0.8501 (m) cc_final: 0.8256 (t)
REVERT: A 1185 ARG cc_start: 0.8593 (mtp85) cc_final: 0.8260 (mtt-85)
REVERT: A 1307 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7654 (mt-10)
REVERT: A 1360 ASP cc_start: 0.8010 (t0) cc_final: 0.7512 (m-30)
REVERT: A 1420 ILE cc_start: 0.8023 (mt) cc_final: 0.7786 (pp)
REVERT: A 1425 ASN cc_start: 0.8064 (m-40) cc_final: 0.7512 (p0)
  outliers start: 26
  outliers final: 11
  residues processed: 154
  average time/residue: 1.6769
  time to fit residues: 278.0790
Evaluate side-chains
  150 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 135
  time to evaluate  : 1.656 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  235 ILE
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  485 SER
Chi-restraints excluded: chain A residue  764 GLU
Chi-restraints excluded: chain A residue  771 SER
Chi-restraints excluded: chain A residue  833 ASP
Chi-restraints excluded: chain A residue  840 ILE
Chi-restraints excluded: chain A residue  973 MET
Chi-restraints excluded: chain A residue 1005 VAL
Chi-restraints excluded: chain A residue 1073 ILE
Chi-restraints excluded: chain A residue 1089 LEU
Chi-restraints excluded: chain A residue 1281 PHE
Chi-restraints excluded: chain A residue 1318 GLU
Chi-restraints excluded: chain A residue 1460 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 27 optimal weight:    0.7980
   chunk 28 optimal weight:    0.8980
   chunk 88 optimal weight:    0.6980
   chunk 96 optimal weight:    0.9990
   chunk 109 optimal weight:    0.0030
   chunk 44 optimal weight:    2.9990
   chunk 66 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9990
   chunk 91 optimal weight:    0.0270
   chunk 110 optimal weight:    0.0270
   chunk 54 optimal weight:    2.9990
   overall best weight:    0.3106

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

Flipped N/Q/H residues before XYZ refinement:
A 478 GLN
A 719 GLN
A1256 ASN
A1319 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.145970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.113316 restraints weight = 10246.580|
|-----------------------------------------------------------------------------|
r_work (start): 0.3182 rms_B_bonded: 1.57
r_work: 0.3046 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.2896 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.2896
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8309
moved from start:          0.1962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   9675  Z= 0.108
  Angle     :  0.444   6.655  13146  Z= 0.233
  Chirality :  0.037   0.158   1560
  Planarity :  0.003   0.040   1613
  Dihedral  :  9.158 163.546   1378
  Min Nonbonded Distance : 2.008

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.76 %
    Favored  : 99.24 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 14.29 %
    Favored  : 83.65 %
  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:  2.88 (0.24), residues: 1190
  helix:  2.59 (0.18), residues: 821
  sheet:  0.91 (0.64), residues: 59
  loop :  0.27 (0.34), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.001   TRP A 980 
 HIS   0.002   0.000   HIS A1001 
 PHE   0.019   0.001   PHE A1445 
 TYR   0.014   0.001   TYR A 532 
 ARG   0.010   0.000   ARG A1494 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04208 (  648)
  hydrogen bonds       : angle       3.75546 ( 1908)
  covalent geometry    : bond        0.00216 ( 9675)
  covalent geometry    : angle       0.44391 (13146)

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 146
  time to evaluate  : 1.041 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  225 LYS cc_start: 0.8437 (mttm) cc_final: 0.8030 (mmtt)
REVERT: A  235 ILE cc_start: 0.8976 (OUTLIER) cc_final: 0.8414 (mp)
REVERT: A  241 LYS cc_start: 0.7941 (pttm) cc_final: 0.7172 (tttm)
REVERT: A  514 SER cc_start: 0.8959 (t) cc_final: 0.8723 (p)
REVERT: A  525 SER cc_start: 0.8660 (t) cc_final: 0.8183 (m)
REVERT: A  527 LYS cc_start: 0.8279 (ttpt) cc_final: 0.7755 (tttt)
REVERT: A  797 ASP cc_start: 0.8582 (m-30) cc_final: 0.8329 (m-30)
REVERT: A  827 ASN cc_start: 0.8196 (t0) cc_final: 0.7801 (t0)
REVERT: A  853 LYS cc_start: 0.8962 (tttt) cc_final: 0.8445 (ttpt)
REVERT: A  893 LYS cc_start: 0.8492 (mptt) cc_final: 0.8086 (mmtm)
REVERT: A  896 GLN cc_start: 0.7731 (tt0) cc_final: 0.7450 (tt0)
REVERT: A  973 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.7465 (tpt)
REVERT: A  976 LYS cc_start: 0.8408 (mttt) cc_final: 0.7791 (mmpt)
REVERT: A 1055 TRP cc_start: 0.7825 (t60) cc_final: 0.7056 (t-100)
REVERT: A 1185 ARG cc_start: 0.8380 (mtp85) cc_final: 0.8036 (mtt-85)
REVERT: A 1277 LYS cc_start: 0.7799 (mttm) cc_final: 0.7376 (mttt)
REVERT: A 1309 LYS cc_start: 0.8016 (mttm) cc_final: 0.7768 (mptt)
REVERT: A 1360 ASP cc_start: 0.7845 (t0) cc_final: 0.7320 (m-30)
REVERT: A 1425 ASN cc_start: 0.7911 (m-40) cc_final: 0.7388 (p0)
REVERT: A 1463 SER cc_start: 0.8051 (t) cc_final: 0.7677 (p)
  outliers start: 21
  outliers final: 9
  residues processed: 156
  average time/residue: 1.2037
  time to fit residues: 201.7573
Evaluate side-chains
  141 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 130
  time to evaluate  : 1.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  235 ILE
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  771 SER
Chi-restraints excluded: chain A residue  840 ILE
Chi-restraints excluded: chain A residue  971 THR
Chi-restraints excluded: chain A residue  973 MET
Chi-restraints excluded: chain A residue 1005 VAL
Chi-restraints excluded: chain A residue 1073 ILE
Chi-restraints excluded: chain A residue 1281 PHE
Chi-restraints excluded: chain A residue 1460 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 102 optimal weight:    5.9990
   chunk 4 optimal weight:    0.7980
   chunk 40 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9990
   chunk 7 optimal weight:    0.5980
   chunk 97 optimal weight:    2.9990
   chunk 110 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9990
   chunk 114 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9990
   overall best weight:    0.8786

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

Flipped N/Q/H residues before XYZ refinement:
A 540 ASN
** A 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1157 GLN
A1319 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.139693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.109250 restraints weight = 10323.431|
|-----------------------------------------------------------------------------|
r_work (start): 0.3141 rms_B_bonded: 1.48
r_work: 0.2962 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.2819 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.2819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8420
moved from start:          0.1906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9675  Z= 0.145
  Angle     :  0.487   6.660  13146  Z= 0.253
  Chirality :  0.039   0.165   1560
  Planarity :  0.004   0.044   1613
  Dihedral  :  9.372 166.007   1378
  Min Nonbonded Distance : 1.918

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 14.88 %
    Favored  : 83.05 %
  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:  2.70 (0.24), residues: 1190
  helix:  2.42 (0.18), residues: 818
  sheet:  0.47 (0.64), residues: 65
  loop :  0.41 (0.34), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 980 
 HIS   0.005   0.001   HIS A1001 
 PHE   0.019   0.001   PHE A1445 
 TYR   0.025   0.001   TYR A 532 
 ARG   0.010   0.000   ARG A1494 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04643 (  648)
  hydrogen bonds       : angle       3.86746 ( 1908)
  covalent geometry    : bond        0.00329 ( 9675)
  covalent geometry    : angle       0.48662 (13146)

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 131
  time to evaluate  : 1.175 
Fit side-chains
   revert: symmetry clash
REVERT: A  225 LYS cc_start: 0.8569 (mttm) cc_final: 0.8171 (mmtt)
REVERT: A  235 ILE cc_start: 0.9063 (OUTLIER) cc_final: 0.8473 (mp)
REVERT: A  241 LYS cc_start: 0.8102 (pttm) cc_final: 0.7341 (tttm)
REVERT: A  482 LEU cc_start: 0.8841 (tp) cc_final: 0.8638 (tp)
REVERT: A  514 SER cc_start: 0.9049 (t) cc_final: 0.8796 (p)
REVERT: A  525 SER cc_start: 0.8738 (t) cc_final: 0.8253 (m)
REVERT: A  527 LYS cc_start: 0.8353 (ttpt) cc_final: 0.7869 (tttt)
REVERT: A  764 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7736 (mt-10)
REVERT: A  797 ASP cc_start: 0.8614 (m-30) cc_final: 0.8367 (m-30)
REVERT: A  827 ASN cc_start: 0.8301 (t0) cc_final: 0.7901 (t0)
REVERT: A  853 LYS cc_start: 0.9026 (tttt) cc_final: 0.8578 (ttpt)
REVERT: A  893 LYS cc_start: 0.8517 (mptt) cc_final: 0.8147 (mmtm)
REVERT: A  896 GLN cc_start: 0.7787 (tt0) cc_final: 0.7548 (tt0)
REVERT: A  973 MET cc_start: 0.8304 (OUTLIER) cc_final: 0.7603 (tpt)
REVERT: A  976 LYS cc_start: 0.8505 (mttt) cc_final: 0.7911 (mmpt)
REVERT: A 1055 TRP cc_start: 0.7935 (t60) cc_final: 0.7199 (t-100)
REVERT: A 1185 ARG cc_start: 0.8534 (mtp85) cc_final: 0.8214 (mtt-85)
REVERT: A 1316 ARG cc_start: 0.8296 (ptp90) cc_final: 0.7739 (ptt90)
REVERT: A 1360 ASP cc_start: 0.7947 (t0) cc_final: 0.7619 (m-30)
REVERT: A 1393 ILE cc_start: 0.8818 (mt) cc_final: 0.8416 (tt)
REVERT: A 1425 ASN cc_start: 0.7980 (m-40) cc_final: 0.7475 (p0)
REVERT: A 1463 SER cc_start: 0.8118 (t) cc_final: 0.7740 (p)
  outliers start: 21
  outliers final: 9
  residues processed: 143
  average time/residue: 1.2057
  time to fit residues: 185.4769
Evaluate side-chains
  139 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 127
  time to evaluate  : 1.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  235 ILE
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  764 GLU
Chi-restraints excluded: chain A residue  771 SER
Chi-restraints excluded: chain A residue  840 ILE
Chi-restraints excluded: chain A residue  971 THR
Chi-restraints excluded: chain A residue  973 MET
Chi-restraints excluded: chain A residue 1005 VAL
Chi-restraints excluded: chain A residue 1073 ILE
Chi-restraints excluded: chain A residue 1281 PHE
Chi-restraints excluded: chain A residue 1460 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 39 optimal weight:    2.9990
   chunk 4 optimal weight:    0.6980
   chunk 67 optimal weight:    0.9980
   chunk 93 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9980
   chunk 22 optimal weight:    0.7980
   chunk 119 optimal weight:    6.9990
   chunk 19 optimal weight:    0.5980
   chunk 25 optimal weight:    0.6980
   chunk 88 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 540 ASN
** A 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1319 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.142680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.109889 restraints weight = 10293.208|
|-----------------------------------------------------------------------------|
r_work (start): 0.3078 rms_B_bonded: 1.56
r_work: 0.2940 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.2791 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.2791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8347
moved from start:          0.1945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9675  Z= 0.134
  Angle     :  0.485   6.670  13146  Z= 0.252
  Chirality :  0.039   0.162   1560
  Planarity :  0.003   0.043   1613
  Dihedral  :  9.389 166.077   1378
  Min Nonbonded Distance : 1.937

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 15.27 %
    Favored  : 82.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.69 (0.24), residues: 1190
  helix:  2.40 (0.18), residues: 818
  sheet:  0.75 (0.67), residues: 60
  loop :  0.37 (0.34), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 980 
 HIS   0.004   0.000   HIS A1001 
 PHE   0.019   0.001   PHE A1445 
 TYR   0.025   0.001   TYR A 532 
 ARG   0.010   0.000   ARG A1494 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04571 (  648)
  hydrogen bonds       : angle       3.87071 ( 1908)
  covalent geometry    : bond        0.00298 ( 9675)
  covalent geometry    : angle       0.48453 (13146)

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 129
  time to evaluate  : 1.048 
Fit side-chains
   revert: symmetry clash
REVERT: A  225 LYS cc_start: 0.8502 (mttm) cc_final: 0.8060 (mmtt)
REVERT: A  235 ILE cc_start: 0.9003 (OUTLIER) cc_final: 0.8392 (mp)
REVERT: A  514 SER cc_start: 0.9005 (t) cc_final: 0.8704 (p)
REVERT: A  525 SER cc_start: 0.8676 (t) cc_final: 0.8213 (m)
REVERT: A  527 LYS cc_start: 0.8297 (ttpt) cc_final: 0.7777 (tttt)
REVERT: A  607 LEU cc_start: 0.8213 (mm) cc_final: 0.7482 (pp)
REVERT: A  672 ASN cc_start: 0.8569 (OUTLIER) cc_final: 0.8065 (t0)
REVERT: A  764 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7686 (mt-10)
REVERT: A  797 ASP cc_start: 0.8533 (m-30) cc_final: 0.8285 (m-30)
REVERT: A  827 ASN cc_start: 0.8303 (t0) cc_final: 0.7865 (t0)
REVERT: A  853 LYS cc_start: 0.8965 (tttt) cc_final: 0.8461 (ttpt)
REVERT: A  893 LYS cc_start: 0.8535 (mptt) cc_final: 0.8125 (mmtm)
REVERT: A  896 GLN cc_start: 0.7716 (tt0) cc_final: 0.7471 (tt0)
REVERT: A  973 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.7526 (tpt)
REVERT: A  976 LYS cc_start: 0.8405 (mttt) cc_final: 0.7782 (mmpt)
REVERT: A 1055 TRP cc_start: 0.7847 (t60) cc_final: 0.7074 (t-100)
REVERT: A 1185 ARG cc_start: 0.8487 (mtp85) cc_final: 0.8133 (mtt-85)
REVERT: A 1316 ARG cc_start: 0.8229 (ptp90) cc_final: 0.7636 (ptt90)
REVERT: A 1360 ASP cc_start: 0.7910 (t0) cc_final: 0.7546 (m-30)
REVERT: A 1393 ILE cc_start: 0.8813 (mt) cc_final: 0.8411 (tt)
REVERT: A 1425 ASN cc_start: 0.7915 (m-40) cc_final: 0.7409 (p0)
REVERT: A 1463 SER cc_start: 0.8123 (t) cc_final: 0.7751 (p)
  outliers start: 19
  outliers final: 10
  residues processed: 137
  average time/residue: 1.1852
  time to fit residues: 174.7508
Evaluate side-chains
  141 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 127
  time to evaluate  : 1.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  235 ILE
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  672 ASN
Chi-restraints excluded: chain A residue  764 GLU
Chi-restraints excluded: chain A residue  771 SER
Chi-restraints excluded: chain A residue  840 ILE
Chi-restraints excluded: chain A residue  971 THR
Chi-restraints excluded: chain A residue  973 MET
Chi-restraints excluded: chain A residue  987 PHE
Chi-restraints excluded: chain A residue 1005 VAL
Chi-restraints excluded: chain A residue 1073 ILE
Chi-restraints excluded: chain A residue 1281 PHE
Chi-restraints excluded: chain A residue 1460 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 100 optimal weight:    0.9980
   chunk 116 optimal weight:    1.9990
   chunk 97 optimal weight:    0.7980
   chunk 104 optimal weight:    3.9990
   chunk 58 optimal weight:    3.9990
   chunk 27 optimal weight:    0.8980
   chunk 46 optimal weight:    2.9990
   chunk 72 optimal weight:    0.5980
   chunk 106 optimal weight:    0.0770
   chunk 8 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   overall best weight:    0.6738

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

Flipped N/Q/H residues before XYZ refinement:
A 540 ASN
** A 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1319 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.141090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.107702 restraints weight = 10274.511|
|-----------------------------------------------------------------------------|
r_work (start): 0.3089 rms_B_bonded: 1.59
r_work: 0.2951 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.2805 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.2805
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8343
moved from start:          0.1958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9675  Z= 0.131
  Angle     :  0.479   6.666  13146  Z= 0.250
  Chirality :  0.039   0.162   1560
  Planarity :  0.003   0.043   1613
  Dihedral  :  9.373 166.232   1378
  Min Nonbonded Distance : 1.940

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 15.37 %
    Favored  : 82.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.67 (0.24), residues: 1190
  helix:  2.40 (0.18), residues: 817
  sheet:  0.52 (0.61), residues: 70
  loop :  0.39 (0.35), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 980 
 HIS   0.004   0.000   HIS A1001 
 PHE   0.019   0.001   PHE A1445 
 TYR   0.027   0.001   TYR A 532 
 ARG   0.010   0.000   ARG A1494 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04542 (  648)
  hydrogen bonds       : angle       3.87579 ( 1908)
  covalent geometry    : bond        0.00288 ( 9675)
  covalent geometry    : angle       0.47914 (13146)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7403.12 seconds
wall clock time: 131 minutes 42.94 seconds (7902.94 seconds total)