Starting phenix.real_space_refine
on Sun May  3 07:01:42 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jn1_61618/05_2026/9jn1_61618.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jn1_61618/05_2026/9jn1_61618.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.56
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jn1_61618/05_2026/9jn1_61618.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jn1_61618/05_2026/9jn1_61618.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jn1_61618/05_2026/9jn1_61618.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jn1_61618/05_2026/9jn1_61618.map"
  }
  resolution = 3.56
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.027
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      52      5.16       5
     C    7194      2.51       5
     N    1845      2.21       5
     O    2019      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11118
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 11054
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1435, 11054
          Classifications: {'peptide': 1435}
          Incomplete info: {'truncation_to_alanine': 95}
          Link IDs: {'PTRANS': 42, 'TRANS': 1392}
          Chain breaks: 2
          Unresolved chain link angles: 3
          Unresolved non-hydrogen bonds: 346
          Unresolved non-hydrogen angles: 416
          Unresolved non-hydrogen dihedrals: 287
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'ASN:plan1': 7, 'GLU:plan': 15, 'ARG:plan': 12, 'ASP:plan': 12, 'PHE:plan': 2, 'GLN:plan1': 3, 'HIS:plan': 2}
          Unresolved non-hydrogen planarities: 211
    Chain: "A"
      Number of atoms: 64
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 64
          Unusual residues: {' MG': 2, 'ANP': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
  Time building chain proxies: 2.91, per 1000 atoms: 0.26
  Number of scatterers: 11118
  At special positions: 0
  Unit cell: (95.23, 97.37, 155.15, 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      52     16.00
     P       6     15.00
     Mg      2     11.99
     O    2019      8.00
     N    1845      7.00
     C    7194      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A   6 " - pdb=" SG  CYS A  26 " distance=2.05

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.98
  Conformation dependent library (CDL) restraints added in 654.6 milliseconds
  

  2858 Ramachandran restraints generated.
    1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2714

  Finding SS restraints...
    Secondary structure from input PDB file:
      57 helices and 6 sheets defined
      71.1% alpha, 6.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.39
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 7
    Processing helix  chain 'A' and resid 12 through 17
      removed outlier: 4.072A  pdb=" N   LEU A  16 " --> pdb=" O   ASN A  12 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 24 through 30
    Processing helix  chain 'A' and resid 30 through 54
      Proline residue:  A  36  - end of helix
      removed outlier: 3.594A  pdb=" N   LEU A  43 " --> pdb=" O   TYR A  39 " (cutoff:3.500A)
      Proline residue:  A  45  - end of helix
    Processing helix  chain 'A' and resid 62 through 89
    Processing helix  chain 'A' and resid 97 through 122
      Proline residue:  A 104  - end of helix
    Processing helix  chain 'A' and resid 129 through 157
      removed outlier: 4.330A  pdb=" N   PHE A 145 " --> pdb=" O   LEU A 141 " (cutoff:3.500A)
      removed outlier: 4.498A  pdb=" N   GLN A 146 " --> pdb=" O   CYS A 142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 161 through 184
      removed outlier: 3.515A  pdb=" N   ILE A 180 " --> pdb=" O   ILE A 176 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   PHE A 181 " --> pdb=" O   LEU A 177 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   PHE A 184 " --> pdb=" O   ILE A 180 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 199 through 206
    Processing helix  chain 'A' and resid 209 through 219
    Processing helix  chain 'A' and resid 230 through 233
    Processing helix  chain 'A' and resid 234 through 256
      removed outlier: 3.781A  pdb=" N   HIS A 245 " --> pdb=" O   LYS A 241 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   ALA A 256 " --> pdb=" O   LYS A 252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 309 through 318
      removed outlier: 3.576A  pdb=" N   ALA A 313 " --> pdb=" O   TRP A 309 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 318 through 337
      removed outlier: 3.996A  pdb=" N   PHE A 337 " --> pdb=" O   ASP A 333 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 352
      removed outlier: 3.853A  pdb=" N   GLN A 341 " --> pdb=" O   PHE A 337 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   LEU A 345 " --> pdb=" O   GLN A 341 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 356 through 407
      removed outlier: 4.021A  pdb=" N   GLY A 360 " --> pdb=" O   TYR A 356 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   LEU A 405 " --> pdb=" O   TYR A 401 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   THR A 406 " --> pdb=" O   LYS A 402 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 408 through 415
      removed outlier: 4.085A  pdb=" N   GLU A 414 " --> pdb=" O   LEU A 410 " (cutoff:3.500A)
      removed outlier: 4.091A  pdb=" N   TYR A 415 " --> pdb=" O   ALA A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 426
      removed outlier: 4.130A  pdb=" N   MET A 424 " --> pdb=" O   THR A 420 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 426 through 437
      removed outlier: 3.611A  pdb=" N   PHE A 437 " --> pdb=" O   ASP A 433 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 439 through 459
      removed outlier: 3.628A  pdb=" N   VAL A 445 " --> pdb=" O   LEU A 441 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 461 through 507
      removed outlier: 4.119A  pdb=" N   ALA A 465 " --> pdb=" O   PRO A 461 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   VAL A 469 " --> pdb=" O   ALA A 465 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   MET A 470 " --> pdb=" O   GLY A 466 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   ILE A 474 " --> pdb=" O   MET A 470 " (cutoff:3.500A)
      Proline residue:  A 475  - end of helix
      removed outlier: 3.526A  pdb=" N   ASN A 494 " --> pdb=" O   LYS A 490 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 508 through 515
      removed outlier: 3.574A  pdb=" N   LEU A 512 " --> pdb=" O   GLY A 508 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 517 through 569
      removed outlier: 3.721A  pdb=" N   LYS A 531 " --> pdb=" O   ASN A 527 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   GLU A 532 " --> pdb=" O   LEU A 528 " (cutoff:3.500A)
      Proline residue:  A 554  - end of helix
      removed outlier: 4.094A  pdb=" N   ASP A 569 " --> pdb=" O   TYR A 565 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 575 through 618
      removed outlier: 3.756A  pdb=" N   THR A 581 " --> pdb=" O   GLN A 577 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   SER A 582 " --> pdb=" O   LYS A 578 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ILE A 588 " --> pdb=" O   THR A 584 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   PHE A 591 " --> pdb=" O   ASN A 587 " (cutoff:3.500A)
      Proline residue:  A 592  - end of helix
      Proline residue:  A 597  - end of helix
      removed outlier: 3.776A  pdb=" N   VAL A 608 " --> pdb=" O   LEU A 604 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 676 through 685
      removed outlier: 4.151A  pdb=" N   ILE A 681 " --> pdb=" O   LYS A 677 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 715 through 721
    Processing helix  chain 'A' and resid 726 through 737
    Processing helix  chain 'A' and resid 738 through 746
      removed outlier: 4.462A  pdb=" N   ASP A 742 " --> pdb=" O   ALA A 738 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   MET A 745 " --> pdb=" O   PRO A 741 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 748 through 751
    Processing helix  chain 'A' and resid 762 through 778
    Processing helix  chain 'A' and resid 792 through 804
    Processing helix  chain 'A' and resid 844 through 851
    Processing helix  chain 'A' and resid 853 through 862
    Processing helix  chain 'A' and resid 890 through 896
      Proline residue:  A 895  - end of helix
    Processing helix  chain 'A' and resid 897 through 914
    Processing helix  chain 'A' and resid 964 through 974
    Processing helix  chain 'A' and resid 975 through 1010
      removed outlier: 3.778A  pdb=" N   SER A1007 " --> pdb=" O   TRP A1003 " (cutoff:3.500A)
      removed outlier: 4.376A  pdb=" N   LYS A1008 " --> pdb=" O   THR A1004 " (cutoff:3.500A)
      removed outlier: 4.076A  pdb=" N   ILE A1009 " --> pdb=" O   SER A1005 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1016 through 1066
      removed outlier: 3.676A  pdb=" N   VAL A1038 " --> pdb=" O   GLN A1034 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1068 through 1075
      removed outlier: 3.640A  pdb=" N   PHE A1072 " --> pdb=" O   PRO A1068 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1076 through 1093
      removed outlier: 3.566A  pdb=" N   ILE A1080 " --> pdb=" O   PRO A1076 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   ASP A1087 " --> pdb=" O   ARG A1083 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   ILE A1088 " --> pdb=" O   PHE A1084 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1093 through 1120
      removed outlier: 4.073A  pdb=" N   GLN A1097 " --> pdb=" O   ASP A1093 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1123 through 1169
      removed outlier: 4.050A  pdb=" N   ILE A1128 " --> pdb=" O   THR A1124 " (cutoff:3.500A)
      Proline residue:  A1129  - end of helix
      removed outlier: 3.776A  pdb=" N   GLN A1147 " --> pdb=" O   SER A1143 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   SER A1157 " --> pdb=" O   SER A1153 " (cutoff:3.500A)
      Proline residue:  A1158  - end of helix
    Processing helix  chain 'A' and resid 1169 through 1176
    Processing helix  chain 'A' and resid 1178 through 1229
      removed outlier: 3.513A  pdb=" N   ASN A1193 " --> pdb=" O   ARG A1189 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   CYS A1196 " --> pdb=" O   THR A1192 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1234 through 1247
      removed outlier: 3.643A  pdb=" N   ASN A1244 " --> pdb=" O   PHE A1240 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   ASN A1247 " --> pdb=" O   SER A1243 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1247 through 1277
      removed outlier: 3.640A  pdb=" N   THR A1251 " --> pdb=" O   ASN A1247 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   ASN A1253 " --> pdb=" O   THR A1249 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   VAL A1256 " --> pdb=" O   LEU A1252 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   VAL A1267 " --> pdb=" O   GLU A1263 " (cutoff:3.500A)
      removed outlier: 4.545A  pdb=" N   ALA A1268 " --> pdb=" O   THR A1264 " (cutoff:3.500A)
      removed outlier: 4.295A  pdb=" N   VAL A1269 " --> pdb=" O   ASN A1265 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1292 through 1297
      removed outlier: 3.519A  pdb=" N   SER A1296 " --> pdb=" O   PRO A1292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1339 through 1348
      removed outlier: 3.515A  pdb=" N   LEU A1343 " --> pdb=" O   GLY A1339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1369 through 1376
    Processing helix  chain 'A' and resid 1390 through 1396
    Processing helix  chain 'A' and resid 1402 through 1414
      removed outlier: 3.660A  pdb=" N   ILE A1406 " --> pdb=" O   SER A1402 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1415 through 1422
    Processing helix  chain 'A' and resid 1424 through 1428
    Processing helix  chain 'A' and resid 1431 through 1435
    Processing helix  chain 'A' and resid 1438 through 1454
    Processing helix  chain 'A' and resid 1468 through 1483
    Processing helix  chain 'A' and resid 1494 through 1501
      removed outlier: 3.839A  pdb=" N   ILE A1498 " --> pdb=" O   ARG A1494 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 627 through 629
      removed outlier: 6.048A  pdb=" N   ARG A 628 " --> pdb=" O   ILE A 697 " (cutoff:3.500A)
      removed outlier: 7.177A  pdb=" N   ASN A 690 " --> pdb=" O   PHE A 644 " (cutoff:3.500A)
      removed outlier: 6.797A  pdb=" N   PHE A 644 " --> pdb=" O   ASN A 690 " (cutoff:3.500A)
      removed outlier: 6.716A  pdb=" N   HIS A 692 " --> pdb=" O   ALA A 642 " (cutoff:3.500A)
      removed outlier: 4.636A  pdb=" N   ALA A 642 " --> pdb=" O   HIS A 692 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   MET A 637 " --> pdb=" O   ILE A 661 " (cutoff:3.500A)
      removed outlier: 5.003A  pdb=" N   VAL A 657 " --> pdb=" O   GLU A 641 " (cutoff:3.500A)
      removed outlier: 6.291A  pdb=" N   SER A 643 " --> pdb=" O   ARG A 655 " (cutoff:3.500A)
      removed outlier: 6.747A  pdb=" N   ARG A 655 " --> pdb=" O   SER A 643 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 701 through 704
      removed outlier: 6.031A  pdb=" N   ALA A 702 " --> pdb=" O   LEU A 783 " (cutoff:3.500A)
      removed outlier: 7.569A  pdb=" N   ASP A 785 " --> pdb=" O   ALA A 702 " (cutoff:3.500A)
      removed outlier: 6.300A  pdb=" N   VAL A 704 " --> pdb=" O   ASP A 785 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   VAL A 669 " --> pdb=" O   LEU A 817 " (cutoff:3.500A)
      removed outlier: 6.862A  pdb=" N   LEU A 666 " --> pdb=" O   GLU A 830 " (cutoff:3.500A)
      removed outlier: 8.028A  pdb=" N   VAL A 832 " --> pdb=" O   LEU A 666 " (cutoff:3.500A)
      removed outlier: 6.310A  pdb=" N   ALA A 668 " --> pdb=" O   VAL A 832 " (cutoff:3.500A)
      removed outlier: 7.391A  pdb=" N   LEU A 834 " --> pdb=" O   ALA A 668 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   ILE A 670 " --> pdb=" O   LEU A 834 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   GLU A 841 " --> pdb=" O   VAL A 833 " (cutoff:3.500A)
      removed outlier: 6.023A  pdb=" N   GLY A 835 " --> pdb=" O   ILE A 839 " (cutoff:3.500A)
      removed outlier: 5.258A  pdb=" N   ILE A 839 " --> pdb=" O   GLY A 835 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 713 through 714
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1323 through 1324
      removed outlier: 4.181A  pdb=" N   GLN A1357 " --> pdb=" O   ASN A1303 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1305 through 1307
      removed outlier: 3.721A  pdb=" N   ILE A1320 " --> pdb=" O   TYR A1305 " (cutoff:3.500A)
      removed outlier: 8.169A  pdb=" N   VAL A1307 " --> pdb=" O   ARG A1318 " (cutoff:3.500A)
      removed outlier: 6.458A  pdb=" N   ARG A1318 " --> pdb=" O   VAL A1307 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1377 through 1380
      removed outlier: 6.171A  pdb=" N   LEU A1458 " --> pdb=" O   ILE A1489 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   ILE A1330 " --> pdb=" O   THR A1490 " (cutoff:3.500A)
      removed outlier: 6.242A  pdb=" N   GLY A1331 " --> pdb=" O   MET A1505 " (cutoff:3.500A)
      removed outlier: 7.391A  pdb=" N   LEU A1507 " --> pdb=" O   GLY A1331 " (cutoff:3.500A)
      removed outlier: 6.087A  pdb=" N   VAL A1333 " --> pdb=" O   LEU A1507 " (cutoff:3.500A)
      removed outlier: 6.183A  pdb=" N   ASP A1508 " --> pdb=" O   ILE A1512 " (cutoff:3.500A)
      removed outlier: 5.166A  pdb=" N   ILE A1512 " --> pdb=" O   ASP A1508 " (cutoff:3.500A)

    739 hydrogen bonds defined for protein.
    2181 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.29

  Time building geometry restraints manager: 1.29 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1874
        1.32 -     1.44: 2931
        1.44 -     1.57: 6451
        1.57 -     1.69: 10
        1.69 -     1.81: 84
  Bond restraints: 11350
  Sorted by residual:
  bond pdb=" N3B ANP A1602 "
       pdb=" PG  ANP A1602 "
    ideal  model  delta    sigma   weight residual
    1.795  1.632  0.163 2.00e-02 2.50e+03 6.66e+01
  bond pdb=" N3B ANP A1604 "
       pdb=" PG  ANP A1604 "
    ideal  model  delta    sigma   weight residual
    1.795  1.633  0.162 2.00e-02 2.50e+03 6.53e+01
  bond pdb=" O3A ANP A1602 "
       pdb=" PB  ANP A1602 "
    ideal  model  delta    sigma   weight residual
    1.700  1.598  0.102 2.00e-02 2.50e+03 2.60e+01
  bond pdb=" O3A ANP A1604 "
       pdb=" PB  ANP A1604 "
    ideal  model  delta    sigma   weight residual
    1.700  1.605  0.095 2.00e-02 2.50e+03 2.26e+01
  bond pdb=" N   VAL A 704 "
       pdb=" CA  VAL A 704 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 7.70e-03 1.69e+04 1.84e+01
  ... (remaining 11345 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.91: 11791
        1.91 -     3.83: 3439
        3.83 -     5.74: 194
        5.74 -     7.66: 20
        7.66 -     9.57: 8
  Bond angle restraints: 15452
  Sorted by residual:
  angle pdb=" CA  GLY A 699 "
        pdb=" C   GLY A 699 "
        pdb=" O   GLY A 699 "
      ideal   model   delta    sigma   weight residual
     122.22  118.14    4.08 6.50e-01 2.37e+00 3.94e+01
  angle pdb=" N   ASP A 780 "
        pdb=" CA  ASP A 780 "
        pdb=" C   ASP A 780 "
      ideal   model   delta    sigma   weight residual
     111.14  116.88   -5.74 1.08e+00 8.57e-01 2.83e+01
  angle pdb=" N   LEU A   2 "
        pdb=" CA  LEU A   2 "
        pdb=" C   LEU A   2 "
      ideal   model   delta    sigma   weight residual
     112.72  106.71    6.01 1.14e+00 7.69e-01 2.78e+01
  angle pdb=" C   ILE A 894 "
        pdb=" CA  ILE A 894 "
        pdb=" CB  ILE A 894 "
      ideal   model   delta    sigma   weight residual
     111.36  120.93   -9.57 1.82e+00 3.02e-01 2.77e+01
  angle pdb=" C   ASN A 422 "
        pdb=" CA  ASN A 422 "
        pdb=" CB  ASN A 422 "
      ideal   model   delta    sigma   weight residual
     110.63  120.14   -9.51 1.85e+00 2.92e-01 2.64e+01
  ... (remaining 15447 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.67: 6471
       31.67 -    63.35: 256
       63.35 -    95.02: 7
       95.02 -   126.69: 0
      126.69 -   158.37: 3
  Dihedral angle restraints: 6737
    sinusoidal: 2553
      harmonic: 4184
  Sorted by residual:
  dihedral pdb=" CB  CYS A   6 "
           pdb=" SG  CYS A   6 "
           pdb=" SG  CYS A  26 "
           pdb=" CB  CYS A  26 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   37.58   55.42     1      1.00e+01 1.00e-02 4.15e+01
  dihedral pdb=" C   ASN A 422 "
           pdb=" N   ASN A 422 "
           pdb=" CA  ASN A 422 "
           pdb=" CB  ASN A 422 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -137.69   15.09     0      2.50e+00 1.60e-01 3.64e+01
  dihedral pdb=" N   ASN A 422 "
           pdb=" C   ASN A 422 "
           pdb=" CA  ASN A 422 "
           pdb=" CB  ASN A 422 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  134.81  -12.01     0      2.50e+00 1.60e-01 2.31e+01
  ... (remaining 6734 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.106: 1215
       0.106 -    0.212: 556
       0.212 -    0.318: 67
       0.318 -    0.424: 4
       0.424 -    0.530: 2
  Chirality restraints: 1844
  Sorted by residual:
  chirality pdb=" CB  ILE A 894 "
            pdb=" CA  ILE A 894 "
            pdb=" CG1 ILE A 894 "
            pdb=" CG2 ILE A 894 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.12    0.53 2.00e-01 2.50e+01 7.01e+00
  chirality pdb=" CA  ASN A 422 "
            pdb=" N   ASN A 422 "
            pdb=" C   ASN A 422 "
            pdb=" CB  ASN A 422 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.03    0.48 2.00e-01 2.50e+01 5.81e+00
  chirality pdb=" CA  TYR A 101 "
            pdb=" N   TYR A 101 "
            pdb=" C   TYR A 101 "
            pdb=" CB  TYR A 101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.12    0.39 2.00e-01 2.50e+01 3.78e+00
  ... (remaining 1841 not shown)

  Planarity restraints: 1908
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A  40 "   -0.010 2.00e-02 2.50e+03   2.00e-02 4.01e+00
        pdb=" C   LEU A  40 "    0.035 2.00e-02 2.50e+03
        pdb=" O   LEU A  40 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   TRP A  41 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 621 "    0.010 2.00e-02 2.50e+03   1.93e-02 3.72e+00
        pdb=" C   ASP A 621 "   -0.033 2.00e-02 2.50e+03
        pdb=" O   ASP A 621 "    0.012 2.00e-02 2.50e+03
        pdb=" N   LEU A 622 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A1173 "    0.008 2.00e-02 2.50e+03   1.59e-02 2.52e+00
        pdb=" C   ILE A1173 "   -0.027 2.00e-02 2.50e+03
        pdb=" O   ILE A1173 "    0.010 2.00e-02 2.50e+03
        pdb=" N   ARG A1174 "    0.009 2.00e-02 2.50e+03
  ... (remaining 1905 not shown)

  Histogram of nonbonded interaction distances:
        1.23 -     1.97: 10
        1.97 -     2.70: 199
        2.70 -     3.43: 16878
        3.43 -     4.17: 25622
        4.17 -     4.90: 45378
  Nonbonded interactions: 88087
  Sorted by model distance:
  nonbonded pdb=" O   GLY A 671 "
            pdb=" NZ  LYS A 677 "
     model   vdw
     1.232 3.120
  nonbonded pdb=" CA  GLY A 671 "
            pdb=" CE  LYS A 677 "
     model   vdw
     1.478 3.840
  nonbonded pdb=" CB  ALA A1338 "
            pdb="MG    MG A1603 "
     model   vdw
     1.607 2.590
  nonbonded pdb=" N   GLY A 671 "
            pdb=" CE  LYS A 677 "
     model   vdw
     1.610 3.520
  nonbonded pdb=" CA  ALA A1338 "
            pdb="MG    MG A1603 "
     model   vdw
     1.714 2.600
  ... (remaining 88082 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.330
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     12.300
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  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:1.650
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.600
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7210
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      :  0.012   0.163  11351  Z= 0.931
  Angle     :  1.563   9.571  15454  Z= 1.244
  Chirality :  0.107   0.530   1844
  Planarity :  0.005   0.033   1908
  Dihedral  : 15.667 158.368   4020
  Min Nonbonded Distance : 1.232

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.05 %
    Favored  : 98.95 %
  Rotamer:
    Outliers :  9.08 %
    Allowed  : 12.05 %
    Favored  : 78.86 %
  Cbeta Deviations :  0.66 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.98 (0.20), residues: 1429
  helix:  3.78 (0.15), residues: 907
  sheet:  2.63 (0.62), residues: 72
  loop :  0.08 (0.26), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 655 
 TYR   0.018   0.002   TYR A 101 
 PHE   0.021   0.002   PHE A1240 
 TRP   0.025   0.002   TRP A1200 
 HIS   0.005   0.001   HIS A 798 

Details of bonding type rmsd
  covalent geometry    : bond        0.01223 (11350)
  covalent geometry    : angle       1.56326 (15452)
  SS BOND              : bond        0.01762 (    1)
  SS BOND              : angle       2.27582 (    2)
  hydrogen bonds       : bond        0.23478 (  739)
  hydrogen bonds       : angle       6.41246 ( 2181)

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

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

  2858 Ramachandran restraints generated.
    1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2858 Ramachandran restraints generated.
    1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  418 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 107
    poor density    : 311
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  148 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.7102 (tp40)
REVERT: A  307 LYS cc_start: 0.6786 (pttp) cc_final: 0.6418 (mtpt)
REVERT: A  410 LEU cc_start: 0.8490 (tp) cc_final: 0.7636 (tt)
REVERT: A  414 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7281 (mp0)
REVERT: A  426 VAL cc_start: 0.8267 (p) cc_final: 0.8041 (t)
REVERT: A  427 ASP cc_start: 0.8280 (m-30) cc_final: 0.7979 (m-30)
REVERT: A  430 LYS cc_start: 0.7453 (tppt) cc_final: 0.6809 (tppt)
REVERT: A  515 PHE cc_start: 0.7970 (m-80) cc_final: 0.7433 (m-80)
REVERT: A  614 GLU cc_start: 0.6719 (pt0) cc_final: 0.6240 (pt0)
REVERT: A  662 MET cc_start: 0.7296 (mmt) cc_final: 0.6852 (mmm)
REVERT: A  688 MET cc_start: 0.7828 (OUTLIER) cc_final: 0.6729 (mmt)
REVERT: A  689 GLU cc_start: 0.6730 (mp0) cc_final: 0.5786 (mp0)
REVERT: A  711 GLN cc_start: 0.7859 (pt0) cc_final: 0.7590 (pt0)
REVERT: A  822 MET cc_start: 0.6806 (mpp) cc_final: 0.6566 (mpp)
REVERT: A  831 ILE cc_start: 0.9148 (mm) cc_final: 0.8731 (pt)
REVERT: A  897 ASP cc_start: 0.6370 (t0) cc_final: 0.6056 (t0)
REVERT: A  988 MET cc_start: 0.8296 (tpp) cc_final: 0.8039 (mmt)
REVERT: A 1015 TYR cc_start: 0.7978 (OUTLIER) cc_final: 0.7429 (t80)
REVERT: A 1043 PHE cc_start: 0.7155 (OUTLIER) cc_final: 0.6645 (t80)
REVERT: A 1151 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.7186 (mt)
REVERT: A 1203 SER cc_start: 0.9404 (t) cc_final: 0.8982 (p)
REVERT: A 1240 PHE cc_start: 0.7503 (OUTLIER) cc_final: 0.6397 (p90)
REVERT: A 1254 TRP cc_start: 0.6751 (OUTLIER) cc_final: 0.6300 (t-100)
REVERT: A 1258 MET cc_start: 0.8091 (mmp) cc_final: 0.7886 (mmm)
REVERT: A 1284 TRP cc_start: 0.7937 (m-10) cc_final: 0.7395 (m-10)
REVERT: A 1320 ILE cc_start: 0.6967 (OUTLIER) cc_final: 0.6645 (mp)
REVERT: A 1327 MET cc_start: 0.4356 (tmm) cc_final: 0.3928 (tpt)
REVERT: A 1392 ARG cc_start: 0.7464 (tpt90) cc_final: 0.7168 (tpt90)
REVERT: A 1472 ASP cc_start: 0.7423 (OUTLIER) cc_final: 0.6387 (t0)
  outliers start: 107
  outliers final: 26
  residues processed: 381
  average time/residue: 0.1054
  time to fit residues: 57.4071
Evaluate side-chains
  219 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 183
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  148 GLN
Chi-restraints excluded: chain A residue  185 SER
Chi-restraints excluded: chain A residue  222 THR
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  385 CYS
Chi-restraints excluded: chain A residue  414 GLU
Chi-restraints excluded: chain A residue  437 PHE
Chi-restraints excluded: chain A residue  491 ASN
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain A residue  532 GLU
Chi-restraints excluded: chain A residue  620 ASP
Chi-restraints excluded: chain A residue  622 LEU
Chi-restraints excluded: chain A residue  627 ILE
Chi-restraints excluded: chain A residue  657 VAL
Chi-restraints excluded: chain A residue  688 MET
Chi-restraints excluded: chain A residue  739 LEU
Chi-restraints excluded: chain A residue  814 THR
Chi-restraints excluded: chain A residue  829 ASP
Chi-restraints excluded: chain A residue  840 VAL
Chi-restraints excluded: chain A residue  874 VAL
Chi-restraints excluded: chain A residue 1015 TYR
Chi-restraints excluded: chain A residue 1043 PHE
Chi-restraints excluded: chain A residue 1060 LEU
Chi-restraints excluded: chain A residue 1107 LEU
Chi-restraints excluded: chain A residue 1151 LEU
Chi-restraints excluded: chain A residue 1200 TRP
Chi-restraints excluded: chain A residue 1240 PHE
Chi-restraints excluded: chain A residue 1254 TRP
Chi-restraints excluded: chain A residue 1320 ILE
Chi-restraints excluded: chain A residue 1371 HIS
Chi-restraints excluded: chain A residue 1391 LEU
Chi-restraints excluded: chain A residue 1439 ILE
Chi-restraints excluded: chain A residue 1472 ASP
Chi-restraints excluded: chain A residue 1507 LEU
Chi-restraints excluded: chain A residue 1515 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 107 optimal weight:    2.9990
   chunk 10 optimal weight:    4.9990
   chunk 66 optimal weight:    0.6980
   chunk 130 optimal weight:    6.9990
   chunk 124 optimal weight:    7.9990
   chunk 103 optimal weight:    0.9980
   chunk 77 optimal weight:    7.9990
   chunk 122 optimal weight:    6.9990
   chunk 91 optimal weight:    0.6980
   chunk 55 optimal weight:    0.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
A  50 HIS
A 159 ASN
** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 409 ASN
A 439 HIS
A 477 ASN
A 491 ASN
A 541 GLN
A 690 ASN
A 694 HIS
A 706 GLN
** A 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 807 ASN
** A1097 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1194 GLN
A1253 ASN
A1399 ASN
A1428 HIS
A1441 GLN
A1443 GLN
A1476 GLN

Total number of N/Q/H flips: 18

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.186271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.145772 restraints weight = 15065.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.144582 restraints weight = 19238.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.146622 restraints weight = 15425.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.145308 restraints weight = 11820.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.145941 restraints weight = 9526.237|
|-----------------------------------------------------------------------------|
r_work (final): 0.3713
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7623
moved from start:          0.3212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  11351  Z= 0.191
  Angle     :  0.637  12.867  15454  Z= 0.354
  Chirality :  0.043   0.234   1844
  Planarity :  0.004   0.041   1908
  Dihedral  : 10.715 156.571   1652
  Min Nonbonded Distance : 2.093

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.56 %
    Favored  : 99.44 %
  Rotamer:
    Outliers :  5.77 %
    Allowed  : 20.20 %
    Favored  : 74.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.66 (0.21), residues: 1429
  helix:  2.67 (0.16), residues: 949
  sheet:  1.92 (0.62), residues: 70
  loop : -0.52 (0.26), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A1146 
 TYR   0.025   0.002   TYR A 101 
 PHE   0.022   0.002   PHE A1240 
 TRP   0.013   0.002   TRP A1200 
 HIS   0.008   0.002   HIS A 798 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 (11350)
  covalent geometry    : angle       0.63650 (15452)
  SS BOND              : bond        0.00595 (    1)
  SS BOND              : angle       2.11994 (    2)
  hydrogen bonds       : bond        0.08394 (  739)
  hydrogen bonds       : angle       4.73531 ( 2181)

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

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

  2858 Ramachandran restraints generated.
    1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2858 Ramachandran restraints generated.
    1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  279 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 211
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  101 TYR cc_start: 0.4697 (p90) cc_final: 0.4454 (p90)
REVERT: A  148 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.7339 (tp40)
REVERT: A  430 LYS cc_start: 0.7777 (tppt) cc_final: 0.7575 (tppt)
REVERT: A  532 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.6450 (tm-30)
REVERT: A  688 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7212 (mmt)
REVERT: A  689 GLU cc_start: 0.6442 (mp0) cc_final: 0.5844 (mp0)
REVERT: A  765 GLN cc_start: 0.7816 (mt0) cc_final: 0.7178 (mt0)
REVERT: A  789 SER cc_start: 0.8325 (p) cc_final: 0.7747 (p)
REVERT: A  988 MET cc_start: 0.7609 (tpp) cc_final: 0.7399 (mmt)
REVERT: A 1015 TYR cc_start: 0.8281 (OUTLIER) cc_final: 0.7601 (t80)
REVERT: A 1043 PHE cc_start: 0.7196 (OUTLIER) cc_final: 0.6714 (t80)
REVERT: A 1327 MET cc_start: 0.3916 (OUTLIER) cc_final: 0.3444 (tpt)
REVERT: A 1442 ARG cc_start: 0.8394 (ptp-170) cc_final: 0.8153 (ptm-80)
  outliers start: 68
  outliers final: 28
  residues processed: 258
  average time/residue: 0.0917
  time to fit residues: 34.8167
Evaluate side-chains
  193 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 159
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 PHE
Chi-restraints excluded: chain A residue  148 GLN
Chi-restraints excluded: chain A residue  222 THR
Chi-restraints excluded: chain A residue  385 CYS
Chi-restraints excluded: chain A residue  435 THR
Chi-restraints excluded: chain A residue  437 PHE
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain A residue  532 GLU
Chi-restraints excluded: chain A residue  544 CYS
Chi-restraints excluded: chain A residue  624 THR
Chi-restraints excluded: chain A residue  640 SER
Chi-restraints excluded: chain A residue  667 VAL
Chi-restraints excluded: chain A residue  669 VAL
Chi-restraints excluded: chain A residue  688 MET
Chi-restraints excluded: chain A residue  739 LEU
Chi-restraints excluded: chain A residue  746 LEU
Chi-restraints excluded: chain A residue  751 LEU
Chi-restraints excluded: chain A residue  814 THR
Chi-restraints excluded: chain A residue  829 ASP
Chi-restraints excluded: chain A residue  874 VAL
Chi-restraints excluded: chain A residue 1015 TYR
Chi-restraints excluded: chain A residue 1043 PHE
Chi-restraints excluded: chain A residue 1064 ILE
Chi-restraints excluded: chain A residue 1107 LEU
Chi-restraints excluded: chain A residue 1194 GLN
Chi-restraints excluded: chain A residue 1200 TRP
Chi-restraints excluded: chain A residue 1218 THR
Chi-restraints excluded: chain A residue 1240 PHE
Chi-restraints excluded: chain A residue 1327 MET
Chi-restraints excluded: chain A residue 1333 VAL
Chi-restraints excluded: chain A residue 1371 HIS
Chi-restraints excluded: chain A residue 1507 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 29 optimal weight:    0.9990
   chunk 92 optimal weight:    0.0170
   chunk 135 optimal weight:    8.9990
   chunk 56 optimal weight:    4.9990
   chunk 7 optimal weight:    0.8980
   chunk 99 optimal weight:    1.9990
   chunk 9 optimal weight:    0.0570
   chunk 35 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   chunk 19 optimal weight:    5.9990
   chunk 114 optimal weight:    2.9990
   overall best weight:    0.5738

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

Flipped N/Q/H residues before XYZ refinement:
A 128 ASN
** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 765 GLN
A 767 GLN
A 997 ASN
** A1097 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1193 ASN
A1244 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.187680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.145544 restraints weight = 15229.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.144246 restraints weight = 18968.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.145706 restraints weight = 16303.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.146118 restraints weight = 10221.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.146272 restraints weight = 8915.274|
|-----------------------------------------------------------------------------|
r_work (final): 0.3711
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7627
moved from start:          0.3955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  11351  Z= 0.155
  Angle     :  0.571  13.919  15454  Z= 0.307
  Chirality :  0.039   0.200   1844
  Planarity :  0.003   0.029   1908
  Dihedral  :  9.280 148.177   1620
  Min Nonbonded Distance : 2.049

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.91 %
    Favored  : 99.09 %
  Rotamer:
    Outliers :  4.75 %
    Allowed  : 21.31 %
    Favored  : 73.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.33 (0.21), residues: 1429
  helix:  2.46 (0.16), residues: 954
  sheet:  1.26 (0.66), residues: 65
  loop : -0.67 (0.26), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1146 
 TYR   0.026   0.001   TYR A 101 
 PHE   0.018   0.001   PHE A 548 
 TRP   0.014   0.001   TRP A1254 
 HIS   0.007   0.001   HIS A 648 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 (11350)
  covalent geometry    : angle       0.56967 (15452)
  SS BOND              : bond        0.01397 (    1)
  SS BOND              : angle       3.38536 (    2)
  hydrogen bonds       : bond        0.07067 (  739)
  hydrogen bonds       : angle       4.28400 ( 2181)

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

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

  2858 Ramachandran restraints generated.
    1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2858 Ramachandran restraints generated.
    1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 176
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  101 TYR cc_start: 0.4680 (p90) cc_final: 0.4407 (p90)
REVERT: A  119 TYR cc_start: 0.7622 (t80) cc_final: 0.7355 (t80)
REVERT: A  148 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.7233 (tp40)
REVERT: A  152 ARG cc_start: 0.4422 (mmt180) cc_final: 0.4217 (mmt180)
REVERT: A  437 PHE cc_start: 0.8369 (OUTLIER) cc_final: 0.8139 (p90)
REVERT: A  504 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.6565 (mp0)
REVERT: A  532 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.6222 (tm-30)
REVERT: A  689 GLU cc_start: 0.6477 (mp0) cc_final: 0.5935 (mp0)
REVERT: A  765 GLN cc_start: 0.7675 (mt0) cc_final: 0.7132 (mt0)
REVERT: A  988 MET cc_start: 0.7513 (tpp) cc_final: 0.7312 (mmt)
REVERT: A 1015 TYR cc_start: 0.8336 (OUTLIER) cc_final: 0.7719 (t80)
REVERT: A 1043 PHE cc_start: 0.7167 (OUTLIER) cc_final: 0.6639 (t80)
REVERT: A 1240 PHE cc_start: 0.8094 (OUTLIER) cc_final: 0.7114 (p90)
REVERT: A 1327 MET cc_start: 0.3704 (OUTLIER) cc_final: 0.3397 (tpt)
  outliers start: 56
  outliers final: 31
  residues processed: 214
  average time/residue: 0.0867
  time to fit residues: 27.4827
Evaluate side-chains
  196 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 157
  time to evaluate  : 0.673 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 PHE
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  148 GLN
Chi-restraints excluded: chain A residue  222 THR
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  437 PHE
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  462 SER
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  467 VAL
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain A residue  504 GLU
Chi-restraints excluded: chain A residue  532 GLU
Chi-restraints excluded: chain A residue  544 CYS
Chi-restraints excluded: chain A residue  575 ASP
Chi-restraints excluded: chain A residue  627 ILE
Chi-restraints excluded: chain A residue  640 SER
Chi-restraints excluded: chain A residue  739 LEU
Chi-restraints excluded: chain A residue  751 LEU
Chi-restraints excluded: chain A residue  809 LEU
Chi-restraints excluded: chain A residue  814 THR
Chi-restraints excluded: chain A residue  829 ASP
Chi-restraints excluded: chain A residue  874 VAL
Chi-restraints excluded: chain A residue 1015 TYR
Chi-restraints excluded: chain A residue 1032 LEU
Chi-restraints excluded: chain A residue 1043 PHE
Chi-restraints excluded: chain A residue 1064 ILE
Chi-restraints excluded: chain A residue 1107 LEU
Chi-restraints excluded: chain A residue 1113 LEU
Chi-restraints excluded: chain A residue 1179 GLN
Chi-restraints excluded: chain A residue 1200 TRP
Chi-restraints excluded: chain A residue 1240 PHE
Chi-restraints excluded: chain A residue 1262 ILE
Chi-restraints excluded: chain A residue 1275 TYR
Chi-restraints excluded: chain A residue 1327 MET
Chi-restraints excluded: chain A residue 1333 VAL
Chi-restraints excluded: chain A residue 1350 ILE
Chi-restraints excluded: chain A residue 1371 HIS
Chi-restraints excluded: chain A residue 1507 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 69 optimal weight:    0.6980
   chunk 71 optimal weight:    0.4980
   chunk 49 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9990
   chunk 131 optimal weight:    8.9990
   chunk 18 optimal weight:    6.9990
   chunk 100 optimal weight:    1.9990
   chunk 101 optimal weight:    0.7980
   chunk 136 optimal weight:    9.9990
   chunk 124 optimal weight:   50.0000
   chunk 34 optimal weight:    0.7980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A 638 GLN
A 767 GLN
A 823 HIS
** A1097 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1371 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.187300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.145093 restraints weight = 15384.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.142946 restraints weight = 21051.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.145015 restraints weight = 15330.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.145381 restraints weight = 10620.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.145417 restraints weight = 9926.997|
|-----------------------------------------------------------------------------|
r_work (final): 0.3694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7648
moved from start:          0.4421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  11351  Z= 0.141
  Angle     :  0.548  11.822  15454  Z= 0.289
  Chirality :  0.040   0.190   1844
  Planarity :  0.003   0.038   1908
  Dihedral  :  8.741 138.700   1616
  Min Nonbonded Distance : 1.999

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.84 %
    Favored  : 99.16 %
  Rotamer:
    Outliers :  5.01 %
    Allowed  : 22.50 %
    Favored  : 72.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.23 (0.21), residues: 1429
  helix:  2.38 (0.16), residues: 954
  sheet:  1.10 (0.66), residues: 65
  loop : -0.68 (0.26), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  58 
 TYR   0.022   0.001   TYR A 101 
 PHE   0.020   0.001   PHE A 633 
 TRP   0.012   0.001   TRP A1200 
 HIS   0.007   0.001   HIS A 648 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 (11350)
  covalent geometry    : angle       0.54648 (15452)
  SS BOND              : bond        0.00790 (    1)
  SS BOND              : angle       3.30095 (    2)
  hydrogen bonds       : bond        0.06345 (  739)
  hydrogen bonds       : angle       4.09657 ( 2181)

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

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

  2858 Ramachandran restraints generated.
    1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2858 Ramachandran restraints generated.
    1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 169
  time to evaluate  : 0.418 
Fit side-chains
   revert: symmetry clash
REVERT: A  101 TYR cc_start: 0.4802 (p90) cc_final: 0.4481 (p90)
REVERT: A  148 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.7250 (tp40)
REVERT: A  437 PHE cc_start: 0.8594 (OUTLIER) cc_final: 0.8341 (p90)
REVERT: A  504 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6565 (mp0)
REVERT: A  532 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.6192 (tm-30)
REVERT: A  689 GLU cc_start: 0.6441 (mp0) cc_final: 0.5643 (mp0)
REVERT: A  765 GLN cc_start: 0.7592 (mt0) cc_final: 0.7066 (mt0)
REVERT: A  988 MET cc_start: 0.7488 (tpp) cc_final: 0.7287 (mmt)
REVERT: A 1015 TYR cc_start: 0.8346 (OUTLIER) cc_final: 0.7906 (t80)
REVERT: A 1043 PHE cc_start: 0.7132 (OUTLIER) cc_final: 0.6626 (t80)
REVERT: A 1170 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8379 (mt)
REVERT: A 1189 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.8067 (mmt-90)
REVERT: A 1240 PHE cc_start: 0.8351 (OUTLIER) cc_final: 0.7428 (p90)
REVERT: A 1327 MET cc_start: 0.3823 (OUTLIER) cc_final: 0.3554 (tpt)
  outliers start: 59
  outliers final: 34
  residues processed: 210
  average time/residue: 0.0877
  time to fit residues: 27.5679
Evaluate side-chains
  197 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 153
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 PHE
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  148 GLN
Chi-restraints excluded: chain A residue  222 THR
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  434 VAL
Chi-restraints excluded: chain A residue  437 PHE
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  462 SER
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain A residue  504 GLU
Chi-restraints excluded: chain A residue  532 GLU
Chi-restraints excluded: chain A residue  544 CYS
Chi-restraints excluded: chain A residue  627 ILE
Chi-restraints excluded: chain A residue  700 THR
Chi-restraints excluded: chain A residue  739 LEU
Chi-restraints excluded: chain A residue  751 LEU
Chi-restraints excluded: chain A residue  809 LEU
Chi-restraints excluded: chain A residue  814 THR
Chi-restraints excluded: chain A residue  829 ASP
Chi-restraints excluded: chain A residue  874 VAL
Chi-restraints excluded: chain A residue 1015 TYR
Chi-restraints excluded: chain A residue 1032 LEU
Chi-restraints excluded: chain A residue 1043 PHE
Chi-restraints excluded: chain A residue 1107 LEU
Chi-restraints excluded: chain A residue 1170 LEU
Chi-restraints excluded: chain A residue 1189 ARG
Chi-restraints excluded: chain A residue 1200 TRP
Chi-restraints excluded: chain A residue 1203 SER
Chi-restraints excluded: chain A residue 1211 LEU
Chi-restraints excluded: chain A residue 1240 PHE
Chi-restraints excluded: chain A residue 1262 ILE
Chi-restraints excluded: chain A residue 1275 TYR
Chi-restraints excluded: chain A residue 1307 VAL
Chi-restraints excluded: chain A residue 1327 MET
Chi-restraints excluded: chain A residue 1333 VAL
Chi-restraints excluded: chain A residue 1350 ILE
Chi-restraints excluded: chain A residue 1371 HIS
Chi-restraints excluded: chain A residue 1391 LEU
Chi-restraints excluded: chain A residue 1428 HIS
Chi-restraints excluded: chain A residue 1467 VAL
Chi-restraints excluded: chain A residue 1507 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 45 optimal weight:    4.9990
   chunk 115 optimal weight:    4.9990
   chunk 128 optimal weight:    8.9990
   chunk 83 optimal weight:    0.7980
   chunk 88 optimal weight:    4.9990
   chunk 58 optimal weight:    9.9990
   chunk 113 optimal weight:    0.7980
   chunk 137 optimal weight:   10.0000
   chunk 141 optimal weight:   20.0000
   chunk 59 optimal weight:    0.7980
   chunk 89 optimal weight:    0.7980
   overall best weight:    1.6382

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

Flipped N/Q/H residues before XYZ refinement:
A 648 HIS
** A1097 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1371 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.183395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.141351 restraints weight = 15359.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.138795 restraints weight = 19761.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.141056 restraints weight = 17092.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.140690 restraints weight = 10771.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.141181 restraints weight = 10349.123|
|-----------------------------------------------------------------------------|
r_work (final): 0.3655
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7728
moved from start:          0.4672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  11351  Z= 0.173
  Angle     :  0.566  11.809  15454  Z= 0.298
  Chirality :  0.041   0.189   1844
  Planarity :  0.004   0.031   1908
  Dihedral  :  8.562 133.337   1616
  Min Nonbonded Distance : 1.944

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 22.92 %
    Favored  : 71.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.02 (0.22), residues: 1429
  helix:  2.20 (0.16), residues: 955
  sheet:  1.53 (0.70), residues: 56
  loop : -0.77 (0.26), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1453 
 TYR   0.016   0.001   TYR A 101 
 PHE   0.026   0.001   PHE A 824 
 TRP   0.016   0.001   TRP A1254 
 HIS   0.007   0.001   HIS A 648 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 (11350)
  covalent geometry    : angle       0.56483 (15452)
  SS BOND              : bond        0.00734 (    1)
  SS BOND              : angle       2.90637 (    2)
  hydrogen bonds       : bond        0.06672 (  739)
  hydrogen bonds       : angle       4.15334 ( 2181)

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

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

  2858 Ramachandran restraints generated.
    1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2858 Ramachandran restraints generated.
    1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 164
  time to evaluate  : 0.413 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 TYR cc_start: 0.8908 (t80) cc_final: 0.8620 (t80)
REVERT: A  101 TYR cc_start: 0.4808 (p90) cc_final: 0.4482 (p90)
REVERT: A  148 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.7459 (tp40)
REVERT: A  430 LYS cc_start: 0.7914 (tppt) cc_final: 0.7432 (mmtp)
REVERT: A  437 PHE cc_start: 0.8788 (OUTLIER) cc_final: 0.8496 (p90)
REVERT: A  504 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6690 (mp0)
REVERT: A  988 MET cc_start: 0.7459 (tpp) cc_final: 0.7221 (mmt)
REVERT: A 1015 TYR cc_start: 0.8361 (OUTLIER) cc_final: 0.7982 (t80)
REVERT: A 1043 PHE cc_start: 0.7259 (OUTLIER) cc_final: 0.6677 (t80)
REVERT: A 1170 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8511 (mt)
REVERT: A 1240 PHE cc_start: 0.8510 (OUTLIER) cc_final: 0.7596 (p90)
REVERT: A 1254 TRP cc_start: 0.7087 (OUTLIER) cc_final: 0.6463 (t-100)
REVERT: A 1284 TRP cc_start: 0.7910 (m-10) cc_final: 0.7575 (m-10)
REVERT: A 1327 MET cc_start: 0.3787 (OUTLIER) cc_final: 0.3523 (tpt)
REVERT: A 1392 ARG cc_start: 0.6860 (tpt90) cc_final: 0.6584 (tpt90)
REVERT: A 1442 ARG cc_start: 0.8424 (ptp90) cc_final: 0.8007 (ptt180)
  outliers start: 62
  outliers final: 39
  residues processed: 205
  average time/residue: 0.0844
  time to fit residues: 26.0558
Evaluate side-chains
  203 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 155
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue   74 PHE
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  148 GLN
Chi-restraints excluded: chain A residue  222 THR
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  434 VAL
Chi-restraints excluded: chain A residue  437 PHE
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  462 SER
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain A residue  504 GLU
Chi-restraints excluded: chain A residue  532 GLU
Chi-restraints excluded: chain A residue  544 CYS
Chi-restraints excluded: chain A residue  553 THR
Chi-restraints excluded: chain A residue  627 ILE
Chi-restraints excluded: chain A residue  667 VAL
Chi-restraints excluded: chain A residue  700 THR
Chi-restraints excluded: chain A residue  739 LEU
Chi-restraints excluded: chain A residue  751 LEU
Chi-restraints excluded: chain A residue  809 LEU
Chi-restraints excluded: chain A residue  814 THR
Chi-restraints excluded: chain A residue  829 ASP
Chi-restraints excluded: chain A residue  874 VAL
Chi-restraints excluded: chain A residue 1015 TYR
Chi-restraints excluded: chain A residue 1032 LEU
Chi-restraints excluded: chain A residue 1043 PHE
Chi-restraints excluded: chain A residue 1107 LEU
Chi-restraints excluded: chain A residue 1126 ILE
Chi-restraints excluded: chain A residue 1170 LEU
Chi-restraints excluded: chain A residue 1200 TRP
Chi-restraints excluded: chain A residue 1240 PHE
Chi-restraints excluded: chain A residue 1254 TRP
Chi-restraints excluded: chain A residue 1264 THR
Chi-restraints excluded: chain A residue 1275 TYR
Chi-restraints excluded: chain A residue 1307 VAL
Chi-restraints excluded: chain A residue 1327 MET
Chi-restraints excluded: chain A residue 1333 VAL
Chi-restraints excluded: chain A residue 1350 ILE
Chi-restraints excluded: chain A residue 1371 HIS
Chi-restraints excluded: chain A residue 1391 LEU
Chi-restraints excluded: chain A residue 1428 HIS
Chi-restraints excluded: chain A residue 1431 THR
Chi-restraints excluded: chain A residue 1467 VAL
Chi-restraints excluded: chain A residue 1498 ILE
Chi-restraints excluded: chain A residue 1507 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 46 optimal weight:    9.9990
   chunk 15 optimal weight:    6.9990
   chunk 86 optimal weight:    0.9990
   chunk 4 optimal weight:    0.7980
   chunk 95 optimal weight:    0.6980
   chunk 42 optimal weight:    1.9990
   chunk 37 optimal weight:    5.9990
   chunk 10 optimal weight:    4.9990
   chunk 71 optimal weight:    6.9990
   chunk 124 optimal weight:   50.0000
   chunk 84 optimal weight:    0.7980
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
A 648 HIS
** A1097 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.183499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.140948 restraints weight = 15351.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.138554 restraints weight = 21399.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.140757 restraints weight = 17969.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.140834 restraints weight = 11091.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.141184 restraints weight = 10188.692|
|-----------------------------------------------------------------------------|
r_work (final): 0.3659
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7709
moved from start:          0.4925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  11351  Z= 0.143
  Angle     :  0.538  12.538  15454  Z= 0.282
  Chirality :  0.039   0.213   1844
  Planarity :  0.003   0.034   1908
  Dihedral  :  8.455 129.055   1616
  Min Nonbonded Distance : 1.991

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 23.34 %
    Favored  : 71.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.06 (0.22), residues: 1429
  helix:  2.26 (0.17), residues: 955
  sheet:  1.52 (0.71), residues: 56
  loop : -0.82 (0.27), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1189 
 TYR   0.018   0.001   TYR A 101 
 PHE   0.041   0.001   PHE A 824 
 TRP   0.014   0.001   TRP A1254 
 HIS   0.007   0.001   HIS A 648 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 (11350)
  covalent geometry    : angle       0.53693 (15452)
  SS BOND              : bond        0.00838 (    1)
  SS BOND              : angle       3.18996 (    2)
  hydrogen bonds       : bond        0.06172 (  739)
  hydrogen bonds       : angle       4.02705 ( 2181)

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

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

  2858 Ramachandran restraints generated.
    1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2858 Ramachandran restraints generated.
    1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 163
  time to evaluate  : 0.380 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  101 TYR cc_start: 0.4756 (p90) cc_final: 0.4502 (p90)
REVERT: A  148 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.7192 (tp40)
REVERT: A  218 LYS cc_start: 0.8211 (mtmm) cc_final: 0.7837 (mtmp)
REVERT: A  430 LYS cc_start: 0.7894 (tppt) cc_final: 0.7432 (mmtp)
REVERT: A  437 PHE cc_start: 0.8710 (OUTLIER) cc_final: 0.8475 (p90)
REVERT: A  500 LYS cc_start: 0.8342 (ttmm) cc_final: 0.8025 (ttmm)
REVERT: A  504 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6681 (mp0)
REVERT: A  532 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.6302 (tm-30)
REVERT: A  988 MET cc_start: 0.7454 (tpp) cc_final: 0.7250 (mmt)
REVERT: A 1015 TYR cc_start: 0.8370 (OUTLIER) cc_final: 0.8012 (t80)
REVERT: A 1043 PHE cc_start: 0.7214 (OUTLIER) cc_final: 0.6632 (t80)
REVERT: A 1170 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8523 (mt)
REVERT: A 1240 PHE cc_start: 0.8522 (OUTLIER) cc_final: 0.7594 (p90)
REVERT: A 1254 TRP cc_start: 0.7073 (OUTLIER) cc_final: 0.6404 (t-100)
REVERT: A 1266 ILE cc_start: 0.8100 (OUTLIER) cc_final: 0.7566 (tp)
REVERT: A 1284 TRP cc_start: 0.7895 (m-10) cc_final: 0.7629 (m-10)
REVERT: A 1327 MET cc_start: 0.3803 (OUTLIER) cc_final: 0.3590 (tpt)
REVERT: A 1442 ARG cc_start: 0.8588 (ptp90) cc_final: 0.7634 (ptt180)
  outliers start: 62
  outliers final: 39
  residues processed: 207
  average time/residue: 0.0932
  time to fit residues: 28.5762
Evaluate side-chains
  205 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 155
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 SER
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue   74 PHE
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  117 ILE
Chi-restraints excluded: chain A residue  148 GLN
Chi-restraints excluded: chain A residue  222 THR
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  425 SER
Chi-restraints excluded: chain A residue  434 VAL
Chi-restraints excluded: chain A residue  437 PHE
Chi-restraints excluded: chain A residue  462 SER
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain A residue  504 GLU
Chi-restraints excluded: chain A residue  532 GLU
Chi-restraints excluded: chain A residue  544 CYS
Chi-restraints excluded: chain A residue  553 THR
Chi-restraints excluded: chain A residue  627 ILE
Chi-restraints excluded: chain A residue  667 VAL
Chi-restraints excluded: chain A residue  700 THR
Chi-restraints excluded: chain A residue  751 LEU
Chi-restraints excluded: chain A residue  809 LEU
Chi-restraints excluded: chain A residue  814 THR
Chi-restraints excluded: chain A residue  829 ASP
Chi-restraints excluded: chain A residue  874 VAL
Chi-restraints excluded: chain A residue 1015 TYR
Chi-restraints excluded: chain A residue 1032 LEU
Chi-restraints excluded: chain A residue 1043 PHE
Chi-restraints excluded: chain A residue 1107 LEU
Chi-restraints excluded: chain A residue 1126 ILE
Chi-restraints excluded: chain A residue 1170 LEU
Chi-restraints excluded: chain A residue 1200 TRP
Chi-restraints excluded: chain A residue 1240 PHE
Chi-restraints excluded: chain A residue 1254 TRP
Chi-restraints excluded: chain A residue 1264 THR
Chi-restraints excluded: chain A residue 1266 ILE
Chi-restraints excluded: chain A residue 1275 TYR
Chi-restraints excluded: chain A residue 1307 VAL
Chi-restraints excluded: chain A residue 1327 MET
Chi-restraints excluded: chain A residue 1333 VAL
Chi-restraints excluded: chain A residue 1350 ILE
Chi-restraints excluded: chain A residue 1371 HIS
Chi-restraints excluded: chain A residue 1391 LEU
Chi-restraints excluded: chain A residue 1428 HIS
Chi-restraints excluded: chain A residue 1431 THR
Chi-restraints excluded: chain A residue 1467 VAL
Chi-restraints excluded: chain A residue 1507 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 39 optimal weight:    2.9990
   chunk 138 optimal weight:    8.9990
   chunk 59 optimal weight:    3.9990
   chunk 62 optimal weight:    7.9990
   chunk 61 optimal weight:    4.9990
   chunk 97 optimal weight:    3.9990
   chunk 113 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9990
   chunk 139 optimal weight:    5.9990
   chunk 66 optimal weight:    1.9990
   chunk 110 optimal weight:    0.9990
   overall best weight:    1.5588

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

Flipped N/Q/H residues before XYZ refinement:
A 648 HIS
** A1097 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1428 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.181474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.137241 restraints weight = 15305.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.134239 restraints weight = 17967.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.136198 restraints weight = 14083.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.136562 restraints weight = 10382.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.136584 restraints weight = 9425.107|
|-----------------------------------------------------------------------------|
r_work (final): 0.3617
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
moved from start:          0.5132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  11351  Z= 0.167
  Angle     :  0.561  12.829  15454  Z= 0.295
  Chirality :  0.040   0.175   1844
  Planarity :  0.004   0.033   1908
  Dihedral  :  8.320 126.752   1614
  Min Nonbonded Distance : 1.963

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 23.85 %
    Favored  : 70.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.85 (0.22), residues: 1429
  helix:  2.12 (0.17), residues: 957
  sheet:  1.53 (0.72), residues: 56
  loop : -1.00 (0.26), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A1392 
 TYR   0.014   0.001   TYR A 101 
 PHE   0.021   0.001   PHE A 548 
 TRP   0.016   0.001   TRP A  41 
 HIS   0.008   0.001   HIS A 648 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 (11350)
  covalent geometry    : angle       0.56040 (15452)
  SS BOND              : bond        0.00721 (    1)
  SS BOND              : angle       2.84135 (    2)
  hydrogen bonds       : bond        0.06441 (  739)
  hydrogen bonds       : angle       4.07248 ( 2181)

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

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

  2858 Ramachandran restraints generated.
    1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2858 Ramachandran restraints generated.
    1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 159
  time to evaluate  : 0.370 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  148 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.7233 (tp40)
REVERT: A  430 LYS cc_start: 0.7943 (tppt) cc_final: 0.7426 (mmtp)
REVERT: A  437 PHE cc_start: 0.8859 (OUTLIER) cc_final: 0.8426 (p90)
REVERT: A  500 LYS cc_start: 0.8397 (ttmm) cc_final: 0.8053 (ttmm)
REVERT: A  504 GLU cc_start: 0.7102 (OUTLIER) cc_final: 0.6773 (mp0)
REVERT: A  532 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.6368 (tm-30)
REVERT: A  988 MET cc_start: 0.7364 (tpp) cc_final: 0.7110 (mmt)
REVERT: A 1015 TYR cc_start: 0.8383 (OUTLIER) cc_final: 0.7947 (t80)
REVERT: A 1043 PHE cc_start: 0.7287 (OUTLIER) cc_final: 0.6694 (t80)
REVERT: A 1240 PHE cc_start: 0.8624 (OUTLIER) cc_final: 0.7780 (p90)
REVERT: A 1254 TRP cc_start: 0.7213 (OUTLIER) cc_final: 0.6523 (t-100)
REVERT: A 1266 ILE cc_start: 0.8209 (OUTLIER) cc_final: 0.7787 (tp)
REVERT: A 1284 TRP cc_start: 0.7972 (m-10) cc_final: 0.7712 (m-10)
REVERT: A 1327 MET cc_start: 0.3967 (OUTLIER) cc_final: 0.3707 (tpt)
REVERT: A 1442 ARG cc_start: 0.8349 (ptp90) cc_final: 0.7857 (ptt180)
  outliers start: 62
  outliers final: 43
  residues processed: 206
  average time/residue: 0.0868
  time to fit residues: 27.2169
Evaluate side-chains
  206 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 153
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 SER
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue   74 PHE
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  148 GLN
Chi-restraints excluded: chain A residue  185 SER
Chi-restraints excluded: chain A residue  222 THR
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  394 THR
Chi-restraints excluded: chain A residue  425 SER
Chi-restraints excluded: chain A residue  434 VAL
Chi-restraints excluded: chain A residue  437 PHE
Chi-restraints excluded: chain A residue  462 SER
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  467 VAL
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain A residue  504 GLU
Chi-restraints excluded: chain A residue  532 GLU
Chi-restraints excluded: chain A residue  544 CYS
Chi-restraints excluded: chain A residue  553 THR
Chi-restraints excluded: chain A residue  627 ILE
Chi-restraints excluded: chain A residue  661 ILE
Chi-restraints excluded: chain A residue  751 LEU
Chi-restraints excluded: chain A residue  754 ILE
Chi-restraints excluded: chain A residue  809 LEU
Chi-restraints excluded: chain A residue  814 THR
Chi-restraints excluded: chain A residue  829 ASP
Chi-restraints excluded: chain A residue  874 VAL
Chi-restraints excluded: chain A residue  974 ILE
Chi-restraints excluded: chain A residue 1015 TYR
Chi-restraints excluded: chain A residue 1032 LEU
Chi-restraints excluded: chain A residue 1043 PHE
Chi-restraints excluded: chain A residue 1107 LEU
Chi-restraints excluded: chain A residue 1126 ILE
Chi-restraints excluded: chain A residue 1200 TRP
Chi-restraints excluded: chain A residue 1240 PHE
Chi-restraints excluded: chain A residue 1242 LEU
Chi-restraints excluded: chain A residue 1254 TRP
Chi-restraints excluded: chain A residue 1264 THR
Chi-restraints excluded: chain A residue 1266 ILE
Chi-restraints excluded: chain A residue 1275 TYR
Chi-restraints excluded: chain A residue 1307 VAL
Chi-restraints excluded: chain A residue 1327 MET
Chi-restraints excluded: chain A residue 1333 VAL
Chi-restraints excluded: chain A residue 1350 ILE
Chi-restraints excluded: chain A residue 1359 ILE
Chi-restraints excluded: chain A residue 1371 HIS
Chi-restraints excluded: chain A residue 1431 THR
Chi-restraints excluded: chain A residue 1467 VAL
Chi-restraints excluded: chain A residue 1507 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 70 optimal weight:    0.3980
   chunk 49 optimal weight:    0.9990
   chunk 103 optimal weight:    0.7980
   chunk 46 optimal weight:    7.9990
   chunk 114 optimal weight:    2.9990
   chunk 86 optimal weight:    8.9990
   chunk 104 optimal weight:    0.0050
   chunk 138 optimal weight:    8.9990
   chunk 140 optimal weight:   30.0000
   chunk 2 optimal weight:    3.9990
   chunk 130 optimal weight:    9.9990
   overall best weight:    1.0398

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

Flipped N/Q/H residues before XYZ refinement:
A 638 GLN
A 648 HIS
** A 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1019 GLN
** A1097 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1428 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.183293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.139433 restraints weight = 15406.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.138023 restraints weight = 17021.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.139134 restraints weight = 14377.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.139775 restraints weight = 10173.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.139700 restraints weight = 9195.548|
|-----------------------------------------------------------------------------|
r_work (final): 0.3641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7749
moved from start:          0.5344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  11351  Z= 0.143
  Angle     :  0.545  13.046  15454  Z= 0.282
  Chirality :  0.040   0.232   1844
  Planarity :  0.003   0.036   1908
  Dihedral  :  8.242 124.332   1614
  Min Nonbonded Distance : 1.972

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  5.77 %
    Allowed  : 22.41 %
    Favored  : 71.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.91 (0.22), residues: 1429
  helix:  2.18 (0.17), residues: 958
  sheet:  1.45 (0.71), residues: 56
  loop : -0.99 (0.27), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG A1392 
 TYR   0.009   0.001   TYR A 782 
 PHE   0.021   0.001   PHE A 548 
 TRP   0.015   0.001   TRP A1254 
 HIS   0.008   0.001   HIS A 648 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 (11350)
  covalent geometry    : angle       0.54382 (15452)
  SS BOND              : bond        0.00524 (    1)
  SS BOND              : angle       2.97749 (    2)
  hydrogen bonds       : bond        0.06057 (  739)
  hydrogen bonds       : angle       3.96926 ( 2181)

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

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

  2858 Ramachandran restraints generated.
    1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2858 Ramachandran restraints generated.
    1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 165
  time to evaluate  : 0.379 
Fit side-chains
   revert: symmetry clash
REVERT: A    5 PHE cc_start: 0.7426 (t80) cc_final: 0.7028 (t80)
REVERT: A  148 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.7121 (tp40)
REVERT: A  430 LYS cc_start: 0.7896 (tppt) cc_final: 0.7485 (mmtp)
REVERT: A  437 PHE cc_start: 0.8810 (OUTLIER) cc_final: 0.8556 (p90)
REVERT: A  500 LYS cc_start: 0.8368 (ttmm) cc_final: 0.8024 (ttmm)
REVERT: A  504 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6757 (mp0)
REVERT: A  532 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.6395 (tm-30)
REVERT: A  634 ASP cc_start: 0.7356 (OUTLIER) cc_final: 0.7129 (p0)
REVERT: A  665 GLN cc_start: 0.7216 (OUTLIER) cc_final: 0.6884 (mp10)
REVERT: A  765 GLN cc_start: 0.7585 (mt0) cc_final: 0.6994 (mt0)
REVERT: A  988 MET cc_start: 0.7396 (tpp) cc_final: 0.7173 (mmt)
REVERT: A 1015 TYR cc_start: 0.8457 (OUTLIER) cc_final: 0.8112 (t80)
REVERT: A 1043 PHE cc_start: 0.7278 (OUTLIER) cc_final: 0.6685 (t80)
REVERT: A 1240 PHE cc_start: 0.8549 (OUTLIER) cc_final: 0.7692 (p90)
REVERT: A 1254 TRP cc_start: 0.7120 (OUTLIER) cc_final: 0.6412 (t-100)
REVERT: A 1266 ILE cc_start: 0.8124 (OUTLIER) cc_final: 0.7613 (tp)
REVERT: A 1327 MET cc_start: 0.3857 (OUTLIER) cc_final: 0.3641 (tpt)
REVERT: A 1442 ARG cc_start: 0.8219 (ptp90) cc_final: 0.7825 (ptt180)
  outliers start: 68
  outliers final: 47
  residues processed: 214
  average time/residue: 0.0835
  time to fit residues: 27.2246
Evaluate side-chains
  220 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 161
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 CYS
Chi-restraints excluded: chain A residue   18 SER
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue   74 PHE
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  148 GLN
Chi-restraints excluded: chain A residue  185 SER
Chi-restraints excluded: chain A residue  222 THR
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  385 CYS
Chi-restraints excluded: chain A residue  394 THR
Chi-restraints excluded: chain A residue  425 SER
Chi-restraints excluded: chain A residue  434 VAL
Chi-restraints excluded: chain A residue  437 PHE
Chi-restraints excluded: chain A residue  462 SER
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  467 VAL
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain A residue  504 GLU
Chi-restraints excluded: chain A residue  532 GLU
Chi-restraints excluded: chain A residue  544 CYS
Chi-restraints excluded: chain A residue  553 THR
Chi-restraints excluded: chain A residue  627 ILE
Chi-restraints excluded: chain A residue  634 ASP
Chi-restraints excluded: chain A residue  661 ILE
Chi-restraints excluded: chain A residue  665 GLN
Chi-restraints excluded: chain A residue  669 VAL
Chi-restraints excluded: chain A residue  700 THR
Chi-restraints excluded: chain A residue  746 LEU
Chi-restraints excluded: chain A residue  751 LEU
Chi-restraints excluded: chain A residue  754 ILE
Chi-restraints excluded: chain A residue  814 THR
Chi-restraints excluded: chain A residue  819 THR
Chi-restraints excluded: chain A residue  829 ASP
Chi-restraints excluded: chain A residue  874 VAL
Chi-restraints excluded: chain A residue  974 ILE
Chi-restraints excluded: chain A residue 1015 TYR
Chi-restraints excluded: chain A residue 1032 LEU
Chi-restraints excluded: chain A residue 1043 PHE
Chi-restraints excluded: chain A residue 1084 PHE
Chi-restraints excluded: chain A residue 1107 LEU
Chi-restraints excluded: chain A residue 1126 ILE
Chi-restraints excluded: chain A residue 1200 TRP
Chi-restraints excluded: chain A residue 1240 PHE
Chi-restraints excluded: chain A residue 1242 LEU
Chi-restraints excluded: chain A residue 1254 TRP
Chi-restraints excluded: chain A residue 1264 THR
Chi-restraints excluded: chain A residue 1266 ILE
Chi-restraints excluded: chain A residue 1275 TYR
Chi-restraints excluded: chain A residue 1307 VAL
Chi-restraints excluded: chain A residue 1327 MET
Chi-restraints excluded: chain A residue 1333 VAL
Chi-restraints excluded: chain A residue 1350 ILE
Chi-restraints excluded: chain A residue 1359 ILE
Chi-restraints excluded: chain A residue 1371 HIS
Chi-restraints excluded: chain A residue 1467 VAL
Chi-restraints excluded: chain A residue 1507 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 38 optimal weight:    0.7980
   chunk 85 optimal weight:    0.9980
   chunk 120 optimal weight:   20.0000
   chunk 95 optimal weight:    0.9990
   chunk 25 optimal weight:    7.9990
   chunk 91 optimal weight:    2.9990
   chunk 18 optimal weight:    3.9990
   chunk 55 optimal weight:    0.9980
   chunk 89 optimal weight:    0.6980
   chunk 86 optimal weight:    0.5980
   chunk 61 optimal weight:    5.9990
   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 648 HIS
** A 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1097 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.184377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.142894 restraints weight = 15196.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.141007 restraints weight = 21228.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.142804 restraints weight = 16211.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.142957 restraints weight = 10508.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.143041 restraints weight = 10942.425|
|-----------------------------------------------------------------------------|
r_work (final): 0.3689
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7694
moved from start:          0.5441

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11351  Z= 0.134
  Angle     :  0.539  12.911  15454  Z= 0.278
  Chirality :  0.039   0.235   1844
  Planarity :  0.003   0.036   1908
  Dihedral  :  8.149 122.116   1614
  Min Nonbonded Distance : 2.040

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  5.18 %
    Allowed  : 23.43 %
    Favored  : 71.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.94 (0.22), residues: 1429
  helix:  2.22 (0.17), residues: 958
  sheet:  1.42 (0.72), residues: 55
  loop : -1.03 (0.26), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A1392 
 TYR   0.008   0.001   TYR A 782 
 PHE   0.022   0.001   PHE A 548 
 TRP   0.015   0.001   TRP A1254 
 HIS   0.009   0.001   HIS A 648 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 (11350)
  covalent geometry    : angle       0.53844 (15452)
  SS BOND              : bond        0.00665 (    1)
  SS BOND              : angle       2.63881 (    2)
  hydrogen bonds       : bond        0.05803 (  739)
  hydrogen bonds       : angle       3.91816 ( 2181)

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

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

  2858 Ramachandran restraints generated.
    1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2858 Ramachandran restraints generated.
    1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 165
  time to evaluate  : 0.428 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 PHE cc_start: 0.7233 (t80) cc_final: 0.6904 (t80)
REVERT: A  148 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.7142 (tp40)
REVERT: A  500 LYS cc_start: 0.8336 (ttmm) cc_final: 0.8036 (ttmm)
REVERT: A  504 GLU cc_start: 0.6933 (OUTLIER) cc_final: 0.6615 (mp0)
REVERT: A  532 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.6373 (tm-30)
REVERT: A 1015 TYR cc_start: 0.8404 (OUTLIER) cc_final: 0.8032 (t80)
REVERT: A 1043 PHE cc_start: 0.7274 (OUTLIER) cc_final: 0.6691 (t80)
REVERT: A 1240 PHE cc_start: 0.8595 (OUTLIER) cc_final: 0.7752 (p90)
REVERT: A 1254 TRP cc_start: 0.7020 (OUTLIER) cc_final: 0.6415 (t-100)
REVERT: A 1266 ILE cc_start: 0.8076 (OUTLIER) cc_final: 0.7637 (tp)
REVERT: A 1442 ARG cc_start: 0.8180 (ptp90) cc_final: 0.7815 (ptt180)
  outliers start: 61
  outliers final: 46
  residues processed: 207
  average time/residue: 0.0828
  time to fit residues: 26.5407
Evaluate side-chains
  211 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 157
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 CYS
Chi-restraints excluded: chain A residue   18 SER
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue   74 PHE
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue  101 TYR
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  148 GLN
Chi-restraints excluded: chain A residue  185 SER
Chi-restraints excluded: chain A residue  222 THR
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  385 CYS
Chi-restraints excluded: chain A residue  394 THR
Chi-restraints excluded: chain A residue  434 VAL
Chi-restraints excluded: chain A residue  437 PHE
Chi-restraints excluded: chain A residue  462 SER
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain A residue  504 GLU
Chi-restraints excluded: chain A residue  532 GLU
Chi-restraints excluded: chain A residue  544 CYS
Chi-restraints excluded: chain A residue  553 THR
Chi-restraints excluded: chain A residue  627 ILE
Chi-restraints excluded: chain A residue  700 THR
Chi-restraints excluded: chain A residue  746 LEU
Chi-restraints excluded: chain A residue  751 LEU
Chi-restraints excluded: chain A residue  754 ILE
Chi-restraints excluded: chain A residue  814 THR
Chi-restraints excluded: chain A residue  829 ASP
Chi-restraints excluded: chain A residue  874 VAL
Chi-restraints excluded: chain A residue  974 ILE
Chi-restraints excluded: chain A residue 1015 TYR
Chi-restraints excluded: chain A residue 1032 LEU
Chi-restraints excluded: chain A residue 1043 PHE
Chi-restraints excluded: chain A residue 1084 PHE
Chi-restraints excluded: chain A residue 1107 LEU
Chi-restraints excluded: chain A residue 1126 ILE
Chi-restraints excluded: chain A residue 1200 TRP
Chi-restraints excluded: chain A residue 1240 PHE
Chi-restraints excluded: chain A residue 1242 LEU
Chi-restraints excluded: chain A residue 1254 TRP
Chi-restraints excluded: chain A residue 1264 THR
Chi-restraints excluded: chain A residue 1266 ILE
Chi-restraints excluded: chain A residue 1275 TYR
Chi-restraints excluded: chain A residue 1307 VAL
Chi-restraints excluded: chain A residue 1333 VAL
Chi-restraints excluded: chain A residue 1350 ILE
Chi-restraints excluded: chain A residue 1371 HIS
Chi-restraints excluded: chain A residue 1428 HIS
Chi-restraints excluded: chain A residue 1467 VAL
Chi-restraints excluded: chain A residue 1507 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 73 optimal weight:    4.9990
   chunk 30 optimal weight:    0.9980
   chunk 46 optimal weight:    6.9990
   chunk 131 optimal weight:   10.0000
   chunk 100 optimal weight:    0.6980
   chunk 115 optimal weight:    0.9990
   chunk 98 optimal weight:    6.9990
   chunk 21 optimal weight:    1.9990
   chunk 132 optimal weight:    6.9990
   chunk 81 optimal weight:   30.0000
   chunk 11 optimal weight:    0.9990
   overall best weight:    1.1386

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

Flipped N/Q/H residues before XYZ refinement:
A 648 HIS
** A 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1097 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.183667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.139754 restraints weight = 15410.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.137632 restraints weight = 17519.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.139082 restraints weight = 13998.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.139619 restraints weight = 9837.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.139627 restraints weight = 9001.769|
|-----------------------------------------------------------------------------|
r_work (final): 0.3645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7751
moved from start:          0.5516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  11351  Z= 0.145
  Angle     :  0.569  12.530  15454  Z= 0.289
  Chirality :  0.040   0.223   1844
  Planarity :  0.004   0.060   1908
  Dihedral  :  8.121 120.098   1614
  Min Nonbonded Distance : 2.000

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  4.67 %
    Allowed  : 23.94 %
    Favored  : 71.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.88 (0.22), residues: 1429
  helix:  2.19 (0.17), residues: 957
  sheet:  1.38 (0.73), residues: 55
  loop : -1.09 (0.26), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 815 
 TYR   0.008   0.001   TYR A1141 
 PHE   0.022   0.001   PHE A 548 
 TRP   0.015   0.001   TRP A1254 
 HIS   0.008   0.001   HIS A 648 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 (11350)
  covalent geometry    : angle       0.56829 (15452)
  SS BOND              : bond        0.00585 (    1)
  SS BOND              : angle       2.56343 (    2)
  hydrogen bonds       : bond        0.05904 (  739)
  hydrogen bonds       : angle       3.95109 ( 2181)

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

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

  2858 Ramachandran restraints generated.
    1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2858 Ramachandran restraints generated.
    1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 161
  time to evaluate  : 0.488 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 PHE cc_start: 0.7253 (t80) cc_final: 0.6958 (t80)
REVERT: A  148 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.7162 (tp40)
REVERT: A  333 ASP cc_start: 0.8464 (t70) cc_final: 0.7761 (t0)
REVERT: A  430 LYS cc_start: 0.7911 (tppt) cc_final: 0.7449 (mmtp)
REVERT: A  437 PHE cc_start: 0.8894 (OUTLIER) cc_final: 0.8607 (p90)
REVERT: A  500 LYS cc_start: 0.8423 (ttmm) cc_final: 0.8184 (ttmm)
REVERT: A  504 GLU cc_start: 0.7009 (OUTLIER) cc_final: 0.6717 (mp0)
REVERT: A 1015 TYR cc_start: 0.8353 (OUTLIER) cc_final: 0.8001 (t80)
REVERT: A 1043 PHE cc_start: 0.7271 (OUTLIER) cc_final: 0.6692 (t80)
REVERT: A 1240 PHE cc_start: 0.8569 (OUTLIER) cc_final: 0.7726 (p90)
REVERT: A 1254 TRP cc_start: 0.7050 (OUTLIER) cc_final: 0.6418 (t-100)
REVERT: A 1266 ILE cc_start: 0.8099 (OUTLIER) cc_final: 0.7634 (tp)
REVERT: A 1327 MET cc_start: 0.2741 (tpt) cc_final: 0.2420 (tpt)
REVERT: A 1442 ARG cc_start: 0.8232 (ptp90) cc_final: 0.7878 (ptt180)
  outliers start: 55
  outliers final: 45
  residues processed: 200
  average time/residue: 0.0823
  time to fit residues: 25.0715
Evaluate side-chains
  211 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 158
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 CYS
Chi-restraints excluded: chain A residue   18 SER
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue   74 PHE
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  117 ILE
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  148 GLN
Chi-restraints excluded: chain A residue  185 SER
Chi-restraints excluded: chain A residue  222 THR
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  385 CYS
Chi-restraints excluded: chain A residue  394 THR
Chi-restraints excluded: chain A residue  425 SER
Chi-restraints excluded: chain A residue  434 VAL
Chi-restraints excluded: chain A residue  437 PHE
Chi-restraints excluded: chain A residue  462 SER
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain A residue  504 GLU
Chi-restraints excluded: chain A residue  544 CYS
Chi-restraints excluded: chain A residue  553 THR
Chi-restraints excluded: chain A residue  627 ILE
Chi-restraints excluded: chain A residue  700 THR
Chi-restraints excluded: chain A residue  751 LEU
Chi-restraints excluded: chain A residue  754 ILE
Chi-restraints excluded: chain A residue  788 LEU
Chi-restraints excluded: chain A residue  814 THR
Chi-restraints excluded: chain A residue  829 ASP
Chi-restraints excluded: chain A residue  874 VAL
Chi-restraints excluded: chain A residue  974 ILE
Chi-restraints excluded: chain A residue 1015 TYR
Chi-restraints excluded: chain A residue 1032 LEU
Chi-restraints excluded: chain A residue 1043 PHE
Chi-restraints excluded: chain A residue 1084 PHE
Chi-restraints excluded: chain A residue 1107 LEU
Chi-restraints excluded: chain A residue 1126 ILE
Chi-restraints excluded: chain A residue 1200 TRP
Chi-restraints excluded: chain A residue 1240 PHE
Chi-restraints excluded: chain A residue 1242 LEU
Chi-restraints excluded: chain A residue 1254 TRP
Chi-restraints excluded: chain A residue 1264 THR
Chi-restraints excluded: chain A residue 1266 ILE
Chi-restraints excluded: chain A residue 1275 TYR
Chi-restraints excluded: chain A residue 1307 VAL
Chi-restraints excluded: chain A residue 1333 VAL
Chi-restraints excluded: chain A residue 1350 ILE
Chi-restraints excluded: chain A residue 1371 HIS
Chi-restraints excluded: chain A residue 1428 HIS
Chi-restraints excluded: chain A residue 1467 VAL
Chi-restraints excluded: chain A residue 1507 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 87 optimal weight:    8.9990
   chunk 66 optimal weight:    0.6980
   chunk 59 optimal weight:    5.9990
   chunk 21 optimal weight:    2.9990
   chunk 80 optimal weight:    1.9990
   chunk 132 optimal weight:    4.9990
   chunk 130 optimal weight:    9.9990
   chunk 19 optimal weight:    0.0670
   chunk 118 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 134 optimal weight:    5.9990
   overall best weight:    1.7524

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

Flipped N/Q/H residues before XYZ refinement:
A 648 HIS
** A 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1097 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.181110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.137931 restraints weight = 15371.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.135364 restraints weight = 21323.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.136923 restraints weight = 18645.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.137227 restraints weight = 12416.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.137543 restraints weight = 10755.737|
|-----------------------------------------------------------------------------|
r_work (final): 0.3618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7781
moved from start:          0.5557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  11351  Z= 0.176
  Angle     :  0.593  13.056  15454  Z= 0.304
  Chirality :  0.041   0.211   1844
  Planarity :  0.004   0.053   1908
  Dihedral  :  7.969 117.914   1611
  Min Nonbonded Distance : 1.971

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  4.92 %
    Allowed  : 23.94 %
    Favored  : 71.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.75 (0.22), residues: 1429
  helix:  2.07 (0.17), residues: 958
  sheet:  1.16 (0.72), residues: 55
  loop : -1.04 (0.27), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG A 815 
 TYR   0.010   0.001   TYR A 703 
 PHE   0.022   0.001   PHE A 548 
 TRP   0.016   0.001   TRP A1254 
 HIS   0.008   0.001   HIS A 648 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 (11350)
  covalent geometry    : angle       0.59251 (15452)
  SS BOND              : bond        0.00687 (    1)
  SS BOND              : angle       2.68090 (    2)
  hydrogen bonds       : bond        0.06393 (  739)
  hydrogen bonds       : angle       4.06167 ( 2181)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1649.17 seconds
wall clock time: 29 minutes 19.47 seconds (1759.47 seconds total)