Starting phenix.real_space_refine
on Sun May  3 06:57:12 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jn2_61619/05_2026/9jn2_61619.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jn2_61619/05_2026/9jn2_61619.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.44
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jn2_61619/05_2026/9jn2_61619.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jn2_61619/05_2026/9jn2_61619.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jn2_61619/05_2026/9jn2_61619.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jn2_61619/05_2026/9jn2_61619.map"
  }
  resolution = 3.44
  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=   0.033
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       3      5.49       5
     Mg      2      5.21       5
     S      57      5.16       5
     C    7229      2.51       5
     N    1848      2.21       5
     O    2017      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 84 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: 11156
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 11123
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1400, 11123
          Classifications: {'peptide': 1400}
          Link IDs: {'PTRANS': 43, 'TRANS': 1356}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 33
          Unusual residues: {' MG': 2, 'ANP': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 2.94, per 1000 atoms: 0.26
  Number of scatterers: 11156
  At special positions: 0
  Unit cell: (113.42, 101.65, 154.08, 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      57     16.00
     P       3     15.00
     Mg      2     11.99
     O    2017      8.00
     N    1848      7.00
     C    7229      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=2.02

  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: 0.97
  Conformation dependent library (CDL) restraints added in 553.1 milliseconds
  

  2784 Ramachandran restraints generated.
    1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2650

  Finding SS restraints...
    Secondary structure from input PDB file:
      61 helices and 6 sheets defined
      73.9% alpha, 6.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.50
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 7
    Processing helix  chain 'A' and resid 12 through 18
      removed outlier: 3.961A  pdb=" N   LEU A  16 " --> pdb=" O   ASN A  12 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 24 through 55
      removed outlier: 3.917A  pdb=" N   LEU A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
      removed outlier: 4.290A  pdb=" N   VAL A  33 " --> pdb=" O   GLN A  29 " (cutoff:3.500A)
      Proline residue:  A  36  - end of helix
      Proline residue:  A  45  - end of helix
      removed outlier: 3.511A  pdb=" N   VAL A  51 " --> pdb=" O   GLN A  47 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 62 through 89
    Processing helix  chain 'A' and resid 97 through 121
      removed outlier: 3.765A  pdb=" N   TYR A 101 " --> pdb=" O   PRO A  97 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   ASN A 103 " --> pdb=" O   VAL A  99 " (cutoff:3.500A)
      Proline residue:  A 104  - end of helix
    Processing helix  chain 'A' and resid 129 through 133
    Processing helix  chain 'A' and resid 134 through 157
      removed outlier: 4.434A  pdb=" N   PHE A 145 " --> pdb=" O   LEU A 141 " (cutoff:3.500A)
      removed outlier: 4.504A  pdb=" N   GLN A 146 " --> pdb=" O   CYS A 142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 161 through 184
      removed outlier: 3.622A  pdb=" N   LEU A 167 " --> pdb=" O   ALA A 163 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   PHE A 184 " --> pdb=" O   ILE A 180 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 193 through 198
      removed outlier: 4.434A  pdb=" N   ILE A 197 " --> pdb=" O   ASN A 193 " (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 222 through 226
    Processing helix  chain 'A' and resid 230 through 233
    Processing helix  chain 'A' and resid 234 through 267
      removed outlier: 3.899A  pdb=" N   HIS A 245 " --> pdb=" O   LYS A 241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 308 through 318
      removed outlier: 3.748A  pdb=" N   LYS A 312 " --> pdb=" O   SER A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 318 through 337
      removed outlier: 3.751A  pdb=" N   LEU A 322 " --> pdb=" O   PHE A 318 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   PHE A 337 " --> pdb=" O   ASP A 333 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 349
      removed outlier: 3.775A  pdb=" N   GLN A 341 " --> pdb=" O   PHE A 337 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   LEU A 345 " --> pdb=" O   GLN A 341 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 356 through 405
      removed outlier: 4.005A  pdb=" N   GLY A 360 " --> pdb=" O   TYR A 356 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   PHE A 368 " --> pdb=" O   ALA A 364 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   LEU A 405 " --> pdb=" O   TYR A 401 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 408 through 415
      removed outlier: 3.785A  pdb=" N   GLU A 414 " --> pdb=" O   LEU A 410 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   TYR A 415 " --> pdb=" O   ALA A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 426
      removed outlier: 4.202A  pdb=" N   MET A 424 " --> pdb=" O   THR A 420 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 426 through 437
    Processing helix  chain 'A' and resid 439 through 460
      removed outlier: 4.085A  pdb=" N   VAL A 445 " --> pdb=" O   LEU A 441 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   GLU A 458 " --> pdb=" O   PHE A 454 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 462 through 508
      removed outlier: 4.045A  pdb=" N   GLY A 466 " --> pdb=" O   SER A 462 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   MET A 470 " --> pdb=" O   GLY A 466 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   ILE A 474 " --> pdb=" O   MET A 470 " (cutoff:3.500A)
      Proline residue:  A 475  - end of helix
      removed outlier: 3.591A  pdb=" N   LYS A 493 " --> pdb=" O   VAL A 489 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   ASN A 494 " --> pdb=" O   LYS A 490 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 508 through 515
    Processing helix  chain 'A' and resid 517 through 569
      removed outlier: 3.593A  pdb=" N   VAL A 525 " --> pdb=" O   PHE A 521 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   LEU A 528 " --> pdb=" O   GLN A 524 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   LYS A 531 " --> pdb=" O   ASN A 527 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   PHE A 550 " --> pdb=" O   VAL A 546 " (cutoff:3.500A)
      Proline residue:  A 554  - end of helix
      removed outlier: 4.004A  pdb=" N   ASP A 569 " --> pdb=" O   TYR A 565 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 575 through 618
      removed outlier: 4.185A  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: 4.355A  pdb=" N   LEU A 604 " --> pdb=" O   ILE A 600 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 676 through 686
      removed outlier: 3.658A  pdb=" N   ILE A 681 " --> pdb=" O   LYS A 677 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 714 through 721
    Processing helix  chain 'A' and resid 726 through 737
    Processing helix  chain 'A' and resid 738 through 746
      removed outlier: 4.585A  pdb=" N   ASP A 742 " --> pdb=" O   ALA A 738 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 748 through 752
      removed outlier: 3.948A  pdb=" N   LEU A 751 " --> pdb=" O   GLY A 748 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 762 through 778
      removed outlier: 3.553A  pdb=" N   GLN A 767 " --> pdb=" O   GLY A 763 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ALA A 774 " --> pdb=" O   SER A 770 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 792 through 803
    Processing helix  chain 'A' and resid 844 through 852
      removed outlier: 3.584A  pdb=" N   LYS A 852 " --> pdb=" O   LEU A 848 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 854 through 861
    Processing helix  chain 'A' and resid 963 through 975
      removed outlier: 3.899A  pdb=" N   TYR A 970 " --> pdb=" O   ILE A 966 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 975 through 1005
    Processing helix  chain 'A' and resid 1005 through 1011
      removed outlier: 4.133A  pdb=" N   ILE A1009 " --> pdb=" O   SER A1005 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1016 through 1066
      removed outlier: 4.177A  pdb=" N   PHE A1047 " --> pdb=" O   PHE A1043 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1068 through 1075
    Processing helix  chain 'A' and resid 1076 through 1093
      removed outlier: 3.774A  pdb=" N   PHE A1084 " --> pdb=" O   ILE A1080 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   ILE A1088 " --> pdb=" O   PHE A1084 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   SER A1089 " --> pdb=" O   ALA A1085 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1093 through 1120
      removed outlier: 3.990A  pdb=" N   GLN A1097 " --> pdb=" O   ASP A1093 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   SER A1098 " --> pdb=" O   THR A1094 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   ILE A1103 " --> pdb=" O   LEU A1099 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   THR A1104 " --> pdb=" O   ARG A1100 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1122 through 1169
      removed outlier: 4.298A  pdb=" N   ILE A1126 " --> pdb=" O   VAL A1122 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   ILE A1128 " --> pdb=" O   THR A1124 " (cutoff:3.500A)
      Proline residue:  A1129  - end of helix
      removed outlier: 3.643A  pdb=" N   GLN A1147 " --> pdb=" O   SER A1143 " (cutoff:3.500A)
      removed outlier: 3.815A  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
      removed outlier: 3.534A  pdb=" N   ARG A1174 " --> pdb=" O   LEU A1170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1178 through 1229
      removed outlier: 3.519A  pdb=" N   ASN A1193 " --> pdb=" O   ARG A1189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1234 through 1246
      removed outlier: 3.516A  pdb=" N   VAL A1241 " --> pdb=" O   THR A1237 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   ASN A1244 " --> pdb=" O   PHE A1240 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1247 through 1266
      removed outlier: 3.638A  pdb=" N   THR A1251 " --> pdb=" O   ASN A1247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1266 through 1277
      removed outlier: 3.610A  pdb=" N   GLU A1270 " --> pdb=" O   ILE A1266 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1339 through 1348
    Processing helix  chain 'A' and resid 1370 through 1375
    Processing helix  chain 'A' and resid 1391 through 1396
    Processing helix  chain 'A' and resid 1402 through 1413
    Processing helix  chain 'A' and resid 1415 through 1422
    Processing helix  chain 'A' and resid 1424 through 1427
    Processing helix  chain 'A' and resid 1431 through 1435
      removed outlier: 3.600A  pdb=" N   GLY A1435 " --> pdb=" O   GLU A1432 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1438 through 1454
    Processing helix  chain 'A' and resid 1462 through 1467
    Processing helix  chain 'A' and resid 1468 through 1483
    Processing helix  chain 'A' and resid 1494 through 1501
      removed outlier: 3.847A  pdb=" N   ILE A1498 " --> pdb=" O   ARG A1494 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1517 through 1524
      removed outlier: 3.567A  pdb=" N   LEU A1521 " --> pdb=" O   SER A1517 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1526 through 1536
    Processing sheet with id=AA1, first strand: chain 'A' and resid 627 through 629
      removed outlier: 5.986A  pdb=" N   ARG A 628 " --> pdb=" O   ILE A 697 " (cutoff:3.500A)
      removed outlier: 5.313A  pdb=" N   ASN A 690 " --> pdb=" O   THR A 645 " (cutoff:3.500A)
      removed outlier: 6.401A  pdb=" N   THR A 645 " --> pdb=" O   ASN A 690 " (cutoff:3.500A)
      removed outlier: 5.496A  pdb=" N   HIS A 694 " --> pdb=" O   GLU A 641 " (cutoff:3.500A)
      removed outlier: 5.543A  pdb=" N   GLU A 641 " --> pdb=" O   HIS A 694 " (cutoff:3.500A)
      removed outlier: 6.828A  pdb=" N   THR A 696 " --> pdb=" O   PHE A 639 " (cutoff:3.500A)
      removed outlier: 5.330A  pdb=" N   PHE A 639 " --> pdb=" O   THR A 696 " (cutoff:3.500A)
      removed outlier: 5.333A  pdb=" N   ALA A 642 " --> pdb=" O   ASP A 656 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 627 through 629
      removed outlier: 5.986A  pdb=" N   ARG A 628 " --> pdb=" O   ILE A 697 " (cutoff:3.500A)
      removed outlier: 5.313A  pdb=" N   ASN A 690 " --> pdb=" O   THR A 645 " (cutoff:3.500A)
      removed outlier: 6.401A  pdb=" N   THR A 645 " --> pdb=" O   ASN A 690 " (cutoff:3.500A)
      removed outlier: 5.496A  pdb=" N   HIS A 694 " --> pdb=" O   GLU A 641 " (cutoff:3.500A)
      removed outlier: 5.543A  pdb=" N   GLU A 641 " --> pdb=" O   HIS A 694 " (cutoff:3.500A)
      removed outlier: 6.828A  pdb=" N   THR A 696 " --> pdb=" O   PHE A 639 " (cutoff:3.500A)
      removed outlier: 5.330A  pdb=" N   PHE A 639 " --> pdb=" O   THR A 696 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 701 through 704
      removed outlier: 6.085A  pdb=" N   ALA A 702 " --> pdb=" O   LEU A 783 " (cutoff:3.500A)
      removed outlier: 7.512A  pdb=" N   ASP A 785 " --> pdb=" O   ALA A 702 " (cutoff:3.500A)
      removed outlier: 6.192A  pdb=" N   VAL A 704 " --> pdb=" O   ASP A 785 " (cutoff:3.500A)
      removed outlier: 6.242A  pdb=" N   TYR A 782 " --> pdb=" O   LEU A 816 " (cutoff:3.500A)
      removed outlier: 7.694A  pdb=" N   VAL A 818 " --> pdb=" O   TYR A 782 " (cutoff:3.500A)
      removed outlier: 6.823A  pdb=" N   LEU A 784 " --> pdb=" O   VAL A 818 " (cutoff:3.500A)
      removed outlier: 6.110A  pdb=" N   VAL A 667 " --> pdb=" O   LEU A 817 " (cutoff:3.500A)
      removed outlier: 6.692A  pdb=" N   LEU A 666 " --> pdb=" O   GLU A 830 " (cutoff:3.500A)
      removed outlier: 7.855A  pdb=" N   VAL A 832 " --> pdb=" O   LEU A 666 " (cutoff:3.500A)
      removed outlier: 6.254A  pdb=" N   ALA A 668 " --> pdb=" O   VAL A 832 " (cutoff:3.500A)
      removed outlier: 7.561A  pdb=" N   LEU A 834 " --> pdb=" O   ALA A 668 " (cutoff:3.500A)
      removed outlier: 6.768A  pdb=" N   ILE A 670 " --> pdb=" O   LEU A 834 " (cutoff:3.500A)
      removed outlier: 5.750A  pdb=" N   GLY A 835 " --> pdb=" O   ILE A 839 " (cutoff:3.500A)
      removed outlier: 5.164A  pdb=" N   ILE A 839 " --> pdb=" O   GLY A 835 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1301 through 1307
      removed outlier: 4.625A  pdb=" N   ILE A1320 " --> pdb=" O   ASN A1304 " (cutoff:3.500A)
      removed outlier: 6.237A  pdb=" N   GLN A1306 " --> pdb=" O   ARG A1318 " (cutoff:3.500A)
      removed outlier: 6.723A  pdb=" N   ARG A1318 " --> pdb=" O   GLN A1306 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1458 through 1461
      removed outlier: 6.093A  pdb=" N   LEU A1458 " --> pdb=" O   ILE A1489 " (cutoff:3.500A)
      removed outlier: 7.512A  pdb=" N   ILE A1491 " --> pdb=" O   LEU A1458 " (cutoff:3.500A)
      removed outlier: 6.529A  pdb=" N   LEU A1460 " --> pdb=" O   ILE A1491 " (cutoff:3.500A)
      removed outlier: 6.137A  pdb=" N   VAL A1504 " --> pdb=" O   CYS A1515 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   CYS A1515 " --> pdb=" O   VAL A1504 " (cutoff:3.500A)
      removed outlier: 7.131A  pdb=" N   VAL A1506 " --> pdb=" O   ILE A1513 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1389 through 1390

    730 hydrogen bonds defined for protein.
    2151 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: 2.26

  Time building geometry restraints manager: 1.28 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: 1933
        1.32 -     1.44: 2875
        1.44 -     1.57: 6484
        1.57 -     1.69: 5
        1.69 -     1.81: 94
  Bond restraints: 11391
  Sorted by residual:
  bond pdb=" N3B ANP A1602 "
       pdb=" PG  ANP A1602 "
    ideal  model  delta    sigma   weight residual
    1.795  1.633  0.162 2.00e-02 2.50e+03 6.56e+01
  bond pdb=" O3A ANP A1602 "
       pdb=" PB  ANP A1602 "
    ideal  model  delta    sigma   weight residual
    1.700  1.601  0.099 2.00e-02 2.50e+03 2.43e+01
  bond pdb=" N   ASP A 786 "
       pdb=" CA  ASP A 786 "
    ideal  model  delta    sigma   weight residual
    1.458  1.488 -0.031 7.40e-03 1.83e+04 1.71e+01
  bond pdb=" N   ILE A1380 "
       pdb=" CA  ILE A1380 "
    ideal  model  delta    sigma   weight residual
    1.457  1.494 -0.037 9.00e-03 1.23e+04 1.70e+01
  bond pdb=" N   ARG A 219 "
       pdb=" CA  ARG A 219 "
    ideal  model  delta    sigma   weight residual
    1.455  1.490 -0.035 9.60e-03 1.09e+04 1.32e+01
  ... (remaining 11386 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.57: 13778
        2.57 -     5.14: 1602
        5.14 -     7.72: 62
        7.72 -    10.29: 9
       10.29 -    12.86: 1
  Bond angle restraints: 15452
  Sorted by residual:
  angle pdb=" C   PHE A1010 "
        pdb=" CA  PHE A1010 "
        pdb=" CB  PHE A1010 "
      ideal   model   delta    sigma   weight residual
     111.45   98.59   12.86 1.72e+00 3.38e-01 5.59e+01
  angle pdb=" N   SER A 351 "
        pdb=" CA  SER A 351 "
        pdb=" C   SER A 351 "
      ideal   model   delta    sigma   weight residual
     113.41  105.16    8.25 1.22e+00 6.72e-01 4.58e+01
  angle pdb=" CA  PHE A1176 "
        pdb=" CB  PHE A1176 "
        pdb=" CG  PHE A1176 "
      ideal   model   delta    sigma   weight residual
     113.80  120.39   -6.59 1.00e+00 1.00e+00 4.35e+01
  angle pdb=" CA  GLY A 693 "
        pdb=" C   GLY A 693 "
        pdb=" O   GLY A 693 "
      ideal   model   delta    sigma   weight residual
     122.23  117.72    4.51 6.90e-01 2.10e+00 4.27e+01
  angle pdb=" N   LEU A 106 "
        pdb=" CA  LEU A 106 "
        pdb=" C   LEU A 106 "
      ideal   model   delta    sigma   weight residual
     111.28  104.88    6.40 1.09e+00 8.42e-01 3.44e+01
  ... (remaining 15447 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.64: 6442
       26.64 -    53.28: 312
       53.28 -    79.93: 50
       79.93 -   106.57: 1
      106.57 -   133.21: 1
  Dihedral angle restraints: 6806
    sinusoidal: 2722
      harmonic: 4084
  Sorted by residual:
  dihedral pdb=" C   PHE A1176 "
           pdb=" N   PHE A1176 "
           pdb=" CA  PHE A1176 "
           pdb=" CB  PHE A1176 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -107.80  -14.80     0      2.50e+00 1.60e-01 3.51e+01
  dihedral pdb=" C   PHE A1240 "
           pdb=" N   PHE A1240 "
           pdb=" CA  PHE A1240 "
           pdb=" CB  PHE A1240 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -135.27   12.67     0      2.50e+00 1.60e-01 2.57e+01
  dihedral pdb=" C   PHE A1010 "
           pdb=" N   PHE A1010 "
           pdb=" CA  PHE A1010 "
           pdb=" CB  PHE A1010 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -110.45  -12.15     0      2.50e+00 1.60e-01 2.36e+01
  ... (remaining 6803 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.090: 967
       0.090 -    0.180: 672
       0.180 -    0.270: 153
       0.270 -    0.360: 15
       0.360 -    0.450: 2
  Chirality restraints: 1809
  Sorted by residual:
  chirality pdb=" CA  PHE A1176 "
            pdb=" N   PHE A1176 "
            pdb=" C   PHE A1176 "
            pdb=" CB  PHE A1176 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.96   -0.45 2.00e-01 2.50e+01 5.07e+00
  chirality pdb=" CA  PHE A1240 "
            pdb=" N   PHE A1240 "
            pdb=" C   PHE A1240 "
            pdb=" CB  PHE A1240 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.36 2.00e-01 2.50e+01 3.31e+00
  chirality pdb=" CA  ASN A 103 "
            pdb=" N   ASN A 103 "
            pdb=" C   ASN A 103 "
            pdb=" CB  ASN A 103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.36 2.00e-01 2.50e+01 3.24e+00
  ... (remaining 1806 not shown)

  Planarity restraints: 1911
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 307 "   -0.018 2.00e-02 2.50e+03   3.80e-02 1.45e+01
        pdb=" C   LYS A 307 "    0.066 2.00e-02 2.50e+03
        pdb=" O   LYS A 307 "   -0.025 2.00e-02 2.50e+03
        pdb=" N   SER A 308 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 349 "   -0.012 2.00e-02 2.50e+03   2.54e-02 6.45e+00
        pdb=" C   PHE A 349 "    0.044 2.00e-02 2.50e+03
        pdb=" O   PHE A 349 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   ALA A 350 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 346 "    0.010 2.00e-02 2.50e+03   2.11e-02 4.44e+00
        pdb=" C   LEU A 346 "   -0.036 2.00e-02 2.50e+03
        pdb=" O   LEU A 346 "    0.013 2.00e-02 2.50e+03
        pdb=" N   ILE A 347 "    0.013 2.00e-02 2.50e+03
  ... (remaining 1908 not shown)

  Histogram of nonbonded interaction distances:
        2.33 -     2.85: 3664
        2.85 -     3.36: 11232
        3.36 -     3.87: 18055
        3.87 -     4.39: 21114
        4.39 -     4.90: 34400
  Nonbonded interactions: 88465
  Sorted by model distance:
  nonbonded pdb=" O   VAL A 673 "
            pdb="MG    MG A1601 "
     model   vdw
     2.335 2.170
  nonbonded pdb=" O   PHE A1010 "
            pdb=" CB  PHE A1010 "
     model   vdw
     2.365 2.752
  nonbonded pdb=" N   VAL A 305 "
            pdb=" O   VAL A 305 "
     model   vdw
     2.453 2.496
  nonbonded pdb=" N   PHE A 349 "
            pdb=" O   PHE A 349 "
     model   vdw
     2.455 2.496
  nonbonded pdb=" C   THR A1013 "
            pdb=" OG1 THR A1013 "
     model   vdw
     2.503 2.616
  ... (remaining 88460 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.270
  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:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     12.510
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5967
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   0.162  11392  Z= 0.925
  Angle     :  1.596  12.860  15454  Z= 1.269
  Chirality :  0.109   0.450   1809
  Planarity :  0.005   0.038   1911
  Dihedral  : 15.185 133.210   4153
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.01 %
    Favored  : 98.99 %
  Rotamer:
    Outliers :  7.17 %
    Allowed  :  7.65 %
    Favored  : 85.19 %
  Cbeta Deviations :  0.30 %
  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:  3.66 (0.21), residues: 1392
  helix:  3.29 (0.15), residues: 936
  sheet:  1.53 (0.58), residues: 81
  loop :  0.31 (0.30), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A1205 
 TYR   0.022   0.002   TYR A  39 
 PHE   0.035   0.002   PHE A1176 
 TRP   0.029   0.002   TRP A 358 
 HIS   0.004   0.001   HIS A 439 

Details of bonding type rmsd
  covalent geometry    : bond        0.01216 (11391)
  covalent geometry    : angle       1.59641 (15452)
  SS BOND              : bond        0.00756 (    1)
  SS BOND              : angle       1.04753 (    2)
  hydrogen bonds       : bond        0.24484 (  728)
  hydrogen bonds       : angle       6.55539 ( 2151)

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

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

  2784 Ramachandran restraints generated.
    1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2784 Ramachandran restraints generated.
    1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  292 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 89
    poor density    : 203
  time to evaluate  : 0.408 
Fit side-chains
   revert: symmetry clash
REVERT: A   63 LYS cc_start: 0.5318 (ptmt) cc_final: 0.4983 (mmtt)
REVERT: A   82 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.7313 (mt-10)
REVERT: A   87 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7996 (mp)
REVERT: A  123 TRP cc_start: 0.6503 (m-90) cc_final: 0.5951 (m-10)
REVERT: A  153 THR cc_start: 0.8438 (m) cc_final: 0.8061 (p)
REVERT: A  156 GLN cc_start: 0.7113 (OUTLIER) cc_final: 0.6861 (tt0)
REVERT: A  246 MET cc_start: 0.6814 (OUTLIER) cc_final: 0.6572 (ttt)
REVERT: A  317 THR cc_start: 0.8362 (m) cc_final: 0.8156 (p)
REVERT: A  355 THR cc_start: 0.7393 (OUTLIER) cc_final: 0.7145 (p)
REVERT: A  523 ASP cc_start: 0.7501 (m-30) cc_final: 0.7221 (t0)
REVERT: A  605 GLN cc_start: 0.7288 (mt0) cc_final: 0.6721 (mp10)
REVERT: A  703 TYR cc_start: 0.7993 (t80) cc_final: 0.7599 (t80)
REVERT: A  770 SER cc_start: 0.8930 (t) cc_final: 0.8704 (p)
REVERT: A  776 TYR cc_start: 0.8086 (t80) cc_final: 0.7436 (t80)
REVERT: A  782 TYR cc_start: 0.8340 (m-80) cc_final: 0.7853 (m-80)
REVERT: A 1022 MET cc_start: 0.7613 (ttp) cc_final: 0.6852 (ttm)
REVERT: A 1057 HIS cc_start: 0.7542 (t-90) cc_final: 0.7116 (t70)
REVERT: A 1149 ARG cc_start: 0.7606 (mtp180) cc_final: 0.7329 (ttm-80)
REVERT: A 1156 ARG cc_start: 0.7434 (ttm-80) cc_final: 0.6863 (ttp80)
REVERT: A 1198 PHE cc_start: 0.6883 (t80) cc_final: 0.6593 (t80)
REVERT: A 1210 ARG cc_start: 0.7113 (OUTLIER) cc_final: 0.6691 (mpt180)
REVERT: A 1226 MET cc_start: 0.7061 (mmt) cc_final: 0.6803 (mmp)
REVERT: A 1257 ARG cc_start: 0.7661 (OUTLIER) cc_final: 0.7388 (ttm170)
REVERT: A 1264 THR cc_start: 0.7973 (m) cc_final: 0.7542 (p)
REVERT: A 1279 GLU cc_start: 0.5616 (OUTLIER) cc_final: 0.5125 (mt-10)
REVERT: A 1305 TYR cc_start: 0.1566 (OUTLIER) cc_final: 0.1091 (t80)
  outliers start: 89
  outliers final: 20
  residues processed: 275
  average time/residue: 0.1211
  time to fit residues: 45.9434
Evaluate side-chains
  163 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 134
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue   82 GLU
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue  128 ASN
Chi-restraints excluded: chain A residue  156 GLN
Chi-restraints excluded: chain A residue  229 VAL
Chi-restraints excluded: chain A residue  238 LEU
Chi-restraints excluded: chain A residue  246 MET
Chi-restraints excluded: chain A residue  305 VAL
Chi-restraints excluded: chain A residue  355 THR
Chi-restraints excluded: chain A residue  661 ILE
Chi-restraints excluded: chain A residue  677 LYS
Chi-restraints excluded: chain A residue  734 LEU
Chi-restraints excluded: chain A residue  989 ASN
Chi-restraints excluded: chain A residue 1013 THR
Chi-restraints excluded: chain A residue 1015 TYR
Chi-restraints excluded: chain A residue 1210 ARG
Chi-restraints excluded: chain A residue 1227 VAL
Chi-restraints excluded: chain A residue 1236 ASP
Chi-restraints excluded: chain A residue 1257 ARG
Chi-restraints excluded: chain A residue 1279 GLU
Chi-restraints excluded: chain A residue 1300 ILE
Chi-restraints excluded: chain A residue 1305 TYR
Chi-restraints excluded: chain A residue 1358 ILE
Chi-restraints excluded: chain A residue 1365 ILE
Chi-restraints excluded: chain A residue 1373 LEU
Chi-restraints excluded: chain A residue 1379 ILE
Chi-restraints excluded: chain A residue 1452 LEU
Chi-restraints excluded: chain A residue 1493 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 107 optimal weight:    0.6980
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    5.9990
   chunk 130 optimal weight:   10.0000
   chunk 124 optimal weight:    3.9990
   chunk 103 optimal weight:    0.6980
   chunk 77 optimal weight:    7.9990
   chunk 122 optimal weight:    7.9990
   chunk 91 optimal weight:    0.9980
   chunk 55 optimal weight:    0.8980
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
A 118 GLN
A 146 GLN
A 332 ASN
A 409 ASN
A 577 GLN
A 711 GLN
A 718 ASN
A 820 HIS
A1054 ASN
A1097 GLN
A1247 ASN
A1253 ASN
A1301 GLN
A1496 HIS

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4522 r_free = 0.4522 target = 0.228098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 99)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.154418 restraints weight = 13850.786|
|-----------------------------------------------------------------------------|
r_work (start): 0.3719 rms_B_bonded: 2.58
r_work: 0.3534 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3534
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7538
moved from start:          0.2675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  11392  Z= 0.174
  Angle     :  0.581   8.965  15454  Z= 0.322
  Chirality :  0.041   0.184   1809
  Planarity :  0.004   0.033   1911
  Dihedral  :  9.773 138.029   1585
  Min Nonbonded Distance : 2.271

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.29 %
    Favored  : 98.71 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 12.48 %
    Favored  : 83.25 %
  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:  2.80 (0.21), residues: 1392
  helix:  2.58 (0.15), residues: 955
  sheet:  0.97 (0.58), residues: 76
  loop :  0.07 (0.31), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 100 
 TYR   0.021   0.001   TYR A  65 
 PHE   0.028   0.002   PHE A1240 
 TRP   0.015   0.001   TRP A 358 
 HIS   0.005   0.001   HIS A 692 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 (11391)
  covalent geometry    : angle       0.58055 (15452)
  SS BOND              : bond        0.00690 (    1)
  SS BOND              : angle       0.82167 (    2)
  hydrogen bonds       : bond        0.08226 (  728)
  hydrogen bonds       : angle       4.68503 ( 2151)

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

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

  2784 Ramachandran restraints generated.
    1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2784 Ramachandran restraints generated.
    1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 146
  time to evaluate  : 0.348 
Fit side-chains
   revert: symmetry clash
REVERT: A   63 LYS cc_start: 0.4560 (ptmt) cc_final: 0.4297 (mmtt)
REVERT: A   82 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.7136 (mt-10)
REVERT: A  156 GLN cc_start: 0.7442 (OUTLIER) cc_final: 0.7167 (tt0)
REVERT: A  352 ASP cc_start: 0.8286 (m-30) cc_final: 0.7829 (t0)
REVERT: A  523 ASP cc_start: 0.7474 (m-30) cc_final: 0.6993 (t0)
REVERT: A  603 MET cc_start: 0.7638 (mmm) cc_final: 0.7330 (mmt)
REVERT: A  677 LYS cc_start: 0.6873 (OUTLIER) cc_final: 0.6545 (mtmm)
REVERT: A  703 TYR cc_start: 0.8188 (t80) cc_final: 0.7978 (t80)
REVERT: A  770 SER cc_start: 0.9032 (t) cc_final: 0.8776 (p)
REVERT: A  782 TYR cc_start: 0.8470 (m-80) cc_final: 0.7993 (m-10)
REVERT: A 1022 MET cc_start: 0.7725 (ttp) cc_final: 0.7490 (ttm)
REVERT: A 1149 ARG cc_start: 0.8254 (mtp180) cc_final: 0.7913 (ttm-80)
REVERT: A 1210 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.8044 (mpt180)
REVERT: A 1257 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7428 (ttm170)
REVERT: A 1279 GLU cc_start: 0.5016 (OUTLIER) cc_final: 0.4719 (mt-10)
  outliers start: 53
  outliers final: 30
  residues processed: 187
  average time/residue: 0.1026
  time to fit residues: 27.7690
Evaluate side-chains
  161 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 125
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   82 GLU
Chi-restraints excluded: chain A residue  105 SER
Chi-restraints excluded: chain A residue  128 ASN
Chi-restraints excluded: chain A residue  156 GLN
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  218 LYS
Chi-restraints excluded: chain A residue  238 LEU
Chi-restraints excluded: chain A residue  305 VAL
Chi-restraints excluded: chain A residue  346 LEU
Chi-restraints excluded: chain A residue  473 VAL
Chi-restraints excluded: chain A residue  546 VAL
Chi-restraints excluded: chain A residue  661 ILE
Chi-restraints excluded: chain A residue  677 LYS
Chi-restraints excluded: chain A residue  710 ILE
Chi-restraints excluded: chain A residue  734 LEU
Chi-restraints excluded: chain A residue  818 VAL
Chi-restraints excluded: chain A residue  820 HIS
Chi-restraints excluded: chain A residue  824 PHE
Chi-restraints excluded: chain A residue  978 SER
Chi-restraints excluded: chain A residue 1013 THR
Chi-restraints excluded: chain A residue 1015 TYR
Chi-restraints excluded: chain A residue 1054 ASN
Chi-restraints excluded: chain A residue 1097 GLN
Chi-restraints excluded: chain A residue 1104 THR
Chi-restraints excluded: chain A residue 1139 MET
Chi-restraints excluded: chain A residue 1210 ARG
Chi-restraints excluded: chain A residue 1236 ASP
Chi-restraints excluded: chain A residue 1257 ARG
Chi-restraints excluded: chain A residue 1279 GLU
Chi-restraints excluded: chain A residue 1305 TYR
Chi-restraints excluded: chain A residue 1358 ILE
Chi-restraints excluded: chain A residue 1373 LEU
Chi-restraints excluded: chain A residue 1379 ILE
Chi-restraints excluded: chain A residue 1415 LEU
Chi-restraints excluded: chain A residue 1493 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 104 optimal weight:    0.7980
   chunk 36 optimal weight:    1.9990
   chunk 19 optimal weight:    0.0070
   chunk 61 optimal weight:    5.9990
   chunk 57 optimal weight:    3.9990
   chunk 74 optimal weight:    0.9990
   chunk 111 optimal weight:    2.9990
   chunk 73 optimal weight:    0.7980
   chunk 12 optimal weight:    0.8980
   chunk 15 optimal weight:    0.8980
   chunk 100 optimal weight:    0.7980
   overall best weight:    0.6598

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

Flipped N/Q/H residues before XYZ refinement:
** A 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 820 HIS
** A1054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1063 ASN
A1097 GLN
A1185 HIS
A1193 ASN
A1216 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4532 r_free = 0.4532 target = 0.228687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.178255 restraints weight = 13917.549|
|-----------------------------------------------------------------------------|
r_work (start): 0.4031 rms_B_bonded: 3.70
r_work: 0.3508 rms_B_bonded: 4.18 restraints_weight: 0.5000
r_work (final): 0.3508
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7552
moved from start:          0.3265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  11392  Z= 0.145
  Angle     :  0.511   8.486  15454  Z= 0.277
  Chirality :  0.038   0.151   1809
  Planarity :  0.003   0.032   1911
  Dihedral  :  8.777 137.815   1568
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 14.65 %
    Favored  : 81.08 %
  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:  2.70 (0.22), residues: 1392
  helix:  2.48 (0.16), residues: 955
  sheet:  1.04 (0.55), residues: 79
  loop :  0.06 (0.31), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 100 
 TYR   0.012   0.001   TYR A  65 
 PHE   0.020   0.001   PHE A1240 
 TRP   0.012   0.001   TRP A1206 
 HIS   0.006   0.001   HIS A 692 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 (11391)
  covalent geometry    : angle       0.51133 (15452)
  SS BOND              : bond        0.00166 (    1)
  SS BOND              : angle       0.89126 (    2)
  hydrogen bonds       : bond        0.06947 (  728)
  hydrogen bonds       : angle       4.35753 ( 2151)

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

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

  2784 Ramachandran restraints generated.
    1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2784 Ramachandran restraints generated.
    1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 134
  time to evaluate  : 0.441 
Fit side-chains
   revert: symmetry clash
REVERT: A   20 GLU cc_start: 0.4294 (tp30) cc_final: 0.3350 (pt0)
REVERT: A   63 LYS cc_start: 0.4493 (ptmt) cc_final: 0.4160 (mmtt)
REVERT: A   82 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.7233 (mt-10)
REVERT: A   87 LEU cc_start: 0.8211 (mp) cc_final: 0.7956 (mp)
REVERT: A  154 LEU cc_start: 0.6964 (OUTLIER) cc_final: 0.6764 (tt)
REVERT: A  156 GLN cc_start: 0.7456 (OUTLIER) cc_final: 0.7247 (tt0)
REVERT: A  166 CYS cc_start: 0.6878 (t) cc_final: 0.6646 (m)
REVERT: A  352 ASP cc_start: 0.8283 (m-30) cc_final: 0.7912 (t0)
REVERT: A  523 ASP cc_start: 0.7606 (m-30) cc_final: 0.7066 (t0)
REVERT: A  603 MET cc_start: 0.7655 (mmm) cc_final: 0.7355 (mmt)
REVERT: A  605 GLN cc_start: 0.8027 (mt0) cc_final: 0.7695 (mp10)
REVERT: A  768 ARG cc_start: 0.7756 (mtm180) cc_final: 0.7466 (mtm180)
REVERT: A  770 SER cc_start: 0.8983 (t) cc_final: 0.8748 (p)
REVERT: A  782 TYR cc_start: 0.8545 (m-80) cc_final: 0.8229 (m-80)
REVERT: A 1022 MET cc_start: 0.7632 (ttp) cc_final: 0.7249 (ttm)
REVERT: A 1101 SER cc_start: 0.7930 (m) cc_final: 0.7603 (m)
REVERT: A 1149 ARG cc_start: 0.8324 (mtp180) cc_final: 0.8007 (ttm-80)
REVERT: A 1210 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.7833 (mpt180)
REVERT: A 1257 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7444 (ttm170)
REVERT: A 1279 GLU cc_start: 0.4890 (OUTLIER) cc_final: 0.4665 (mt-10)
  outliers start: 53
  outliers final: 28
  residues processed: 172
  average time/residue: 0.1002
  time to fit residues: 25.2214
Evaluate side-chains
  157 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 123
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   82 GLU
Chi-restraints excluded: chain A residue  105 SER
Chi-restraints excluded: chain A residue  128 ASN
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  156 GLN
Chi-restraints excluded: chain A residue  218 LYS
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  263 LYS
Chi-restraints excluded: chain A residue  305 VAL
Chi-restraints excluded: chain A residue  546 VAL
Chi-restraints excluded: chain A residue  661 ILE
Chi-restraints excluded: chain A residue  670 ILE
Chi-restraints excluded: chain A residue  720 LEU
Chi-restraints excluded: chain A residue  734 LEU
Chi-restraints excluded: chain A residue  779 LEU
Chi-restraints excluded: chain A residue  818 VAL
Chi-restraints excluded: chain A residue  820 HIS
Chi-restraints excluded: chain A residue  824 PHE
Chi-restraints excluded: chain A residue  989 ASN
Chi-restraints excluded: chain A residue 1013 THR
Chi-restraints excluded: chain A residue 1090 THR
Chi-restraints excluded: chain A residue 1104 THR
Chi-restraints excluded: chain A residue 1210 ARG
Chi-restraints excluded: chain A residue 1236 ASP
Chi-restraints excluded: chain A residue 1257 ARG
Chi-restraints excluded: chain A residue 1269 VAL
Chi-restraints excluded: chain A residue 1279 GLU
Chi-restraints excluded: chain A residue 1305 TYR
Chi-restraints excluded: chain A residue 1358 ILE
Chi-restraints excluded: chain A residue 1373 LEU
Chi-restraints excluded: chain A residue 1379 ILE
Chi-restraints excluded: chain A residue 1415 LEU
Chi-restraints excluded: chain A residue 1493 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 99 optimal weight:    0.6980
   chunk 22 optimal weight:    2.9990
   chunk 19 optimal weight:    0.5980
   chunk 89 optimal weight:    3.9990
   chunk 126 optimal weight:    6.9990
   chunk 121 optimal weight:   40.0000
   chunk 76 optimal weight:    6.9990
   chunk 116 optimal weight:   20.0000
   chunk 70 optimal weight:    7.9990
   chunk 138 optimal weight:    0.9990
   chunk 50 optimal weight:    9.9990
   overall best weight:    1.8586

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

Flipped N/Q/H residues before XYZ refinement:
A 161 ASN
A 447 GLN
** A 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 777 GLN
A 820 HIS
A1054 ASN
A1063 ASN
A1244 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4497 r_free = 0.4497 target = 0.225410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.173735 restraints weight = 14103.364|
|-----------------------------------------------------------------------------|
r_work (start): 0.3973 rms_B_bonded: 4.34
r_work: 0.3455 rms_B_bonded: 4.12 restraints_weight: 0.5000
r_work (final): 0.3455
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7648
moved from start:          0.3578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  11392  Z= 0.184
  Angle     :  0.546   9.473  15454  Z= 0.292
  Chirality :  0.039   0.141   1809
  Planarity :  0.004   0.033   1911
  Dihedral  :  8.120 134.542   1560
  Min Nonbonded Distance : 2.061

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 15.94 %
    Favored  : 80.11 %
  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:  2.32 (0.22), residues: 1392
  helix:  2.20 (0.16), residues: 954
  sheet:  0.63 (0.54), residues: 79
  loop : -0.02 (0.32), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 100 
 TYR   0.014   0.002   TYR A 101 
 PHE   0.023   0.002   PHE A1084 
 TRP   0.014   0.001   TRP A1206 
 HIS   0.011   0.001   HIS A 820 

Details of bonding type rmsd
  covalent geometry    : bond        0.00416 (11391)
  covalent geometry    : angle       0.54630 (15452)
  SS BOND              : bond        0.00005 (    1)
  SS BOND              : angle       0.76149 (    2)
  hydrogen bonds       : bond        0.07004 (  728)
  hydrogen bonds       : angle       4.30487 ( 2151)

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

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

  2784 Ramachandran restraints generated.
    1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2784 Ramachandran restraints generated.
    1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 125
  time to evaluate  : 0.422 
Fit side-chains
   revert: symmetry clash
REVERT: A   87 LEU cc_start: 0.8270 (mp) cc_final: 0.8064 (mp)
REVERT: A  107 TYR cc_start: 0.7887 (OUTLIER) cc_final: 0.7484 (m-10)
REVERT: A  156 GLN cc_start: 0.7290 (OUTLIER) cc_final: 0.7068 (tt0)
REVERT: A  352 ASP cc_start: 0.8213 (m-30) cc_final: 0.7875 (t0)
REVERT: A  441 LEU cc_start: 0.8685 (tt) cc_final: 0.8297 (mt)
REVERT: A  523 ASP cc_start: 0.7644 (m-30) cc_final: 0.7145 (t0)
REVERT: A  605 GLN cc_start: 0.8026 (mt0) cc_final: 0.7757 (mp10)
REVERT: A  768 ARG cc_start: 0.7762 (mtm180) cc_final: 0.7438 (mtm180)
REVERT: A  770 SER cc_start: 0.9020 (t) cc_final: 0.8736 (p)
REVERT: A  782 TYR cc_start: 0.8568 (m-80) cc_final: 0.8271 (m-80)
REVERT: A 1022 MET cc_start: 0.7753 (ttp) cc_final: 0.7229 (ttm)
REVERT: A 1101 SER cc_start: 0.8072 (m) cc_final: 0.7733 (m)
REVERT: A 1149 ARG cc_start: 0.8380 (mtp180) cc_final: 0.8028 (ttm-80)
REVERT: A 1210 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7794 (mpt180)
REVERT: A 1257 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7354 (ttm170)
REVERT: A 1279 GLU cc_start: 0.5005 (OUTLIER) cc_final: 0.4627 (mt-10)
  outliers start: 49
  outliers final: 40
  residues processed: 165
  average time/residue: 0.0928
  time to fit residues: 22.9414
Evaluate side-chains
  161 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 116
  time to evaluate  : 0.439 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 LEU
Chi-restraints excluded: chain A residue  105 SER
Chi-restraints excluded: chain A residue  107 TYR
Chi-restraints excluded: chain A residue  128 ASN
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  156 GLN
Chi-restraints excluded: chain A residue  166 CYS
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  214 LEU
Chi-restraints excluded: chain A residue  218 LYS
Chi-restraints excluded: chain A residue  222 THR
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  263 LYS
Chi-restraints excluded: chain A residue  305 VAL
Chi-restraints excluded: chain A residue  351 SER
Chi-restraints excluded: chain A residue  473 VAL
Chi-restraints excluded: chain A residue  568 VAL
Chi-restraints excluded: chain A residue  661 ILE
Chi-restraints excluded: chain A residue  670 ILE
Chi-restraints excluded: chain A residue  734 LEU
Chi-restraints excluded: chain A residue  751 LEU
Chi-restraints excluded: chain A residue  779 LEU
Chi-restraints excluded: chain A residue  788 LEU
Chi-restraints excluded: chain A residue  818 VAL
Chi-restraints excluded: chain A residue  820 HIS
Chi-restraints excluded: chain A residue  824 PHE
Chi-restraints excluded: chain A residue  989 ASN
Chi-restraints excluded: chain A residue 1013 THR
Chi-restraints excluded: chain A residue 1015 TYR
Chi-restraints excluded: chain A residue 1054 ASN
Chi-restraints excluded: chain A residue 1104 THR
Chi-restraints excluded: chain A residue 1130 LEU
Chi-restraints excluded: chain A residue 1210 ARG
Chi-restraints excluded: chain A residue 1236 ASP
Chi-restraints excluded: chain A residue 1257 ARG
Chi-restraints excluded: chain A residue 1269 VAL
Chi-restraints excluded: chain A residue 1279 GLU
Chi-restraints excluded: chain A residue 1305 TYR
Chi-restraints excluded: chain A residue 1358 ILE
Chi-restraints excluded: chain A residue 1373 LEU
Chi-restraints excluded: chain A residue 1379 ILE
Chi-restraints excluded: chain A residue 1415 LEU
Chi-restraints excluded: chain A residue 1452 LEU
Chi-restraints excluded: chain A residue 1493 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 101 optimal weight:    3.9990
   chunk 130 optimal weight:   10.0000
   chunk 110 optimal weight:    1.9990
   chunk 91 optimal weight:    8.9990
   chunk 65 optimal weight:    2.9990
   chunk 105 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   chunk 5 optimal weight:    0.2980
   chunk 2 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 53 optimal weight:    0.5980
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
** A 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 820 HIS
A1054 ASN
A1063 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4519 r_free = 0.4519 target = 0.227803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.175765 restraints weight = 14030.461|
|-----------------------------------------------------------------------------|
r_work (start): 0.3986 rms_B_bonded: 3.96
r_work: 0.3508 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.3508
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7588
moved from start:          0.3823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  11392  Z= 0.135
  Angle     :  0.497   9.042  15454  Z= 0.263
  Chirality :  0.037   0.132   1809
  Planarity :  0.003   0.036   1911
  Dihedral  :  7.886 131.782   1557
  Min Nonbonded Distance : 2.022

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 16.67 %
    Favored  : 79.39 %
  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:  2.39 (0.22), residues: 1392
  helix:  2.27 (0.16), residues: 956
  sheet:  0.50 (0.55), residues: 79
  loop : -0.01 (0.32), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 100 
 TYR   0.011   0.001   TYR A  39 
 PHE   0.016   0.001   PHE A1240 
 TRP   0.013   0.001   TRP A1206 
 HIS   0.005   0.001   HIS A 692 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 (11391)
  covalent geometry    : angle       0.49700 (15452)
  SS BOND              : bond        0.00042 (    1)
  SS BOND              : angle       0.56467 (    2)
  hydrogen bonds       : bond        0.06304 (  728)
  hydrogen bonds       : angle       4.13563 ( 2151)

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

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

  2784 Ramachandran restraints generated.
    1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2784 Ramachandran restraints generated.
    1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 124
  time to evaluate  : 0.459 
Fit side-chains
   revert: symmetry clash
REVERT: A   82 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.7027 (mt-10)
REVERT: A  107 TYR cc_start: 0.7790 (OUTLIER) cc_final: 0.7265 (m-10)
REVERT: A  156 GLN cc_start: 0.7339 (OUTLIER) cc_final: 0.7099 (tt0)
REVERT: A  352 ASP cc_start: 0.8237 (m-30) cc_final: 0.7857 (t70)
REVERT: A  441 LEU cc_start: 0.8627 (tt) cc_final: 0.8255 (mt)
REVERT: A  523 ASP cc_start: 0.7641 (m-30) cc_final: 0.7164 (t0)
REVERT: A  605 GLN cc_start: 0.7979 (mt0) cc_final: 0.7742 (mp10)
REVERT: A  768 ARG cc_start: 0.7693 (mtm180) cc_final: 0.7376 (mtm180)
REVERT: A  770 SER cc_start: 0.9003 (t) cc_final: 0.8726 (p)
REVERT: A  782 TYR cc_start: 0.8515 (m-80) cc_final: 0.8132 (m-80)
REVERT: A  830 GLU cc_start: 0.7217 (tt0) cc_final: 0.6723 (tm-30)
REVERT: A 1022 MET cc_start: 0.7621 (ttp) cc_final: 0.7014 (ttm)
REVERT: A 1101 SER cc_start: 0.8073 (m) cc_final: 0.7737 (m)
REVERT: A 1149 ARG cc_start: 0.8257 (mtp180) cc_final: 0.7915 (ttm-80)
REVERT: A 1210 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7627 (mpt180)
REVERT: A 1257 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.7420 (ttm170)
REVERT: A 1279 GLU cc_start: 0.5209 (OUTLIER) cc_final: 0.4740 (mt-10)
  outliers start: 49
  outliers final: 35
  residues processed: 159
  average time/residue: 0.0974
  time to fit residues: 23.2818
Evaluate side-chains
  159 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 118
  time to evaluate  : 0.429 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 GLU
Chi-restraints excluded: chain A residue  105 SER
Chi-restraints excluded: chain A residue  107 TYR
Chi-restraints excluded: chain A residue  128 ASN
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  156 GLN
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  218 LYS
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  263 LYS
Chi-restraints excluded: chain A residue  305 VAL
Chi-restraints excluded: chain A residue  568 VAL
Chi-restraints excluded: chain A residue  661 ILE
Chi-restraints excluded: chain A residue  670 ILE
Chi-restraints excluded: chain A residue  688 MET
Chi-restraints excluded: chain A residue  734 LEU
Chi-restraints excluded: chain A residue  751 LEU
Chi-restraints excluded: chain A residue  788 LEU
Chi-restraints excluded: chain A residue  818 VAL
Chi-restraints excluded: chain A residue  820 HIS
Chi-restraints excluded: chain A residue  824 PHE
Chi-restraints excluded: chain A residue  978 SER
Chi-restraints excluded: chain A residue  989 ASN
Chi-restraints excluded: chain A residue 1013 THR
Chi-restraints excluded: chain A residue 1054 ASN
Chi-restraints excluded: chain A residue 1065 LEU
Chi-restraints excluded: chain A residue 1104 THR
Chi-restraints excluded: chain A residue 1130 LEU
Chi-restraints excluded: chain A residue 1139 MET
Chi-restraints excluded: chain A residue 1210 ARG
Chi-restraints excluded: chain A residue 1236 ASP
Chi-restraints excluded: chain A residue 1257 ARG
Chi-restraints excluded: chain A residue 1269 VAL
Chi-restraints excluded: chain A residue 1279 GLU
Chi-restraints excluded: chain A residue 1305 TYR
Chi-restraints excluded: chain A residue 1358 ILE
Chi-restraints excluded: chain A residue 1373 LEU
Chi-restraints excluded: chain A residue 1379 ILE
Chi-restraints excluded: chain A residue 1415 LEU
Chi-restraints excluded: chain A residue 1452 LEU
Chi-restraints excluded: chain A residue 1493 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 38 optimal weight:    3.9990
   chunk 132 optimal weight:   30.0000
   chunk 40 optimal weight:    4.9990
   chunk 91 optimal weight:    8.9990
   chunk 47 optimal weight:   10.0000
   chunk 127 optimal weight:    7.9990
   chunk 106 optimal weight:    0.8980
   chunk 114 optimal weight:   10.0000
   chunk 89 optimal weight:    4.9990
   chunk 88 optimal weight:    0.8980
   chunk 56 optimal weight:    1.9990
   overall best weight:    2.5586

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

Flipped N/Q/H residues before XYZ refinement:
** A 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 820 HIS
A1054 ASN
A1063 ASN
A1216 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4478 r_free = 0.4478 target = 0.223141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.164860 restraints weight = 14164.430|
|-----------------------------------------------------------------------------|
r_work (start): 0.3907 rms_B_bonded: 2.06
r_work: 0.3553 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3413 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3413
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7762
moved from start:          0.3907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  11392  Z= 0.225
  Angle     :  0.582   8.674  15454  Z= 0.310
  Chirality :  0.041   0.141   1809
  Planarity :  0.004   0.040   1911
  Dihedral  :  7.813 126.783   1557
  Min Nonbonded Distance : 1.923

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  4.75 %
    Allowed  : 16.43 %
    Favored  : 78.82 %
  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:  1.94 (0.22), residues: 1392
  helix:  1.94 (0.16), residues: 963
  sheet:  0.27 (0.54), residues: 79
  loop : -0.22 (0.32), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 457 
 TYR   0.025   0.002   TYR A 703 
 PHE   0.024   0.002   PHE A1240 
 TRP   0.015   0.002   TRP A1206 
 HIS   0.005   0.001   HIS A  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00532 (11391)
  covalent geometry    : angle       0.58199 (15452)
  SS BOND              : bond        0.00100 (    1)
  SS BOND              : angle       0.74494 (    2)
  hydrogen bonds       : bond        0.07085 (  728)
  hydrogen bonds       : angle       4.27642 ( 2151)

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

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

  2784 Ramachandran restraints generated.
    1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2784 Ramachandran restraints generated.
    1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 118
  time to evaluate  : 0.550 
Fit side-chains
   revert: symmetry clash
REVERT: A   63 LYS cc_start: 0.4506 (ptmt) cc_final: 0.4140 (mmtt)
REVERT: A   82 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.7287 (mt-10)
REVERT: A   87 LEU cc_start: 0.8311 (mp) cc_final: 0.8041 (mp)
REVERT: A  107 TYR cc_start: 0.8031 (OUTLIER) cc_final: 0.7661 (m-10)
REVERT: A  156 GLN cc_start: 0.7442 (tp40) cc_final: 0.7150 (tt0)
REVERT: A  352 ASP cc_start: 0.8315 (m-30) cc_final: 0.7954 (t70)
REVERT: A  523 ASP cc_start: 0.7669 (m-30) cc_final: 0.7214 (t0)
REVERT: A  605 GLN cc_start: 0.8169 (mt0) cc_final: 0.7896 (mp10)
REVERT: A  770 SER cc_start: 0.9031 (t) cc_final: 0.8698 (p)
REVERT: A  782 TYR cc_start: 0.8670 (m-80) cc_final: 0.8344 (m-80)
REVERT: A  830 GLU cc_start: 0.7303 (tt0) cc_final: 0.6823 (tm-30)
REVERT: A 1101 SER cc_start: 0.8207 (m) cc_final: 0.7897 (m)
REVERT: A 1149 ARG cc_start: 0.8418 (mtp180) cc_final: 0.8066 (ttm-80)
REVERT: A 1210 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.7854 (mpt180)
REVERT: A 1257 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7412 (ttm170)
REVERT: A 1279 GLU cc_start: 0.5197 (OUTLIER) cc_final: 0.4803 (mt-10)
REVERT: A 1423 GLN cc_start: 0.4702 (OUTLIER) cc_final: 0.4494 (pt0)
  outliers start: 59
  outliers final: 44
  residues processed: 163
  average time/residue: 0.0960
  time to fit residues: 23.5050
Evaluate side-chains
  162 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 112
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 GLU
Chi-restraints excluded: chain A residue  105 SER
Chi-restraints excluded: chain A residue  107 TYR
Chi-restraints excluded: chain A residue  128 ASN
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  166 CYS
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  214 LEU
Chi-restraints excluded: chain A residue  218 LYS
Chi-restraints excluded: chain A residue  222 THR
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  263 LYS
Chi-restraints excluded: chain A residue  305 VAL
Chi-restraints excluded: chain A residue  351 SER
Chi-restraints excluded: chain A residue  473 VAL
Chi-restraints excluded: chain A residue  568 VAL
Chi-restraints excluded: chain A residue  653 THR
Chi-restraints excluded: chain A residue  661 ILE
Chi-restraints excluded: chain A residue  670 ILE
Chi-restraints excluded: chain A residue  688 MET
Chi-restraints excluded: chain A residue  734 LEU
Chi-restraints excluded: chain A residue  751 LEU
Chi-restraints excluded: chain A residue  779 LEU
Chi-restraints excluded: chain A residue  788 LEU
Chi-restraints excluded: chain A residue  818 VAL
Chi-restraints excluded: chain A residue  824 PHE
Chi-restraints excluded: chain A residue  832 VAL
Chi-restraints excluded: chain A residue  978 SER
Chi-restraints excluded: chain A residue  989 ASN
Chi-restraints excluded: chain A residue 1013 THR
Chi-restraints excluded: chain A residue 1015 TYR
Chi-restraints excluded: chain A residue 1054 ASN
Chi-restraints excluded: chain A residue 1065 LEU
Chi-restraints excluded: chain A residue 1104 THR
Chi-restraints excluded: chain A residue 1120 THR
Chi-restraints excluded: chain A residue 1130 LEU
Chi-restraints excluded: chain A residue 1154 VAL
Chi-restraints excluded: chain A residue 1210 ARG
Chi-restraints excluded: chain A residue 1236 ASP
Chi-restraints excluded: chain A residue 1257 ARG
Chi-restraints excluded: chain A residue 1269 VAL
Chi-restraints excluded: chain A residue 1279 GLU
Chi-restraints excluded: chain A residue 1305 TYR
Chi-restraints excluded: chain A residue 1358 ILE
Chi-restraints excluded: chain A residue 1373 LEU
Chi-restraints excluded: chain A residue 1379 ILE
Chi-restraints excluded: chain A residue 1415 LEU
Chi-restraints excluded: chain A residue 1423 GLN
Chi-restraints excluded: chain A residue 1452 LEU
Chi-restraints excluded: chain A residue 1493 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 137 optimal weight:   20.0000
   chunk 109 optimal weight:    4.9990
   chunk 74 optimal weight:    0.1980
   chunk 34 optimal weight:    0.7980
   chunk 60 optimal weight:    5.9990
   chunk 121 optimal weight:    0.0040
   chunk 25 optimal weight:    6.9990
   chunk 23 optimal weight:    0.7980
   chunk 134 optimal weight:    9.9990
   chunk 10 optimal weight:    0.9980
   overall best weight:    0.5592

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

Flipped N/Q/H residues before XYZ refinement:
** A 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 820 HIS
A1054 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4524 r_free = 0.4524 target = 0.227920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.176210 restraints weight = 13944.962|
|-----------------------------------------------------------------------------|
r_work (start): 0.3998 rms_B_bonded: 3.72
r_work: 0.3502 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.3502
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7587
moved from start:          0.4129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  11392  Z= 0.124
  Angle     :  0.485   8.310  15454  Z= 0.256
  Chirality :  0.037   0.158   1809
  Planarity :  0.003   0.039   1911
  Dihedral  :  7.489 126.462   1554
  Min Nonbonded Distance : 2.010

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 17.71 %
    Favored  : 78.66 %
  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:  2.32 (0.22), residues: 1392
  helix:  2.25 (0.16), residues: 956
  sheet:  0.26 (0.56), residues: 79
  loop : -0.09 (0.32), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 100 
 TYR   0.012   0.001   TYR A  39 
 PHE   0.013   0.001   PHE A1240 
 TRP   0.027   0.001   TRP A1294 
 HIS   0.005   0.001   HIS A 692 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 (11391)
  covalent geometry    : angle       0.48458 (15452)
  SS BOND              : bond        0.00057 (    1)
  SS BOND              : angle       0.49460 (    2)
  hydrogen bonds       : bond        0.05924 (  728)
  hydrogen bonds       : angle       4.02749 ( 2151)

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

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

  2784 Ramachandran restraints generated.
    1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2784 Ramachandran restraints generated.
    1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 124
  time to evaluate  : 0.409 
Fit side-chains
   revert: symmetry clash
REVERT: A   87 LEU cc_start: 0.8139 (mp) cc_final: 0.7862 (mp)
REVERT: A  107 TYR cc_start: 0.7754 (OUTLIER) cc_final: 0.7132 (m-10)
REVERT: A  156 GLN cc_start: 0.7376 (tp40) cc_final: 0.7125 (tt0)
REVERT: A  352 ASP cc_start: 0.8202 (m-30) cc_final: 0.7877 (t70)
REVERT: A  523 ASP cc_start: 0.7657 (m-30) cc_final: 0.7197 (t0)
REVERT: A  575 ASP cc_start: 0.7873 (OUTLIER) cc_final: 0.7544 (m-30)
REVERT: A  605 GLN cc_start: 0.7870 (mt0) cc_final: 0.7653 (mp10)
REVERT: A  768 ARG cc_start: 0.7619 (mtm110) cc_final: 0.7369 (mtm180)
REVERT: A  770 SER cc_start: 0.9052 (t) cc_final: 0.8695 (p)
REVERT: A  782 TYR cc_start: 0.8567 (m-80) cc_final: 0.8211 (m-80)
REVERT: A  830 GLU cc_start: 0.7285 (tt0) cc_final: 0.6791 (tm-30)
REVERT: A 1006 ASP cc_start: 0.8545 (t70) cc_final: 0.7975 (t0)
REVERT: A 1101 SER cc_start: 0.8134 (m) cc_final: 0.7816 (m)
REVERT: A 1149 ARG cc_start: 0.8274 (mtp180) cc_final: 0.7944 (ttm-80)
REVERT: A 1210 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7504 (mpt180)
REVERT: A 1257 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.7330 (ttm170)
REVERT: A 1275 TYR cc_start: 0.6254 (OUTLIER) cc_final: 0.4311 (t80)
REVERT: A 1279 GLU cc_start: 0.5095 (OUTLIER) cc_final: 0.4654 (mt-10)
  outliers start: 45
  outliers final: 34
  residues processed: 160
  average time/residue: 0.0972
  time to fit residues: 22.8775
Evaluate side-chains
  155 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 115
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 SER
Chi-restraints excluded: chain A residue  107 TYR
Chi-restraints excluded: chain A residue  128 ASN
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  305 VAL
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  568 VAL
Chi-restraints excluded: chain A residue  575 ASP
Chi-restraints excluded: chain A residue  661 ILE
Chi-restraints excluded: chain A residue  670 ILE
Chi-restraints excluded: chain A residue  688 MET
Chi-restraints excluded: chain A residue  734 LEU
Chi-restraints excluded: chain A residue  751 LEU
Chi-restraints excluded: chain A residue  779 LEU
Chi-restraints excluded: chain A residue  818 VAL
Chi-restraints excluded: chain A residue  824 PHE
Chi-restraints excluded: chain A residue  978 SER
Chi-restraints excluded: chain A residue  989 ASN
Chi-restraints excluded: chain A residue 1013 THR
Chi-restraints excluded: chain A residue 1015 TYR
Chi-restraints excluded: chain A residue 1054 ASN
Chi-restraints excluded: chain A residue 1065 LEU
Chi-restraints excluded: chain A residue 1104 THR
Chi-restraints excluded: chain A residue 1120 THR
Chi-restraints excluded: chain A residue 1130 LEU
Chi-restraints excluded: chain A residue 1139 MET
Chi-restraints excluded: chain A residue 1210 ARG
Chi-restraints excluded: chain A residue 1236 ASP
Chi-restraints excluded: chain A residue 1257 ARG
Chi-restraints excluded: chain A residue 1275 TYR
Chi-restraints excluded: chain A residue 1279 GLU
Chi-restraints excluded: chain A residue 1305 TYR
Chi-restraints excluded: chain A residue 1358 ILE
Chi-restraints excluded: chain A residue 1373 LEU
Chi-restraints excluded: chain A residue 1379 ILE
Chi-restraints excluded: chain A residue 1415 LEU
Chi-restraints excluded: chain A residue 1452 LEU
Chi-restraints excluded: chain A residue 1493 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 122 optimal weight:    0.9990
   chunk 96 optimal weight:    0.6980
   chunk 102 optimal weight:    1.9990
   chunk 57 optimal weight:    4.9990
   chunk 135 optimal weight:   40.0000
   chunk 97 optimal weight:    0.6980
   chunk 71 optimal weight:    4.9990
   chunk 92 optimal weight:    5.9990
   chunk 109 optimal weight:    2.9990
   chunk 5 optimal weight:   10.0000
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
A 765 GLN
A1054 ASN
** A1063 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4505 r_free = 0.4505 target = 0.226567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.175422 restraints weight = 14082.405|
|-----------------------------------------------------------------------------|
r_work (start): 0.3996 rms_B_bonded: 4.07
r_work: 0.3487 rms_B_bonded: 4.00 restraints_weight: 0.5000
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7638
moved from start:          0.4205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  11392  Z= 0.155
  Angle     :  0.522   7.958  15454  Z= 0.275
  Chirality :  0.038   0.141   1809
  Planarity :  0.003   0.045   1911
  Dihedral  :  7.401 123.106   1554
  Min Nonbonded Distance : 1.964

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 17.15 %
    Favored  : 78.58 %
  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:  2.20 (0.22), residues: 1392
  helix:  2.18 (0.16), residues: 957
  sheet: -0.00 (0.55), residues: 81
  loop : -0.14 (0.33), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 457 
 TYR   0.011   0.001   TYR A  39 
 PHE   0.019   0.001   PHE A1084 
 TRP   0.015   0.001   TRP A1294 
 HIS   0.005   0.001   HIS A 692 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 (11391)
  covalent geometry    : angle       0.52185 (15452)
  SS BOND              : bond        0.00056 (    1)
  SS BOND              : angle       0.61802 (    2)
  hydrogen bonds       : bond        0.06178 (  728)
  hydrogen bonds       : angle       4.04519 ( 2151)

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

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

  2784 Ramachandran restraints generated.
    1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2784 Ramachandran restraints generated.
    1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 113
  time to evaluate  : 0.364 
Fit side-chains
   revert: symmetry clash
REVERT: A   82 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7042 (mt-10)
REVERT: A   87 LEU cc_start: 0.8169 (mp) cc_final: 0.7958 (mp)
REVERT: A  107 TYR cc_start: 0.7839 (OUTLIER) cc_final: 0.7310 (m-10)
REVERT: A  156 GLN cc_start: 0.7381 (tp40) cc_final: 0.7140 (tt0)
REVERT: A  352 ASP cc_start: 0.8199 (m-30) cc_final: 0.7842 (t70)
REVERT: A  523 ASP cc_start: 0.7735 (m-30) cc_final: 0.7255 (t0)
REVERT: A  575 ASP cc_start: 0.8012 (OUTLIER) cc_final: 0.7545 (t0)
REVERT: A  605 GLN cc_start: 0.7898 (mt0) cc_final: 0.7684 (mp10)
REVERT: A  768 ARG cc_start: 0.7630 (mtm110) cc_final: 0.7400 (mtm180)
REVERT: A  770 SER cc_start: 0.9030 (t) cc_final: 0.8674 (p)
REVERT: A  782 TYR cc_start: 0.8558 (m-80) cc_final: 0.8197 (m-80)
REVERT: A  830 GLU cc_start: 0.7339 (tt0) cc_final: 0.6863 (tm-30)
REVERT: A 1006 ASP cc_start: 0.8587 (t70) cc_final: 0.8034 (t0)
REVERT: A 1101 SER cc_start: 0.8177 (m) cc_final: 0.7856 (m)
REVERT: A 1149 ARG cc_start: 0.8316 (mtp180) cc_final: 0.7960 (ttm-80)
REVERT: A 1210 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7599 (mpt180)
REVERT: A 1257 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.7364 (ttm170)
REVERT: A 1275 TYR cc_start: 0.6516 (OUTLIER) cc_final: 0.4373 (t80)
REVERT: A 1279 GLU cc_start: 0.5287 (OUTLIER) cc_final: 0.4767 (mt-10)
  outliers start: 53
  outliers final: 39
  residues processed: 155
  average time/residue: 0.1003
  time to fit residues: 22.7301
Evaluate side-chains
  155 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 109
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 GLU
Chi-restraints excluded: chain A residue  105 SER
Chi-restraints excluded: chain A residue  107 TYR
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  166 CYS
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  214 LEU
Chi-restraints excluded: chain A residue  222 THR
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  305 VAL
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  473 VAL
Chi-restraints excluded: chain A residue  568 VAL
Chi-restraints excluded: chain A residue  575 ASP
Chi-restraints excluded: chain A residue  653 THR
Chi-restraints excluded: chain A residue  661 ILE
Chi-restraints excluded: chain A residue  670 ILE
Chi-restraints excluded: chain A residue  688 MET
Chi-restraints excluded: chain A residue  734 LEU
Chi-restraints excluded: chain A residue  751 LEU
Chi-restraints excluded: chain A residue  779 LEU
Chi-restraints excluded: chain A residue  788 LEU
Chi-restraints excluded: chain A residue  818 VAL
Chi-restraints excluded: chain A residue  824 PHE
Chi-restraints excluded: chain A residue  978 SER
Chi-restraints excluded: chain A residue  989 ASN
Chi-restraints excluded: chain A residue 1013 THR
Chi-restraints excluded: chain A residue 1015 TYR
Chi-restraints excluded: chain A residue 1054 ASN
Chi-restraints excluded: chain A residue 1065 LEU
Chi-restraints excluded: chain A residue 1104 THR
Chi-restraints excluded: chain A residue 1120 THR
Chi-restraints excluded: chain A residue 1130 LEU
Chi-restraints excluded: chain A residue 1139 MET
Chi-restraints excluded: chain A residue 1210 ARG
Chi-restraints excluded: chain A residue 1226 MET
Chi-restraints excluded: chain A residue 1236 ASP
Chi-restraints excluded: chain A residue 1257 ARG
Chi-restraints excluded: chain A residue 1275 TYR
Chi-restraints excluded: chain A residue 1279 GLU
Chi-restraints excluded: chain A residue 1305 TYR
Chi-restraints excluded: chain A residue 1358 ILE
Chi-restraints excluded: chain A residue 1373 LEU
Chi-restraints excluded: chain A residue 1379 ILE
Chi-restraints excluded: chain A residue 1452 LEU
Chi-restraints excluded: chain A residue 1493 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 57 optimal weight:    0.8980
   chunk 124 optimal weight:   20.0000
   chunk 26 optimal weight:    4.9990
   chunk 115 optimal weight:    7.9990
   chunk 24 optimal weight:    3.9990
   chunk 76 optimal weight:    3.9990
   chunk 85 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9990
   chunk 73 optimal weight:    0.6980
   chunk 70 optimal weight:    2.9990
   chunk 89 optimal weight:    0.9980
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
A1054 ASN
A1063 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4508 r_free = 0.4508 target = 0.226869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.174762 restraints weight = 13956.408|
|-----------------------------------------------------------------------------|
r_work (start): 0.3995 rms_B_bonded: 4.86
r_work: 0.3494 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7623
moved from start:          0.4311

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  11392  Z= 0.146
  Angle     :  0.516   8.520  15454  Z= 0.269
  Chirality :  0.038   0.157   1809
  Planarity :  0.003   0.046   1911
  Dihedral  :  7.317 120.713   1552
  Min Nonbonded Distance : 1.966

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 17.39 %
    Favored  : 78.18 %
  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:  2.21 (0.22), residues: 1392
  helix:  2.20 (0.16), residues: 956
  sheet: -0.05 (0.55), residues: 81
  loop : -0.16 (0.33), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 259 
 TYR   0.011   0.001   TYR A  39 
 PHE   0.017   0.001   PHE A1240 
 TRP   0.013   0.001   TRP A1206 
 HIS   0.005   0.001   HIS A 692 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 (11391)
  covalent geometry    : angle       0.51577 (15452)
  SS BOND              : bond        0.00001 (    1)
  SS BOND              : angle       0.61151 (    2)
  hydrogen bonds       : bond        0.06062 (  728)
  hydrogen bonds       : angle       4.00899 ( 2151)

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

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

  2784 Ramachandran restraints generated.
    1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2784 Ramachandran restraints generated.
    1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 108
  time to evaluate  : 0.400 
Fit side-chains
   revert: symmetry clash
REVERT: A   82 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.7057 (mt-10)
REVERT: A   87 LEU cc_start: 0.8275 (mp) cc_final: 0.8066 (mp)
REVERT: A  107 TYR cc_start: 0.7798 (OUTLIER) cc_final: 0.7281 (m-10)
REVERT: A  156 GLN cc_start: 0.7338 (tp40) cc_final: 0.7041 (tt0)
REVERT: A  251 GLN cc_start: 0.7928 (tt0) cc_final: 0.7423 (mt0)
REVERT: A  352 ASP cc_start: 0.8276 (m-30) cc_final: 0.7847 (t70)
REVERT: A  523 ASP cc_start: 0.7678 (m-30) cc_final: 0.7211 (t0)
REVERT: A  575 ASP cc_start: 0.7984 (OUTLIER) cc_final: 0.7503 (t0)
REVERT: A  605 GLN cc_start: 0.7854 (mt0) cc_final: 0.7646 (mp10)
REVERT: A  770 SER cc_start: 0.9029 (t) cc_final: 0.8641 (p)
REVERT: A  782 TYR cc_start: 0.8549 (m-80) cc_final: 0.8165 (m-80)
REVERT: A  830 GLU cc_start: 0.7310 (tt0) cc_final: 0.6791 (tm-30)
REVERT: A 1006 ASP cc_start: 0.8644 (t0) cc_final: 0.8086 (t0)
REVERT: A 1101 SER cc_start: 0.8159 (m) cc_final: 0.7840 (m)
REVERT: A 1149 ARG cc_start: 0.8314 (mtp180) cc_final: 0.7958 (ttm-80)
REVERT: A 1210 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7564 (mpt180)
REVERT: A 1257 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.7376 (ttm170)
REVERT: A 1275 TYR cc_start: 0.6368 (OUTLIER) cc_final: 0.4053 (t80)
REVERT: A 1279 GLU cc_start: 0.5177 (OUTLIER) cc_final: 0.4786 (mt-10)
  outliers start: 55
  outliers final: 44
  residues processed: 152
  average time/residue: 0.0917
  time to fit residues: 20.7181
Evaluate side-chains
  159 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 108
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 GLU
Chi-restraints excluded: chain A residue  105 SER
Chi-restraints excluded: chain A residue  107 TYR
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  166 CYS
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  214 LEU
Chi-restraints excluded: chain A residue  218 LYS
Chi-restraints excluded: chain A residue  222 THR
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  263 LYS
Chi-restraints excluded: chain A residue  305 VAL
Chi-restraints excluded: chain A residue  346 LEU
Chi-restraints excluded: chain A residue  351 SER
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  473 VAL
Chi-restraints excluded: chain A residue  568 VAL
Chi-restraints excluded: chain A residue  575 ASP
Chi-restraints excluded: chain A residue  653 THR
Chi-restraints excluded: chain A residue  661 ILE
Chi-restraints excluded: chain A residue  670 ILE
Chi-restraints excluded: chain A residue  688 MET
Chi-restraints excluded: chain A residue  734 LEU
Chi-restraints excluded: chain A residue  751 LEU
Chi-restraints excluded: chain A residue  779 LEU
Chi-restraints excluded: chain A residue  788 LEU
Chi-restraints excluded: chain A residue  818 VAL
Chi-restraints excluded: chain A residue  824 PHE
Chi-restraints excluded: chain A residue  978 SER
Chi-restraints excluded: chain A residue  989 ASN
Chi-restraints excluded: chain A residue 1013 THR
Chi-restraints excluded: chain A residue 1015 TYR
Chi-restraints excluded: chain A residue 1054 ASN
Chi-restraints excluded: chain A residue 1065 LEU
Chi-restraints excluded: chain A residue 1104 THR
Chi-restraints excluded: chain A residue 1120 THR
Chi-restraints excluded: chain A residue 1130 LEU
Chi-restraints excluded: chain A residue 1210 ARG
Chi-restraints excluded: chain A residue 1226 MET
Chi-restraints excluded: chain A residue 1236 ASP
Chi-restraints excluded: chain A residue 1257 ARG
Chi-restraints excluded: chain A residue 1275 TYR
Chi-restraints excluded: chain A residue 1279 GLU
Chi-restraints excluded: chain A residue 1305 TYR
Chi-restraints excluded: chain A residue 1358 ILE
Chi-restraints excluded: chain A residue 1373 LEU
Chi-restraints excluded: chain A residue 1379 ILE
Chi-restraints excluded: chain A residue 1415 LEU
Chi-restraints excluded: chain A residue 1452 LEU
Chi-restraints excluded: chain A residue 1493 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 74 optimal weight:    0.0980
   chunk 44 optimal weight:    0.5980
   chunk 82 optimal weight:    5.9990
   chunk 24 optimal weight:    4.9990
   chunk 93 optimal weight:    7.9990
   chunk 90 optimal weight:    0.8980
   chunk 101 optimal weight:    3.9990
   chunk 94 optimal weight:    0.9990
   chunk 12 optimal weight:    7.9990
   chunk 41 optimal weight:    2.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
A1054 ASN
** A1063 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4515 r_free = 0.4515 target = 0.226924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.170107 restraints weight = 13989.441|
|-----------------------------------------------------------------------------|
r_work (start): 0.3900 rms_B_bonded: 4.80
r_work: 0.3513 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.3513
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7637
moved from start:          0.4388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  11392  Z= 0.136
  Angle     :  0.510   8.247  15454  Z= 0.265
  Chirality :  0.038   0.140   1809
  Planarity :  0.003   0.048   1911
  Dihedral  :  7.252 118.545   1552
  Min Nonbonded Distance : 1.971

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 17.47 %
    Favored  : 78.34 %
  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:  2.29 (0.22), residues: 1392
  helix:  2.25 (0.16), residues: 955
  sheet:  0.07 (0.56), residues: 81
  loop : -0.13 (0.33), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 259 
 TYR   0.011   0.001   TYR A  39 
 PHE   0.016   0.001   PHE A1240 
 TRP   0.013   0.001   TRP A1206 
 HIS   0.005   0.001   HIS A 692 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 (11391)
  covalent geometry    : angle       0.51021 (15452)
  SS BOND              : bond        0.00015 (    1)
  SS BOND              : angle       0.61477 (    2)
  hydrogen bonds       : bond        0.05888 (  728)
  hydrogen bonds       : angle       3.95398 ( 2151)

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

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

  2784 Ramachandran restraints generated.
    1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2784 Ramachandran restraints generated.
    1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 109
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7098 (mt-10)
REVERT: A  107 TYR cc_start: 0.7791 (OUTLIER) cc_final: 0.7278 (m-10)
REVERT: A  156 GLN cc_start: 0.7343 (tp40) cc_final: 0.7034 (tt0)
REVERT: A  251 GLN cc_start: 0.7940 (tt0) cc_final: 0.7445 (mt0)
REVERT: A  259 ARG cc_start: 0.7463 (tmm160) cc_final: 0.7155 (ttp80)
REVERT: A  352 ASP cc_start: 0.8257 (m-30) cc_final: 0.7866 (t70)
REVERT: A  523 ASP cc_start: 0.7747 (m-30) cc_final: 0.7328 (t0)
REVERT: A  575 ASP cc_start: 0.7920 (OUTLIER) cc_final: 0.7543 (m-30)
REVERT: A  768 ARG cc_start: 0.7631 (mtm110) cc_final: 0.7411 (mtm180)
REVERT: A  770 SER cc_start: 0.9018 (t) cc_final: 0.8644 (p)
REVERT: A  782 TYR cc_start: 0.8575 (m-80) cc_final: 0.8215 (m-80)
REVERT: A 1006 ASP cc_start: 0.8621 (t0) cc_final: 0.8099 (t0)
REVERT: A 1101 SER cc_start: 0.8173 (m) cc_final: 0.7863 (m)
REVERT: A 1149 ARG cc_start: 0.8304 (mtp180) cc_final: 0.7997 (ttm-80)
REVERT: A 1210 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7569 (mpt180)
REVERT: A 1257 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.7431 (ttm170)
REVERT: A 1275 TYR cc_start: 0.6331 (OUTLIER) cc_final: 0.3962 (t80)
REVERT: A 1279 GLU cc_start: 0.5167 (OUTLIER) cc_final: 0.4709 (mt-10)
  outliers start: 52
  outliers final: 44
  residues processed: 151
  average time/residue: 0.0910
  time to fit residues: 20.4702
Evaluate side-chains
  155 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 104
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 GLU
Chi-restraints excluded: chain A residue  105 SER
Chi-restraints excluded: chain A residue  107 TYR
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  166 CYS
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  214 LEU
Chi-restraints excluded: chain A residue  218 LYS
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  263 LYS
Chi-restraints excluded: chain A residue  305 VAL
Chi-restraints excluded: chain A residue  346 LEU
Chi-restraints excluded: chain A residue  351 SER
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  473 VAL
Chi-restraints excluded: chain A residue  568 VAL
Chi-restraints excluded: chain A residue  575 ASP
Chi-restraints excluded: chain A residue  653 THR
Chi-restraints excluded: chain A residue  661 ILE
Chi-restraints excluded: chain A residue  670 ILE
Chi-restraints excluded: chain A residue  688 MET
Chi-restraints excluded: chain A residue  734 LEU
Chi-restraints excluded: chain A residue  751 LEU
Chi-restraints excluded: chain A residue  779 LEU
Chi-restraints excluded: chain A residue  788 LEU
Chi-restraints excluded: chain A residue  818 VAL
Chi-restraints excluded: chain A residue  824 PHE
Chi-restraints excluded: chain A residue  978 SER
Chi-restraints excluded: chain A residue  989 ASN
Chi-restraints excluded: chain A residue 1013 THR
Chi-restraints excluded: chain A residue 1015 TYR
Chi-restraints excluded: chain A residue 1054 ASN
Chi-restraints excluded: chain A residue 1065 LEU
Chi-restraints excluded: chain A residue 1104 THR
Chi-restraints excluded: chain A residue 1120 THR
Chi-restraints excluded: chain A residue 1130 LEU
Chi-restraints excluded: chain A residue 1139 MET
Chi-restraints excluded: chain A residue 1210 ARG
Chi-restraints excluded: chain A residue 1226 MET
Chi-restraints excluded: chain A residue 1236 ASP
Chi-restraints excluded: chain A residue 1257 ARG
Chi-restraints excluded: chain A residue 1275 TYR
Chi-restraints excluded: chain A residue 1279 GLU
Chi-restraints excluded: chain A residue 1305 TYR
Chi-restraints excluded: chain A residue 1358 ILE
Chi-restraints excluded: chain A residue 1373 LEU
Chi-restraints excluded: chain A residue 1379 ILE
Chi-restraints excluded: chain A residue 1415 LEU
Chi-restraints excluded: chain A residue 1452 LEU
Chi-restraints excluded: chain A residue 1493 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 105 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 46 optimal weight:   10.0000
   chunk 42 optimal weight:    0.0770
   chunk 27 optimal weight:    0.6980
   chunk 96 optimal weight:    0.6980
   chunk 129 optimal weight:   40.0000
   chunk 13 optimal weight:    0.8980
   chunk 38 optimal weight:    0.3980
   chunk 133 optimal weight:    0.5980
   chunk 126 optimal weight:   10.0000
   overall best weight:    0.4938

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

Flipped N/Q/H residues before XYZ refinement:
A1054 ASN
** A1063 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4491 r_free = 0.4491 target = 0.226700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.173781 restraints weight = 13991.663|
|-----------------------------------------------------------------------------|
r_work (start): 0.3957 rms_B_bonded: 4.62
r_work: 0.3481 rms_B_bonded: 4.00 restraints_weight: 0.5000
r_work (final): 0.3481
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7522
moved from start:          0.4536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  11392  Z= 0.117
  Angle     :  0.498  10.264  15454  Z= 0.256
  Chirality :  0.037   0.139   1809
  Planarity :  0.003   0.050   1911
  Dihedral  :  7.179 116.899   1552
  Min Nonbonded Distance : 2.013

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 18.12 %
    Favored  : 78.34 %
  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:  2.44 (0.22), residues: 1392
  helix:  2.37 (0.16), residues: 957
  sheet:  0.11 (0.57), residues: 83
  loop : -0.09 (0.33), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 259 
 TYR   0.011   0.001   TYR A  39 
 PHE   0.012   0.001   PHE A1240 
 TRP   0.012   0.001   TRP A 358 
 HIS   0.005   0.001   HIS A 692 

Details of bonding type rmsd
  covalent geometry    : bond        0.00217 (11391)
  covalent geometry    : angle       0.49805 (15452)
  SS BOND              : bond        0.00061 (    1)
  SS BOND              : angle       0.55584 (    2)
  hydrogen bonds       : bond        0.05437 (  728)
  hydrogen bonds       : angle       3.88493 ( 2151)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3065.02 seconds
wall clock time: 53 minutes 7.88 seconds (3187.88 seconds total)