Starting phenix.real_space_refine
on Fri May 16 00:08:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jzn_36748/05_2025/8jzn_36748.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jzn_36748/05_2025/8jzn_36748.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.47
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jzn_36748/05_2025/8jzn_36748.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jzn_36748/05_2025/8jzn_36748.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jzn_36748/05_2025/8jzn_36748.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jzn_36748/05_2025/8jzn_36748.cif"
  }
  resolution = 2.47
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.094
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: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      72      5.16       5
     C    8520      2.51       5
     N    2042      2.21       5
     O    2195      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 89 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 12831
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 12155
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1489, 12155
          Classifications: {'peptide': 1489}
          Link IDs: {'PTRANS': 66, 'TRANS': 1422}
          Chain breaks: 13
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 648
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 18, 648
          Unusual residues: {'AV0': 2, 'ERG': 14, 'POV': 2}
          Classifications: {'undetermined': 18}
          Link IDs: {None: 17}
  Time building chain proxies: 8.00, per 1000 atoms: 0.62
  Number of scatterers: 12831
  At special positions: 0
  Unit cell: (100.244, 117.127, 135.066, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      72     16.00
     P       2     15.00
     O    2195      8.00
     N    2042      7.00
     C    8520      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 658 " - pdb=" SG  CYS A 669 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1328 " - pdb=" SG  CYS A1345 " distance=2.03

  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
  Links applied
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
    NAG-ASN
      " NAG B   1 " - " ASN A1849 "
  Time building additional restraints: 3.87
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2828

  Finding SS restraints...
    Secondary structure from input PDB file:
      78 helices and 3 sheets defined
      67.0% alpha, 4.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.52
  Creating SS restraints...
    Processing helix  chain 'A' and resid 148 through 153
    Processing helix  chain 'A' and resid 160 through 176
    Processing helix  chain 'A' and resid 178 through 197
    Processing helix  chain 'A' and resid 201 through 214
    Processing helix  chain 'A' and resid 219 through 229
    Processing helix  chain 'A' and resid 232 through 245
      removed outlier: 3.764A  pdb=" N   LYS A 245 " --> pdb=" O   MET A 241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 295
      removed outlier: 3.560A  pdb=" N   GLN A 295 " --> pdb=" O   ALA A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 313
    Processing helix  chain 'A' and resid 321 through 337
      removed outlier: 3.511A  pdb=" N   LEU A 325 " --> pdb=" O   THR A 321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 343
    Processing helix  chain 'A' and resid 351 through 357
    Processing helix  chain 'A' and resid 357 through 369
      removed outlier: 3.981A  pdb=" N   ILE A 361 " --> pdb=" O   VAL A 357 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   VAL A 369 " --> pdb=" O   ILE A 365 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 395
    Processing helix  chain 'A' and resid 396 through 398
      No H-bonds generated for 'chain 'A' and resid 396 through 398'
    Processing helix  chain 'A' and resid 399 through 404
    Processing helix  chain 'A' and resid 413 through 417
    Processing helix  chain 'A' and resid 418 through 426
      removed outlier: 3.713A  pdb=" N   ARG A 422 " --> pdb=" O   LEU A 419 " (cutoff:3.500A)
      removed outlier: 4.871A  pdb=" N   TYR A 423 " --> pdb=" O   GLU A 420 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   LEU A 424 " --> pdb=" O   GLU A 421 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 434
    Processing helix  chain 'A' and resid 443 through 452
      removed outlier: 3.696A  pdb=" N   HIS A 447 " --> pdb=" O   ARG A 443 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   THR A 450 " --> pdb=" O   LEU A 446 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 452 through 470
      removed outlier: 3.663A  pdb=" N   MET A 458 " --> pdb=" O   ARG A 454 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   HIS A 459 " --> pdb=" O   ILE A 455 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   MET A 465 " --> pdb=" O   SER A 461 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 471 through 475
      removed outlier: 3.505A  pdb=" N   TYR A 475 " --> pdb=" O   PRO A 472 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 488 through 497
      removed outlier: 4.060A  pdb=" N   LYS A 492 " --> pdb=" O   LEU A 488 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 497 through 515
      removed outlier: 4.061A  pdb=" N   THR A 501 " --> pdb=" O   ALA A 497 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 526 through 552
      Proline residue:  A 545  - end of helix
    Processing helix  chain 'A' and resid 559 through 583
      removed outlier: 4.736A  pdb=" N   VAL A 565 " --> pdb=" O   ALA A 561 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   PHE A 571 " --> pdb=" O   ALA A 567 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 603 through 608
    Processing helix  chain 'A' and resid 615 through 639
      removed outlier: 3.587A  pdb=" N   TRP A 625 " --> pdb=" O   SER A 621 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   TYR A 637 " --> pdb=" O   TYR A 633 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   TYR A 638 " --> pdb=" O   SER A 634 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 641 through 643
      No H-bonds generated for 'chain 'A' and resid 641 through 643'
    Processing helix  chain 'A' and resid 644 through 652
    Processing helix  chain 'A' and resid 671 through 711
      removed outlier: 3.608A  pdb=" N   ILE A 686 " --> pdb=" O   ALA A 682 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   PHE A 689 " --> pdb=" O   PHE A 685 " (cutoff:3.500A)
      removed outlier: 4.078A  pdb=" N   THR A 692 " --> pdb=" O   PHE A 688 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   TYR A 693 " --> pdb=" O   PHE A 689 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   SER A 708 " --> pdb=" O   SER A 704 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 718 through 725
      removed outlier: 3.761A  pdb=" N   ILE A 722 " --> pdb=" O   PRO A 718 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   ARG A 725 " --> pdb=" O   ASN A 721 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 725 through 734
      removed outlier: 3.543A  pdb=" N   TYR A 731 " --> pdb=" O   PRO A 727 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 745 through 764
      removed outlier: 3.737A  pdb=" N   LEU A 749 " --> pdb=" O   LYS A 745 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   ALA A 756 " --> pdb=" O   GLN A 752 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 768 through 774
      removed outlier: 3.906A  pdb=" N   LYS A 774 " --> pdb=" O   ASP A 770 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 794 through 799
      removed outlier: 3.992A  pdb=" N   GLN A 799 " --> pdb=" O   PHE A 795 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 813 through 826
    Processing helix  chain 'A' and resid 835 through 839
    Processing helix  chain 'A' and resid 856 through 862
    Processing helix  chain 'A' and resid 871 through 880
      removed outlier: 3.556A  pdb=" N   GLN A 878 " --> pdb=" O   GLU A 874 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 880 through 899
    Processing helix  chain 'A' and resid 933 through 945
      removed outlier: 3.596A  pdb=" N   THR A 939 " --> pdb=" O   TYR A 935 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 949 through 958
      removed outlier: 3.563A  pdb=" N   THR A 953 " --> pdb=" O   THR A 949 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 958 through 971
    Processing helix  chain 'A' and resid 972 through 980
      removed outlier: 3.556A  pdb=" N   PHE A 979 " --> pdb=" O   ILE A 975 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 982 through 997
      removed outlier: 3.520A  pdb=" N   GLU A 989 " --> pdb=" O   GLY A 985 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1006 through 1010
    Processing helix  chain 'A' and resid 1011 through 1025
    Processing helix  chain 'A' and resid 1081 through 1089
    Processing helix  chain 'A' and resid 1090 through 1093
    Processing helix  chain 'A' and resid 1108 through 1113
    Processing helix  chain 'A' and resid 1114 through 1119
    Processing helix  chain 'A' and resid 1120 through 1123
    Processing helix  chain 'A' and resid 1138 through 1142
    Processing helix  chain 'A' and resid 1172 through 1187
      removed outlier: 3.993A  pdb=" N   THR A1178 " --> pdb=" O   GLN A1174 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   LEU A1179 " --> pdb=" O   THR A1175 " (cutoff:3.500A)
      removed outlier: 4.913A  pdb=" N   ARG A1182 " --> pdb=" O   THR A1178 " (cutoff:3.500A)
      removed outlier: 5.282A  pdb=" N   THR A1183 " --> pdb=" O   LEU A1179 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1201 through 1206
      removed outlier: 3.547A  pdb=" N   THR A1206 " --> pdb=" O   THR A1202 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1227 through 1232
    Processing helix  chain 'A' and resid 1267 through 1271
      removed outlier: 3.927A  pdb=" N   MET A1270 " --> pdb=" O   GLY A1267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1272 through 1280
      removed outlier: 3.661A  pdb=" N   TYR A1276 " --> pdb=" O   SER A1272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1283 through 1294
      removed outlier: 3.531A  pdb=" N   THR A1289 " --> pdb=" O   ASP A1285 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   HIS A1294 " --> pdb=" O   PHE A1290 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1294 through 1325
      removed outlier: 3.625A  pdb=" N   HIS A1298 " --> pdb=" O   HIS A1294 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   ASN A1317 " --> pdb=" O   LEU A1313 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   GLU A1324 " --> pdb=" O   SER A1320 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1348 through 1353
    Processing helix  chain 'A' and resid 1353 through 1368
    Processing helix  chain 'A' and resid 1370 through 1381
    Processing helix  chain 'A' and resid 1384 through 1397
      removed outlier: 3.768A  pdb=" N   GLN A1388 " --> pdb=" O   TRP A1384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1437 through 1445
      removed outlier: 4.119A  pdb=" N   SER A1443 " --> pdb=" O   SER A1439 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   PHE A1445 " --> pdb=" O   LEU A1441 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1449 through 1467
    Processing helix  chain 'A' and resid 1471 through 1485
      removed outlier: 4.171A  pdb=" N   PHE A1475 " --> pdb=" O   PRO A1471 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   LEU A1482 " --> pdb=" O   SER A1478 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1495 through 1512
      removed outlier: 3.610A  pdb=" N   PHE A1500 " --> pdb=" O   TRP A1496 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   LEU A1501 " --> pdb=" O   GLU A1497 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1560 through 1565
    Processing helix  chain 'A' and resid 1565 through 1583
    Processing helix  chain 'A' and resid 1597 through 1623
      removed outlier: 3.813A  pdb=" N   ARG A1601 " --> pdb=" O   ASN A1597 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   ILE A1602 " --> pdb=" O   SER A1598 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   ALA A1608 " --> pdb=" O   ILE A1604 " (cutoff:3.500A)
      Proline residue:  A1609  - end of helix
      removed outlier: 3.698A  pdb=" N   LEU A1617 " --> pdb=" O   ASN A1613 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   PHE A1619 " --> pdb=" O   GLY A1615 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1640 through 1665
      removed outlier: 3.645A  pdb=" N   ILE A1645 " --> pdb=" O   VAL A1641 " (cutoff:3.500A)
      removed outlier: 4.468A  pdb=" N   ALA A1646 " --> pdb=" O   MET A1642 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1668 through 1694
      removed outlier: 3.652A  pdb=" N   ILE A1674 " --> pdb=" O   VAL A1670 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1725 through 1753
      removed outlier: 3.739A  pdb=" N   GLU A1729 " --> pdb=" O   GLN A1725 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   LEU A1730 " --> pdb=" O   PRO A1726 " (cutoff:3.500A)
      removed outlier: 4.253A  pdb=" N   ALA A1732 " --> pdb=" O   ARG A1728 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   LYS A1733 " --> pdb=" O   GLU A1729 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   GLU A1736 " --> pdb=" O   ALA A1732 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   SER A1738 " --> pdb=" O   VAL A1734 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1754 through 1759
      removed outlier: 3.778A  pdb=" N   ILE A1759 " --> pdb=" O   LEU A1755 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1763 through 1774
      removed outlier: 4.276A  pdb=" N   MET A1770 " --> pdb=" O   PHE A1766 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   LEU A1774 " --> pdb=" O   MET A1770 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1786 through 1800
      removed outlier: 3.949A  pdb=" N   ARG A1791 " --> pdb=" O   LEU A1787 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   LEU A1792 " --> pdb=" O   LYS A1788 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1800 through 1821
      removed outlier: 3.755A  pdb=" N   LEU A1806 " --> pdb=" O   SER A1802 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   ILE A1815 " --> pdb=" O   PHE A1811 " (cutoff:3.500A)
      Proline residue:  A1818  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 370 through 373
      removed outlier: 3.728A  pdb=" N   ARG A 376 " --> pdb=" O   VAL A 373 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 778 through 781
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1068 through 1071
      removed outlier: 3.759A  pdb=" N   PHE A1068 " --> pdb=" O   LEU A1051 " (cutoff:3.500A)
      removed outlier: 4.094A  pdb=" N   LEU A1033 " --> pdb=" O   MET A1004 " (cutoff:3.500A)
      removed outlier: 6.584A  pdb=" N   PHE A 842 " --> pdb=" O   LYS A 999 " (cutoff:3.500A)
      removed outlier: 7.712A  pdb=" N   LEU A1001 " --> pdb=" O   PHE A 842 " (cutoff:3.500A)
      removed outlier: 5.948A  pdb=" N   VAL A 844 " --> pdb=" O   LEU A1001 " (cutoff:3.500A)
      removed outlier: 7.190A  pdb=" N   SER A1003 " --> pdb=" O   VAL A 844 " (cutoff:3.500A)
      removed outlier: 6.766A  pdb=" N   THR A 846 " --> pdb=" O   SER A1003 " (cutoff:3.500A)
      removed outlier: 6.515A  pdb=" N   THR A 843 " --> pdb=" O   GLN A1099 " (cutoff:3.500A)
      removed outlier: 6.642A  pdb=" N   ALA A1149 " --> pdb=" O   ASN A1200 " (cutoff:3.500A)
      removed outlier: 12.749A  pdb=" N   VAL A1148 " --> pdb=" O   HIS A1238 " (cutoff:3.500A)
      removed outlier: 15.753A  pdb=" N   GLU A1240 " --> pdb=" O   VAL A1148 " (cutoff:3.500A)
      removed outlier: 16.918A  pdb=" N   ILE A1150 " --> pdb=" O   GLU A1240 " (cutoff:3.500A)
      removed outlier: 13.110A  pdb=" N   TYR A1242 " --> pdb=" O   ILE A1150 " (cutoff:3.500A)
      removed outlier: 8.859A  pdb=" N   GLY A1152 " --> pdb=" O   TYR A1242 " (cutoff:3.500A)
      removed outlier: 9.289A  pdb=" N   CYS A1244 " --> pdb=" O   GLY A1152 " (cutoff:3.500A)
      removed outlier: 6.886A  pdb=" N   ARG A1154 " --> pdb=" O   CYS A1244 " (cutoff:3.500A)
      removed outlier: 7.491A  pdb=" N   LYS A1246 " --> pdb=" O   ARG A1154 " (cutoff:3.500A)
      removed outlier: 5.682A  pdb=" N   TYR A1156 " --> pdb=" O   LYS A1246 " (cutoff:3.500A)

    640 hydrogen bonds defined for protein.
    1857 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: 5.07

  Time building geometry restraints manager: 4.39 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1892
        1.31 -     1.43: 3698
        1.43 -     1.56: 7258
        1.56 -     1.68: 229
        1.68 -     1.81: 126
  Bond restraints: 13203
  Sorted by residual:
  bond pdb=" C5  ERG A1912 "
       pdb=" C6  ERG A1912 "
    ideal  model  delta    sigma   weight residual
    1.338  1.617 -0.279 2.00e-02 2.50e+03 1.95e+02
  bond pdb=" C5  ERG A1908 "
       pdb=" C6  ERG A1908 "
    ideal  model  delta    sigma   weight residual
    1.338  1.612 -0.274 2.00e-02 2.50e+03 1.88e+02
  bond pdb=" C5  ERG A1913 "
       pdb=" C6  ERG A1913 "
    ideal  model  delta    sigma   weight residual
    1.338  1.612 -0.274 2.00e-02 2.50e+03 1.87e+02
  bond pdb=" C5  ERG A1915 "
       pdb=" C6  ERG A1915 "
    ideal  model  delta    sigma   weight residual
    1.338  1.611 -0.273 2.00e-02 2.50e+03 1.86e+02
  bond pdb=" C5  ERG A1906 "
       pdb=" C6  ERG A1906 "
    ideal  model  delta    sigma   weight residual
    1.338  1.611 -0.273 2.00e-02 2.50e+03 1.86e+02
  ... (remaining 13198 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.66: 17289
        2.66 -     5.33: 518
        5.33 -     7.99: 115
        7.99 -    10.65: 45
       10.65 -    13.32: 11
  Bond angle restraints: 17978
  Sorted by residual:
  angle pdb=" N   VAL A 705 "
        pdb=" CA  VAL A 705 "
        pdb=" C   VAL A 705 "
      ideal   model   delta    sigma   weight residual
     111.90  107.98    3.92 8.10e-01 1.52e+00 2.34e+01
  angle pdb=" C14 ERG A1917 "
        pdb=" C8  ERG A1917 "
        pdb=" C9  ERG A1917 "
      ideal   model   delta    sigma   weight residual
     116.25  102.93   13.32 3.00e+00 1.11e-01 1.97e+01
  angle pdb=" C14 ERG A1904 "
        pdb=" C8  ERG A1904 "
        pdb=" C9  ERG A1904 "
      ideal   model   delta    sigma   weight residual
     116.25  103.29   12.96 3.00e+00 1.11e-01 1.86e+01
  angle pdb=" C14 ERG A1909 "
        pdb=" C8  ERG A1909 "
        pdb=" C9  ERG A1909 "
      ideal   model   delta    sigma   weight residual
     116.25  103.98   12.27 3.00e+00 1.11e-01 1.67e+01
  angle pdb=" N   MET A 458 "
        pdb=" CA  MET A 458 "
        pdb=" C   MET A 458 "
      ideal   model   delta    sigma   weight residual
     111.14  115.49   -4.35 1.08e+00 8.57e-01 1.62e+01
  ... (remaining 17973 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.37: 8138
       34.37 -    68.74: 434
       68.74 -   103.11: 64
      103.11 -   137.48: 26
      137.48 -   171.85: 3
  Dihedral angle restraints: 8665
    sinusoidal: 4292
      harmonic: 4373
  Sorted by residual:
  dihedral pdb=" CA  HIS A1826 "
           pdb=" C   HIS A1826 "
           pdb=" N   LYS A1827 "
           pdb=" CA  LYS A1827 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.86  -28.14     0      5.00e+00 4.00e-02 3.17e+01
  dihedral pdb=" CA  ALA A 525 "
           pdb=" C   ALA A 525 "
           pdb=" N   GLN A 526 "
           pdb=" CA  GLN A 526 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.35   25.65     0      5.00e+00 4.00e-02 2.63e+01
  dihedral pdb=" CA  LEU A1340 "
           pdb=" C   LEU A1340 "
           pdb=" N   VAL A1341 "
           pdb=" CA  VAL A1341 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.58  -23.42     0      5.00e+00 4.00e-02 2.19e+01
  ... (remaining 8662 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.125: 1924
       0.125 -    0.250: 59
       0.250 -    0.375: 16
       0.375 -    0.500: 6
       0.500 -    0.625: 19
  Chirality restraints: 2024
  Sorted by residual:
  chirality pdb=" C13 ERG A1905 "
            pdb=" C12 ERG A1905 "
            pdb=" C14 ERG A1905 "
            pdb=" C17 ERG A1905 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -2.30   -0.63 2.00e-01 2.50e+01 9.77e+00
  chirality pdb=" C13 ERG A1911 "
            pdb=" C12 ERG A1911 "
            pdb=" C14 ERG A1911 "
            pdb=" C17 ERG A1911 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -2.30   -0.62 2.00e-01 2.50e+01 9.64e+00
  chirality pdb=" C13 ERG A1916 "
            pdb=" C12 ERG A1916 "
            pdb=" C14 ERG A1916 "
            pdb=" C17 ERG A1916 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -2.31   -0.62 2.00e-01 2.50e+01 9.58e+00
  ... (remaining 2021 not shown)

  Planarity restraints: 2148
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A1036 "    0.044 5.00e-02 4.00e+02   6.66e-02 7.09e+00
        pdb=" N   PRO A1037 "   -0.115 5.00e-02 4.00e+02
        pdb=" CA  PRO A1037 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO A1037 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A1775 "    0.037 5.00e-02 4.00e+02   5.62e-02 5.06e+00
        pdb=" N   PRO A1776 "   -0.097 5.00e-02 4.00e+02
        pdb=" CA  PRO A1776 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A1776 "    0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 544 "   -0.036 5.00e-02 4.00e+02   5.52e-02 4.87e+00
        pdb=" N   PRO A 545 "    0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO A 545 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 545 "   -0.031 5.00e-02 4.00e+02
  ... (remaining 2145 not shown)

  Histogram of nonbonded interaction distances:
        1.78 -     2.41: 37
        2.41 -     3.03: 7321
        3.03 -     3.65: 18792
        3.65 -     4.28: 30717
        4.28 -     4.90: 49456
  Nonbonded interactions: 106323
  Sorted by model distance:
  nonbonded pdb=" OAI AV0 A1902 "
            pdb=" OAS AV0 A1902 "
     model   vdw
     1.784 3.040
  nonbonded pdb=" OG1 THR A1040 "
            pdb=" OE1 GLU A1043 "
     model   vdw
     2.199 3.040
  nonbonded pdb=" O4  AV0 A1902 "
            pdb=" OAQ AV0 A1902 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" OE2 GLU A 984 "
            pdb=" NH1 ARG A 988 "
     model   vdw
     2.207 3.120
  nonbonded pdb=" OE1 GLU A 661 "
            pdb=" OG  SER A1598 "
     model   vdw
     2.216 3.040
  ... (remaining 106318 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== 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:             2.750
  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:          0.510
  Check model and map are aligned:         0.090
  Set scattering table:                    0.130
  Process input model:                     32.450
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:10.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   47.080
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7628
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      :  0.019   0.279  13207  Z= 0.929
  Angle     :  1.122  13.317  17988  Z= 0.472
  Chirality :  0.084   0.625   2024
  Planarity :  0.005   0.067   2147
  Dihedral  : 21.229 171.849   5831
  Min Nonbonded Distance : 1.784

Molprobity Statistics.
  All-atom Clashscore : 9.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 16.42 %
    Favored  : 81.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.06 (0.20), residues: 1461
  helix: -1.58 (0.15), residues: 863
  sheet: -0.39 (0.57), residues: 76
  loop : -0.77 (0.27), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 493 
 HIS   0.010   0.001   HIS A1195 
 PHE   0.027   0.002   PHE A1657 
 TYR   0.017   0.002   TYR A1804 
 ARG   0.021   0.001   ARG A 791 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00116 (    1)
  link_NAG-ASN         : angle       2.54639 (    3)
  link_BETA1-4         : bond        0.00487 (    1)
  link_BETA1-4         : angle       3.09471 (    3)
  hydrogen bonds       : bond        0.25260 (  640)
  hydrogen bonds       : angle       8.66458 ( 1857)
  SS BOND              : bond        0.00377 (    2)
  SS BOND              : angle       0.74026 (    4)
  covalent geometry    : bond        0.01889 (13203)
  covalent geometry    : angle       1.12131 (17978)

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

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

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 150
  time to evaluate  : 1.442 
Fit side-chains
REVERT: A  601 VAL cc_start: 0.8113 (t) cc_final: 0.7873 (m)
REVERT: A  745 LYS cc_start: 0.7991 (ttmt) cc_final: 0.7718 (mptt)
REVERT: A  763 ARG cc_start: 0.7699 (mmt180) cc_final: 0.7022 (mtm-85)
REVERT: A  791 ARG cc_start: 0.7728 (ptp-110) cc_final: 0.6985 (ptm-80)
REVERT: A 1202 THR cc_start: 0.8871 (OUTLIER) cc_final: 0.8544 (m)
REVERT: A 1770 MET cc_start: 0.6790 (mpt) cc_final: 0.5661 (mmp)
  outliers start: 25
  outliers final: 17
  residues processed: 167
  average time/residue: 1.2652
  time to fit residues: 231.3346
Evaluate side-chains
  164 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 146
  time to evaluate  : 1.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 ILE
Chi-restraints excluded: chain A residue  444 THR
Chi-restraints excluded: chain A residue  473 THR
Chi-restraints excluded: chain A residue  527 HIS
Chi-restraints excluded: chain A residue  607 THR
Chi-restraints excluded: chain A residue  610 PHE
Chi-restraints excluded: chain A residue  616 LEU
Chi-restraints excluded: chain A residue  634 SER
Chi-restraints excluded: chain A residue 1088 HIS
Chi-restraints excluded: chain A residue 1130 VAL
Chi-restraints excluded: chain A residue 1154 ARG
Chi-restraints excluded: chain A residue 1202 THR
Chi-restraints excluded: chain A residue 1308 LEU
Chi-restraints excluded: chain A residue 1316 VAL
Chi-restraints excluded: chain A residue 1378 LEU
Chi-restraints excluded: chain A residue 1566 ILE
Chi-restraints excluded: chain A residue 1751 LEU
Chi-restraints excluded: chain A residue 1752 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 124 optimal weight:    0.8980
   chunk 112 optimal weight:    2.9990
   chunk 62 optimal weight:    5.9990
   chunk 38 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9980
   chunk 59 optimal weight:    1.9990
   chunk 116 optimal weight:    0.9980
   chunk 44 optimal weight:    0.6980
   chunk 70 optimal weight:    6.9990
   chunk 86 optimal weight:    0.9990
   chunk 134 optimal weight:    0.7980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 453 ASN
A 459 HIS
A 507 GLN
A 721 ASN
** A1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1228 ASN
A1269 GLN
A1388 GLN
A1688 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.156829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.106019 restraints weight = 14262.833|
|-----------------------------------------------------------------------------|
r_work (start): 0.3255 rms_B_bonded: 2.63
r_work: 0.3092 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.2948 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.2948
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7412
moved from start:          0.1354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  13207  Z= 0.152
  Angle     :  0.674   9.872  17988  Z= 0.326
  Chirality :  0.044   0.187   2024
  Planarity :  0.005   0.055   2147
  Dihedral  : 15.945 167.596   2984
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 15.28 %
    Favored  : 81.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.42 (0.21), residues: 1461
  helix: -0.07 (0.16), residues: 892
  sheet:  0.43 (0.65), residues: 66
  loop : -0.49 (0.28), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 664 
 HIS   0.010   0.001   HIS A1195 
 PHE   0.017   0.002   PHE A1581 
 TYR   0.017   0.001   TYR A1503 
 ARG   0.008   0.000   ARG A 791 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00207 (    1)
  link_NAG-ASN         : angle       1.82261 (    3)
  link_BETA1-4         : bond        0.00101 (    1)
  link_BETA1-4         : angle       1.80825 (    3)
  hydrogen bonds       : bond        0.05243 (  640)
  hydrogen bonds       : angle       4.91333 ( 1857)
  SS BOND              : bond        0.00385 (    2)
  SS BOND              : angle       0.50479 (    4)
  covalent geometry    : bond        0.00341 (13203)
  covalent geometry    : angle       0.67361 (17978)

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

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

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 159
  time to evaluate  : 1.247 
Fit side-chains
   revert: symmetry clash
REVERT: A  386 LYS cc_start: 0.8585 (mmmt) cc_final: 0.7765 (mmtt)
REVERT: A  443 ARG cc_start: 0.7761 (mtm180) cc_final: 0.6236 (mtm110)
REVERT: A  518 VAL cc_start: 0.8619 (OUTLIER) cc_final: 0.8357 (m)
REVERT: A  533 TRP cc_start: 0.7149 (t60) cc_final: 0.5486 (m100)
REVERT: A  640 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8060 (mp)
REVERT: A  645 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.7674 (ttm110)
REVERT: A  725 ARG cc_start: 0.6067 (OUTLIER) cc_final: 0.5634 (mtm180)
REVERT: A  745 LYS cc_start: 0.7692 (ttmt) cc_final: 0.7164 (mptt)
REVERT: A  791 ARG cc_start: 0.7523 (ptp-110) cc_final: 0.6385 (ptm-80)
REVERT: A  794 THR cc_start: 0.8420 (p) cc_final: 0.8124 (t)
REVERT: A  809 PHE cc_start: 0.7906 (OUTLIER) cc_final: 0.7087 (p90)
REVERT: A  974 GLU cc_start: 0.7487 (pm20) cc_final: 0.7265 (pm20)
REVERT: A 1088 HIS cc_start: 0.8116 (OUTLIER) cc_final: 0.7041 (t70)
REVERT: A 1202 THR cc_start: 0.8866 (t) cc_final: 0.8611 (m)
REVERT: A 1269 GLN cc_start: 0.7358 (OUTLIER) cc_final: 0.6235 (mm-40)
REVERT: A 1642 MET cc_start: 0.6559 (tmm) cc_final: 0.5980 (pmm)
REVERT: A 1739 GLU cc_start: 0.7217 (mm-30) cc_final: 0.6975 (tp30)
REVERT: A 1836 VAL cc_start: 0.8041 (m) cc_final: 0.7772 (p)
  outliers start: 38
  outliers final: 11
  residues processed: 181
  average time/residue: 1.1117
  time to fit residues: 221.2316
Evaluate side-chains
  160 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 142
  time to evaluate  : 1.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 ILE
Chi-restraints excluded: chain A residue  473 THR
Chi-restraints excluded: chain A residue  518 VAL
Chi-restraints excluded: chain A residue  527 HIS
Chi-restraints excluded: chain A residue  607 THR
Chi-restraints excluded: chain A residue  610 PHE
Chi-restraints excluded: chain A residue  616 LEU
Chi-restraints excluded: chain A residue  640 LEU
Chi-restraints excluded: chain A residue  645 ARG
Chi-restraints excluded: chain A residue  667 VAL
Chi-restraints excluded: chain A residue  725 ARG
Chi-restraints excluded: chain A residue  741 GLU
Chi-restraints excluded: chain A residue  809 PHE
Chi-restraints excluded: chain A residue 1088 HIS
Chi-restraints excluded: chain A residue 1269 GLN
Chi-restraints excluded: chain A residue 1316 VAL
Chi-restraints excluded: chain A residue 1649 VAL
Chi-restraints excluded: chain A residue 1847 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 52 optimal weight:    0.9990
   chunk 55 optimal weight:    5.9990
   chunk 105 optimal weight:    0.9990
   chunk 143 optimal weight:    0.7980
   chunk 116 optimal weight:    1.9990
   chunk 28 optimal weight:    0.7980
   chunk 140 optimal weight:    0.1980
   chunk 45 optimal weight:    3.9990
   chunk 120 optimal weight:    2.9990
   chunk 26 optimal weight:    0.8980
   chunk 115 optimal weight:    0.1980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 721 ASN
** A1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1269 GLN
A1688 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.157985 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.106602 restraints weight = 14246.630|
|-----------------------------------------------------------------------------|
r_work (start): 0.3265 rms_B_bonded: 2.77
r_work: 0.3107 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.2963 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.2963
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7378
moved from start:          0.1690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  13207  Z= 0.121
  Angle     :  0.592   9.511  17988  Z= 0.288
  Chirality :  0.040   0.155   2024
  Planarity :  0.004   0.052   2147
  Dihedral  : 13.754 172.596   2966
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 15.81 %
    Favored  : 80.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.34 (0.22), residues: 1461
  helix:  0.64 (0.17), residues: 887
  sheet:  0.54 (0.66), residues: 66
  loop : -0.39 (0.28), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 664 
 HIS   0.009   0.001   HIS A1195 
 PHE   0.014   0.001   PHE A1581 
 TYR   0.016   0.001   TYR A1503 
 ARG   0.008   0.000   ARG A 852 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00199 (    1)
  link_NAG-ASN         : angle       1.76143 (    3)
  link_BETA1-4         : bond        0.00333 (    1)
  link_BETA1-4         : angle       1.87228 (    3)
  hydrogen bonds       : bond        0.04600 (  640)
  hydrogen bonds       : angle       4.50400 ( 1857)
  SS BOND              : bond        0.00398 (    2)
  SS BOND              : angle       0.50877 (    4)
  covalent geometry    : bond        0.00265 (13203)
  covalent geometry    : angle       0.59145 (17978)

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

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

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 156
  time to evaluate  : 1.564 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  386 LYS cc_start: 0.8585 (mmmt) cc_final: 0.7788 (mmtt)
REVERT: A  443 ARG cc_start: 0.7768 (mtm180) cc_final: 0.6230 (mtm110)
REVERT: A  518 VAL cc_start: 0.8588 (OUTLIER) cc_final: 0.8363 (m)
REVERT: A  533 TRP cc_start: 0.7297 (t60) cc_final: 0.5461 (m100)
REVERT: A  719 TRP cc_start: 0.6788 (m100) cc_final: 0.6564 (m100)
REVERT: A  741 GLU cc_start: 0.6047 (OUTLIER) cc_final: 0.5836 (pt0)
REVERT: A  745 LYS cc_start: 0.7576 (ttmt) cc_final: 0.7112 (mptt)
REVERT: A  763 ARG cc_start: 0.7652 (mmt180) cc_final: 0.6721 (mtm-85)
REVERT: A  791 ARG cc_start: 0.7428 (ptp-110) cc_final: 0.6378 (ptm-80)
REVERT: A  794 THR cc_start: 0.8333 (p) cc_final: 0.8054 (t)
REVERT: A  809 PHE cc_start: 0.7941 (OUTLIER) cc_final: 0.6966 (p90)
REVERT: A 1088 HIS cc_start: 0.8103 (OUTLIER) cc_final: 0.7015 (t70)
REVERT: A 1202 THR cc_start: 0.8861 (t) cc_final: 0.8596 (m)
REVERT: A 1268 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.6968 (tt0)
REVERT: A 1269 GLN cc_start: 0.7377 (OUTLIER) cc_final: 0.6254 (mm-40)
REVERT: A 1690 MET cc_start: 0.6168 (OUTLIER) cc_final: 0.5922 (mtt)
REVERT: A 1694 MET cc_start: 0.5444 (OUTLIER) cc_final: 0.4775 (mpt)
REVERT: A 1836 VAL cc_start: 0.7737 (m) cc_final: 0.7452 (p)
  outliers start: 48
  outliers final: 15
  residues processed: 185
  average time/residue: 1.1746
  time to fit residues: 238.5609
Evaluate side-chains
  167 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 144
  time to evaluate  : 1.459 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 ILE
Chi-restraints excluded: chain A residue  348 MET
Chi-restraints excluded: chain A residue  440 LYS
Chi-restraints excluded: chain A residue  473 THR
Chi-restraints excluded: chain A residue  518 VAL
Chi-restraints excluded: chain A residue  527 HIS
Chi-restraints excluded: chain A residue  541 ILE
Chi-restraints excluded: chain A residue  610 PHE
Chi-restraints excluded: chain A residue  616 LEU
Chi-restraints excluded: chain A residue  667 VAL
Chi-restraints excluded: chain A residue  734 ILE
Chi-restraints excluded: chain A residue  741 GLU
Chi-restraints excluded: chain A residue  761 MET
Chi-restraints excluded: chain A residue  809 PHE
Chi-restraints excluded: chain A residue 1088 HIS
Chi-restraints excluded: chain A residue 1268 GLU
Chi-restraints excluded: chain A residue 1269 GLN
Chi-restraints excluded: chain A residue 1308 LEU
Chi-restraints excluded: chain A residue 1316 VAL
Chi-restraints excluded: chain A residue 1690 MET
Chi-restraints excluded: chain A residue 1694 MET
Chi-restraints excluded: chain A residue 1751 LEU
Chi-restraints excluded: chain A residue 1847 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 77 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 67 optimal weight:    3.9990
   chunk 87 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 133 optimal weight:    3.9990
   chunk 69 optimal weight:    4.9990
   chunk 53 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9980
   chunk 56 optimal weight:    0.9990
   chunk 82 optimal weight:    2.9990
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
A 721 ASN
** A1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1688 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.154660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.101992 restraints weight = 14210.015|
|-----------------------------------------------------------------------------|
r_work (start): 0.3208 rms_B_bonded: 2.28
r_work: 0.3063 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.2920 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.2920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7425
moved from start:          0.1554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.050  13207  Z= 0.232
  Angle     :  0.676  10.994  17988  Z= 0.330
  Chirality :  0.045   0.185   2024
  Planarity :  0.005   0.052   2147
  Dihedral  : 13.272 177.539   2965
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 16.50 %
    Favored  : 79.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.28 (0.22), residues: 1461
  helix:  0.66 (0.17), residues: 884
  sheet:  0.36 (0.65), residues: 66
  loop : -0.51 (0.28), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 625 
 HIS   0.007   0.001   HIS A1195 
 PHE   0.016   0.002   PHE A1581 
 TYR   0.019   0.002   TYR A 308 
 ARG   0.006   0.001   ARG A 852 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00320 (    1)
  link_NAG-ASN         : angle       1.90613 (    3)
  link_BETA1-4         : bond        0.00284 (    1)
  link_BETA1-4         : angle       2.50124 (    3)
  hydrogen bonds       : bond        0.05174 (  640)
  hydrogen bonds       : angle       4.57876 ( 1857)
  SS BOND              : bond        0.00410 (    2)
  SS BOND              : angle       0.51878 (    4)
  covalent geometry    : bond        0.00562 (13203)
  covalent geometry    : angle       0.67506 (17978)

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

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

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 148
  time to evaluate  : 1.506 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  230 LEU cc_start: 0.7635 (OUTLIER) cc_final: 0.7232 (mt)
REVERT: A  386 LYS cc_start: 0.8583 (mmmt) cc_final: 0.7764 (mmtt)
REVERT: A  443 ARG cc_start: 0.7802 (mtm180) cc_final: 0.6226 (mtm110)
REVERT: A  518 VAL cc_start: 0.8632 (OUTLIER) cc_final: 0.8368 (m)
REVERT: A  533 TRP cc_start: 0.7234 (t60) cc_final: 0.5454 (m100)
REVERT: A  640 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8125 (mp)
REVERT: A  725 ARG cc_start: 0.6042 (OUTLIER) cc_final: 0.5598 (mtm180)
REVERT: A  745 LYS cc_start: 0.7592 (ttmt) cc_final: 0.7120 (mptt)
REVERT: A  763 ARG cc_start: 0.7525 (mmt180) cc_final: 0.6486 (mtm-85)
REVERT: A  791 ARG cc_start: 0.7370 (ptp-110) cc_final: 0.6573 (ptt-90)
REVERT: A  794 THR cc_start: 0.8412 (p) cc_final: 0.8042 (t)
REVERT: A  809 PHE cc_start: 0.8022 (OUTLIER) cc_final: 0.6971 (p90)
REVERT: A 1057 GLU cc_start: 0.7415 (tm-30) cc_final: 0.7204 (tm-30)
REVERT: A 1088 HIS cc_start: 0.8344 (OUTLIER) cc_final: 0.7032 (t70)
REVERT: A 1202 THR cc_start: 0.8794 (t) cc_final: 0.8521 (m)
REVERT: A 1268 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.7039 (tt0)
REVERT: A 1269 GLN cc_start: 0.7389 (OUTLIER) cc_final: 0.5841 (mm-40)
REVERT: A 1642 MET cc_start: 0.6221 (OUTLIER) cc_final: 0.5651 (pmm)
REVERT: A 1690 MET cc_start: 0.6210 (OUTLIER) cc_final: 0.5984 (mtt)
REVERT: A 1694 MET cc_start: 0.5484 (OUTLIER) cc_final: 0.4862 (mpt)
REVERT: A 1836 VAL cc_start: 0.7786 (m) cc_final: 0.7489 (p)
  outliers start: 48
  outliers final: 18
  residues processed: 175
  average time/residue: 1.1903
  time to fit residues: 228.8093
Evaluate side-chains
  176 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 147
  time to evaluate  : 1.437 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 ILE
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  348 MET
Chi-restraints excluded: chain A residue  430 VAL
Chi-restraints excluded: chain A residue  440 LYS
Chi-restraints excluded: chain A residue  473 THR
Chi-restraints excluded: chain A residue  518 VAL
Chi-restraints excluded: chain A residue  607 THR
Chi-restraints excluded: chain A residue  610 PHE
Chi-restraints excluded: chain A residue  616 LEU
Chi-restraints excluded: chain A residue  640 LEU
Chi-restraints excluded: chain A residue  667 VAL
Chi-restraints excluded: chain A residue  725 ARG
Chi-restraints excluded: chain A residue  734 ILE
Chi-restraints excluded: chain A residue  741 GLU
Chi-restraints excluded: chain A residue  809 PHE
Chi-restraints excluded: chain A residue 1088 HIS
Chi-restraints excluded: chain A residue 1130 VAL
Chi-restraints excluded: chain A residue 1268 GLU
Chi-restraints excluded: chain A residue 1269 GLN
Chi-restraints excluded: chain A residue 1308 LEU
Chi-restraints excluded: chain A residue 1316 VAL
Chi-restraints excluded: chain A residue 1339 VAL
Chi-restraints excluded: chain A residue 1380 GLU
Chi-restraints excluded: chain A residue 1642 MET
Chi-restraints excluded: chain A residue 1690 MET
Chi-restraints excluded: chain A residue 1694 MET
Chi-restraints excluded: chain A residue 1751 LEU
Chi-restraints excluded: chain A residue 1847 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 75 optimal weight:    0.7980
   chunk 145 optimal weight:    5.9990
   chunk 78 optimal weight:    2.9990
   chunk 107 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 21 optimal weight:    0.4980
   chunk 121 optimal weight:    2.9990
   chunk 128 optimal weight:    3.9990
   chunk 60 optimal weight:    7.9990
   chunk 7 optimal weight:    0.3980
   chunk 55 optimal weight:    5.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
** A1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1269 GLN
A1688 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.156327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.105063 restraints weight = 14252.407|
|-----------------------------------------------------------------------------|
r_work (start): 0.3243 rms_B_bonded: 2.79
r_work: 0.3080 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.2935 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.2935
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7396
moved from start:          0.1777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  13207  Z= 0.152
  Angle     :  0.601   9.831  17988  Z= 0.296
  Chirality :  0.041   0.159   2024
  Planarity :  0.004   0.051   2147
  Dihedral  : 12.481 159.979   2963
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 17.11 %
    Favored  : 79.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.57 (0.22), residues: 1461
  helix:  0.93 (0.17), residues: 882
  sheet:  0.45 (0.65), residues: 66
  loop : -0.47 (0.28), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 625 
 HIS   0.008   0.001   HIS A1195 
 PHE   0.017   0.001   PHE A1581 
 TYR   0.019   0.001   TYR A1503 
 ARG   0.008   0.000   ARG A 852 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00101 (    1)
  link_NAG-ASN         : angle       1.73832 (    3)
  link_BETA1-4         : bond        0.00088 (    1)
  link_BETA1-4         : angle       2.13043 (    3)
  hydrogen bonds       : bond        0.04536 (  640)
  hydrogen bonds       : angle       4.40939 ( 1857)
  SS BOND              : bond        0.00382 (    2)
  SS BOND              : angle       0.45139 (    4)
  covalent geometry    : bond        0.00358 (13203)
  covalent geometry    : angle       0.60010 (17978)

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

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

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 153
  time to evaluate  : 1.472 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  386 LYS cc_start: 0.8576 (mmmt) cc_final: 0.7734 (mmtt)
REVERT: A  443 ARG cc_start: 0.7792 (mtm180) cc_final: 0.6190 (mtm110)
REVERT: A  518 VAL cc_start: 0.8592 (OUTLIER) cc_final: 0.8338 (m)
REVERT: A  533 TRP cc_start: 0.7281 (t60) cc_final: 0.5451 (m100)
REVERT: A  640 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8106 (mp)
REVERT: A  725 ARG cc_start: 0.5982 (OUTLIER) cc_final: 0.5560 (mtm180)
REVERT: A  745 LYS cc_start: 0.7521 (ttmt) cc_final: 0.7070 (mptt)
REVERT: A  791 ARG cc_start: 0.7415 (ptp-110) cc_final: 0.6640 (ptt-90)
REVERT: A  794 THR cc_start: 0.8367 (p) cc_final: 0.8020 (t)
REVERT: A  809 PHE cc_start: 0.7908 (OUTLIER) cc_final: 0.6895 (p90)
REVERT: A  862 ARG cc_start: 0.4621 (OUTLIER) cc_final: 0.3299 (tpm170)
REVERT: A 1057 GLU cc_start: 0.7404 (tm-30) cc_final: 0.7134 (tm-30)
REVERT: A 1088 HIS cc_start: 0.8297 (OUTLIER) cc_final: 0.7133 (t70)
REVERT: A 1202 THR cc_start: 0.8808 (OUTLIER) cc_final: 0.8557 (m)
REVERT: A 1268 GLU cc_start: 0.7539 (mt-10) cc_final: 0.7078 (tt0)
REVERT: A 1269 GLN cc_start: 0.7377 (OUTLIER) cc_final: 0.6280 (mm-40)
REVERT: A 1380 GLU cc_start: 0.6297 (OUTLIER) cc_final: 0.6060 (pt0)
REVERT: A 1504 ARG cc_start: 0.7324 (tmm160) cc_final: 0.7115 (tmm160)
REVERT: A 1694 MET cc_start: 0.5433 (OUTLIER) cc_final: 0.4879 (mpt)
REVERT: A 1836 VAL cc_start: 0.7753 (m) cc_final: 0.7452 (p)
  outliers start: 45
  outliers final: 21
  residues processed: 177
  average time/residue: 1.1780
  time to fit residues: 229.7330
Evaluate side-chains
  182 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 151
  time to evaluate  : 1.415 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 ILE
Chi-restraints excluded: chain A residue  348 MET
Chi-restraints excluded: chain A residue  430 VAL
Chi-restraints excluded: chain A residue  440 LYS
Chi-restraints excluded: chain A residue  473 THR
Chi-restraints excluded: chain A residue  518 VAL
Chi-restraints excluded: chain A residue  537 ILE
Chi-restraints excluded: chain A residue  541 ILE
Chi-restraints excluded: chain A residue  607 THR
Chi-restraints excluded: chain A residue  610 PHE
Chi-restraints excluded: chain A residue  616 LEU
Chi-restraints excluded: chain A residue  640 LEU
Chi-restraints excluded: chain A residue  667 VAL
Chi-restraints excluded: chain A residue  725 ARG
Chi-restraints excluded: chain A residue  734 ILE
Chi-restraints excluded: chain A residue  761 MET
Chi-restraints excluded: chain A residue  809 PHE
Chi-restraints excluded: chain A residue  862 ARG
Chi-restraints excluded: chain A residue 1088 HIS
Chi-restraints excluded: chain A residue 1130 VAL
Chi-restraints excluded: chain A residue 1202 THR
Chi-restraints excluded: chain A residue 1269 GLN
Chi-restraints excluded: chain A residue 1308 LEU
Chi-restraints excluded: chain A residue 1316 VAL
Chi-restraints excluded: chain A residue 1378 LEU
Chi-restraints excluded: chain A residue 1380 GLU
Chi-restraints excluded: chain A residue 1612 VAL
Chi-restraints excluded: chain A residue 1642 MET
Chi-restraints excluded: chain A residue 1653 VAL
Chi-restraints excluded: chain A residue 1694 MET
Chi-restraints excluded: chain A residue 1847 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 19 optimal weight:    0.9990
   chunk 117 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 10 optimal weight:    0.5980
   chunk 13 optimal weight:    2.9990
   chunk 5 optimal weight:    0.7980
   chunk 38 optimal weight:    5.9990
   chunk 144 optimal weight:    3.9990
   chunk 54 optimal weight:    2.9990
   chunk 4 optimal weight:    0.6980
   chunk 112 optimal weight:    4.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A 385 ASN
A 721 ASN
A 824 GLN
** A1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.157282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.106103 restraints weight = 14314.830|
|-----------------------------------------------------------------------------|
r_work (start): 0.3258 rms_B_bonded: 2.80
r_work: 0.3097 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.2952 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.2952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7380
moved from start:          0.1915

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  13207  Z= 0.125
  Angle     :  0.576   9.199  17988  Z= 0.284
  Chirality :  0.040   0.163   2024
  Planarity :  0.004   0.050   2147
  Dihedral  : 11.952 146.030   2963
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 17.88 %
    Favored  : 79.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.83 (0.22), residues: 1461
  helix:  1.16 (0.17), residues: 882
  sheet:  0.57 (0.66), residues: 66
  loop : -0.42 (0.28), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 625 
 HIS   0.008   0.001   HIS A1195 
 PHE   0.014   0.001   PHE A1581 
 TYR   0.019   0.001   TYR A1503 
 ARG   0.007   0.000   ARG A 852 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00147 (    1)
  link_NAG-ASN         : angle       1.69843 (    3)
  link_BETA1-4         : bond        0.00192 (    1)
  link_BETA1-4         : angle       1.95421 (    3)
  hydrogen bonds       : bond        0.04255 (  640)
  hydrogen bonds       : angle       4.29124 ( 1857)
  SS BOND              : bond        0.00361 (    2)
  SS BOND              : angle       0.42049 (    4)
  covalent geometry    : bond        0.00285 (13203)
  covalent geometry    : angle       0.57491 (17978)

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

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

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 153
  time to evaluate  : 1.575 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  386 LYS cc_start: 0.8546 (mmmt) cc_final: 0.7729 (mmtt)
REVERT: A  443 ARG cc_start: 0.7763 (mtm180) cc_final: 0.6183 (mtm110)
REVERT: A  518 VAL cc_start: 0.8598 (OUTLIER) cc_final: 0.8356 (m)
REVERT: A  533 TRP cc_start: 0.7277 (t60) cc_final: 0.5436 (m100)
REVERT: A  640 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8095 (mp)
REVERT: A  725 ARG cc_start: 0.5934 (OUTLIER) cc_final: 0.5535 (mtm180)
REVERT: A  745 LYS cc_start: 0.7483 (ttmt) cc_final: 0.7052 (mptt)
REVERT: A  791 ARG cc_start: 0.7425 (ptp-110) cc_final: 0.6347 (ptm-80)
REVERT: A  794 THR cc_start: 0.8327 (p) cc_final: 0.8022 (t)
REVERT: A  862 ARG cc_start: 0.4461 (OUTLIER) cc_final: 0.3112 (tpm170)
REVERT: A 1057 GLU cc_start: 0.7432 (tm-30) cc_final: 0.7093 (tm-30)
REVERT: A 1088 HIS cc_start: 0.8306 (OUTLIER) cc_final: 0.7153 (t70)
REVERT: A 1202 THR cc_start: 0.8820 (t) cc_final: 0.8570 (m)
REVERT: A 1269 GLN cc_start: 0.7347 (mt0) cc_final: 0.6396 (mm-40)
REVERT: A 1694 MET cc_start: 0.5397 (OUTLIER) cc_final: 0.4825 (mpt)
REVERT: A 1836 VAL cc_start: 0.7733 (m) cc_final: 0.7447 (p)
REVERT: A 1848 ASN cc_start: 0.7972 (p0) cc_final: 0.7716 (p0)
  outliers start: 40
  outliers final: 21
  residues processed: 178
  average time/residue: 1.2368
  time to fit residues: 242.6118
Evaluate side-chains
  175 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 148
  time to evaluate  : 1.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 ILE
Chi-restraints excluded: chain A residue  348 MET
Chi-restraints excluded: chain A residue  430 VAL
Chi-restraints excluded: chain A residue  440 LYS
Chi-restraints excluded: chain A residue  473 THR
Chi-restraints excluded: chain A residue  518 VAL
Chi-restraints excluded: chain A residue  527 HIS
Chi-restraints excluded: chain A residue  537 ILE
Chi-restraints excluded: chain A residue  610 PHE
Chi-restraints excluded: chain A residue  616 LEU
Chi-restraints excluded: chain A residue  640 LEU
Chi-restraints excluded: chain A residue  667 VAL
Chi-restraints excluded: chain A residue  725 ARG
Chi-restraints excluded: chain A residue  734 ILE
Chi-restraints excluded: chain A residue  761 MET
Chi-restraints excluded: chain A residue  862 ARG
Chi-restraints excluded: chain A residue 1083 SER
Chi-restraints excluded: chain A residue 1088 HIS
Chi-restraints excluded: chain A residue 1223 ILE
Chi-restraints excluded: chain A residue 1308 LEU
Chi-restraints excluded: chain A residue 1316 VAL
Chi-restraints excluded: chain A residue 1328 CYS
Chi-restraints excluded: chain A residue 1339 VAL
Chi-restraints excluded: chain A residue 1378 LEU
Chi-restraints excluded: chain A residue 1612 VAL
Chi-restraints excluded: chain A residue 1694 MET
Chi-restraints excluded: chain A residue 1847 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 120 optimal weight:    5.9990
   chunk 143 optimal weight:    2.9990
   chunk 99 optimal weight:    3.9990
   chunk 76 optimal weight:    3.9990
   chunk 98 optimal weight:    8.9990
   chunk 125 optimal weight:    0.0670
   chunk 45 optimal weight:    0.0970
   chunk 66 optimal weight:    0.8980
   chunk 3 optimal weight:    2.9990
   chunk 75 optimal weight:    0.4980
   overall best weight:    0.7118

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

Flipped N/Q/H residues before XYZ refinement:
A 700 ASN
A 824 GLN
** A1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1269 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.157980 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.106922 restraints weight = 14086.897|
|-----------------------------------------------------------------------------|
r_work (start): 0.3271 rms_B_bonded: 2.72
r_work: 0.3108 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.2963 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.2963
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7366
moved from start:          0.2078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  13207  Z= 0.121
  Angle     :  0.560   9.032  17988  Z= 0.278
  Chirality :  0.040   0.154   2024
  Planarity :  0.004   0.050   2147
  Dihedral  : 11.533 135.825   2963
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 17.42 %
    Favored  : 79.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.98 (0.22), residues: 1461
  helix:  1.26 (0.18), residues: 884
  sheet:  0.72 (0.67), residues: 66
  loop : -0.33 (0.29), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 625 
 HIS   0.008   0.001   HIS A1195 
 PHE   0.013   0.001   PHE A1581 
 TYR   0.019   0.001   TYR A1503 
 ARG   0.009   0.000   ARG A 852 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00134 (    1)
  link_NAG-ASN         : angle       1.69926 (    3)
  link_BETA1-4         : bond        0.00199 (    1)
  link_BETA1-4         : angle       1.89739 (    3)
  hydrogen bonds       : bond        0.04124 (  640)
  hydrogen bonds       : angle       4.22188 ( 1857)
  SS BOND              : bond        0.00327 (    2)
  SS BOND              : angle       0.42921 (    4)
  covalent geometry    : bond        0.00274 (13203)
  covalent geometry    : angle       0.55912 (17978)

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

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

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 156
  time to evaluate  : 1.447 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  371 GLU cc_start: 0.6955 (tp30) cc_final: 0.6477 (pt0)
REVERT: A  386 LYS cc_start: 0.8562 (mmmt) cc_final: 0.7749 (mmtt)
REVERT: A  443 ARG cc_start: 0.7762 (mtm180) cc_final: 0.6181 (mtm110)
REVERT: A  518 VAL cc_start: 0.8614 (OUTLIER) cc_final: 0.8395 (m)
REVERT: A  533 TRP cc_start: 0.7320 (t60) cc_final: 0.5325 (m100)
REVERT: A  640 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8091 (mp)
REVERT: A  725 ARG cc_start: 0.5902 (OUTLIER) cc_final: 0.5518 (mtm180)
REVERT: A  745 LYS cc_start: 0.7413 (ttmt) cc_final: 0.6945 (mptt)
REVERT: A  791 ARG cc_start: 0.7381 (ptp-110) cc_final: 0.6293 (ptm-80)
REVERT: A  794 THR cc_start: 0.8297 (p) cc_final: 0.8020 (t)
REVERT: A  862 ARG cc_start: 0.4497 (OUTLIER) cc_final: 0.3250 (tpm170)
REVERT: A  974 GLU cc_start: 0.7646 (pm20) cc_final: 0.7409 (pm20)
REVERT: A 1088 HIS cc_start: 0.8297 (OUTLIER) cc_final: 0.7216 (t70)
REVERT: A 1202 THR cc_start: 0.8824 (OUTLIER) cc_final: 0.8570 (m)
REVERT: A 1269 GLN cc_start: 0.7298 (OUTLIER) cc_final: 0.6346 (mm-40)
REVERT: A 1694 MET cc_start: 0.5258 (OUTLIER) cc_final: 0.4753 (mpt)
REVERT: A 1836 VAL cc_start: 0.7697 (m) cc_final: 0.7440 (p)
REVERT: A 1848 ASN cc_start: 0.8012 (p0) cc_final: 0.7747 (p0)
  outliers start: 46
  outliers final: 22
  residues processed: 183
  average time/residue: 1.1956
  time to fit residues: 240.2446
Evaluate side-chains
  183 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 153
  time to evaluate  : 1.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 ILE
Chi-restraints excluded: chain A residue  198 SER
Chi-restraints excluded: chain A residue  348 MET
Chi-restraints excluded: chain A residue  430 VAL
Chi-restraints excluded: chain A residue  440 LYS
Chi-restraints excluded: chain A residue  473 THR
Chi-restraints excluded: chain A residue  518 VAL
Chi-restraints excluded: chain A residue  527 HIS
Chi-restraints excluded: chain A residue  537 ILE
Chi-restraints excluded: chain A residue  607 THR
Chi-restraints excluded: chain A residue  610 PHE
Chi-restraints excluded: chain A residue  616 LEU
Chi-restraints excluded: chain A residue  640 LEU
Chi-restraints excluded: chain A residue  667 VAL
Chi-restraints excluded: chain A residue  725 ARG
Chi-restraints excluded: chain A residue  761 MET
Chi-restraints excluded: chain A residue  862 ARG
Chi-restraints excluded: chain A residue  877 LYS
Chi-restraints excluded: chain A residue 1083 SER
Chi-restraints excluded: chain A residue 1088 HIS
Chi-restraints excluded: chain A residue 1202 THR
Chi-restraints excluded: chain A residue 1269 GLN
Chi-restraints excluded: chain A residue 1308 LEU
Chi-restraints excluded: chain A residue 1316 VAL
Chi-restraints excluded: chain A residue 1328 CYS
Chi-restraints excluded: chain A residue 1339 VAL
Chi-restraints excluded: chain A residue 1612 VAL
Chi-restraints excluded: chain A residue 1653 VAL
Chi-restraints excluded: chain A residue 1694 MET
Chi-restraints excluded: chain A residue 1847 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 61 optimal weight:    0.6980
   chunk 20 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 93 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 43 optimal weight:    0.7980
   chunk 71 optimal weight:    0.9980
   chunk 109 optimal weight:    5.9990
   chunk 116 optimal weight:    0.8980
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
A 700 ASN
A 824 GLN
** A1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1269 GLN
A1688 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.157127 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.106644 restraints weight = 14299.667|
|-----------------------------------------------------------------------------|
r_work (start): 0.3263 rms_B_bonded: 2.49
r_work: 0.3102 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.2958 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.2958
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7464
moved from start:          0.2032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  13207  Z= 0.147
  Angle     :  0.589   9.582  17988  Z= 0.289
  Chirality :  0.041   0.158   2024
  Planarity :  0.004   0.050   2147
  Dihedral  : 11.451 131.474   2963
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 18.11 %
    Favored  : 78.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.95 (0.22), residues: 1461
  helix:  1.26 (0.17), residues: 882
  sheet:  0.69 (0.67), residues: 66
  loop : -0.37 (0.28), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 625 
 HIS   0.008   0.001   HIS A1195 
 PHE   0.014   0.001   PHE A1581 
 TYR   0.019   0.001   TYR A1503 
 ARG   0.004   0.000   ARG A 852 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00055 (    1)
  link_NAG-ASN         : angle       1.76193 (    3)
  link_BETA1-4         : bond        0.00055 (    1)
  link_BETA1-4         : angle       1.99497 (    3)
  hydrogen bonds       : bond        0.04315 (  640)
  hydrogen bonds       : angle       4.24890 ( 1857)
  SS BOND              : bond        0.00334 (    2)
  SS BOND              : angle       0.48671 (    4)
  covalent geometry    : bond        0.00346 (13203)
  covalent geometry    : angle       0.58855 (17978)

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

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

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 152
  time to evaluate  : 1.310 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  371 GLU cc_start: 0.6873 (tp30) cc_final: 0.6528 (pt0)
REVERT: A  386 LYS cc_start: 0.8599 (mmmt) cc_final: 0.7782 (mmtt)
REVERT: A  443 ARG cc_start: 0.7855 (mtm180) cc_final: 0.6273 (mtm110)
REVERT: A  518 VAL cc_start: 0.8661 (OUTLIER) cc_final: 0.8444 (m)
REVERT: A  640 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8153 (mp)
REVERT: A  725 ARG cc_start: 0.6009 (OUTLIER) cc_final: 0.5609 (mtm180)
REVERT: A  745 LYS cc_start: 0.7471 (ttmt) cc_final: 0.7015 (mptt)
REVERT: A  791 ARG cc_start: 0.7448 (ptp-110) cc_final: 0.6366 (ptm-80)
REVERT: A  794 THR cc_start: 0.8353 (p) cc_final: 0.8067 (t)
REVERT: A  809 PHE cc_start: 0.7748 (OUTLIER) cc_final: 0.6895 (p90)
REVERT: A  862 ARG cc_start: 0.4629 (OUTLIER) cc_final: 0.3326 (tpm170)
REVERT: A  974 GLU cc_start: 0.7605 (pm20) cc_final: 0.7350 (pm20)
REVERT: A 1088 HIS cc_start: 0.8413 (OUTLIER) cc_final: 0.7219 (t70)
REVERT: A 1202 THR cc_start: 0.8880 (OUTLIER) cc_final: 0.8613 (m)
REVERT: A 1268 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.6989 (tt0)
REVERT: A 1269 GLN cc_start: 0.7167 (OUTLIER) cc_final: 0.6308 (mm-40)
REVERT: A 1388 GLN cc_start: 0.5042 (OUTLIER) cc_final: 0.4645 (mt0)
REVERT: A 1694 MET cc_start: 0.5313 (OUTLIER) cc_final: 0.4804 (mpt)
REVERT: A 1836 VAL cc_start: 0.7736 (m) cc_final: 0.7477 (p)
REVERT: A 1848 ASN cc_start: 0.8015 (p0) cc_final: 0.7749 (p0)
  outliers start: 41
  outliers final: 25
  residues processed: 176
  average time/residue: 1.1821
  time to fit residues: 228.4100
Evaluate side-chains
  187 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 151
  time to evaluate  : 1.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 ILE
Chi-restraints excluded: chain A residue  198 SER
Chi-restraints excluded: chain A residue  348 MET
Chi-restraints excluded: chain A residue  430 VAL
Chi-restraints excluded: chain A residue  440 LYS
Chi-restraints excluded: chain A residue  473 THR
Chi-restraints excluded: chain A residue  518 VAL
Chi-restraints excluded: chain A residue  537 ILE
Chi-restraints excluded: chain A residue  607 THR
Chi-restraints excluded: chain A residue  610 PHE
Chi-restraints excluded: chain A residue  616 LEU
Chi-restraints excluded: chain A residue  640 LEU
Chi-restraints excluded: chain A residue  667 VAL
Chi-restraints excluded: chain A residue  725 ARG
Chi-restraints excluded: chain A residue  734 ILE
Chi-restraints excluded: chain A residue  741 GLU
Chi-restraints excluded: chain A residue  761 MET
Chi-restraints excluded: chain A residue  809 PHE
Chi-restraints excluded: chain A residue  862 ARG
Chi-restraints excluded: chain A residue  877 LYS
Chi-restraints excluded: chain A residue 1083 SER
Chi-restraints excluded: chain A residue 1088 HIS
Chi-restraints excluded: chain A residue 1130 VAL
Chi-restraints excluded: chain A residue 1202 THR
Chi-restraints excluded: chain A residue 1268 GLU
Chi-restraints excluded: chain A residue 1269 GLN
Chi-restraints excluded: chain A residue 1308 LEU
Chi-restraints excluded: chain A residue 1316 VAL
Chi-restraints excluded: chain A residue 1328 CYS
Chi-restraints excluded: chain A residue 1339 VAL
Chi-restraints excluded: chain A residue 1388 GLN
Chi-restraints excluded: chain A residue 1612 VAL
Chi-restraints excluded: chain A residue 1653 VAL
Chi-restraints excluded: chain A residue 1694 MET
Chi-restraints excluded: chain A residue 1816 ILE
Chi-restraints excluded: chain A residue 1847 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 42 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 4 optimal weight:    0.6980
   chunk 13 optimal weight:    0.6980
   chunk 131 optimal weight:    3.9990
   chunk 86 optimal weight:    3.9990
   chunk 82 optimal weight:    2.9990
   chunk 73 optimal weight:    0.5980
   chunk 38 optimal weight:    2.9990
   chunk 133 optimal weight:    0.9980
   chunk 134 optimal weight:    0.8980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 700 ASN
A 824 GLN
** A1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1269 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.157781 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.107437 restraints weight = 14187.029|
|-----------------------------------------------------------------------------|
r_work (start): 0.3276 rms_B_bonded: 2.50
r_work: 0.3114 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2969 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.2969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7453
moved from start:          0.2117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  13207  Z= 0.126
  Angle     :  0.571  10.261  17988  Z= 0.281
  Chirality :  0.040   0.154   2024
  Planarity :  0.004   0.050   2147
  Dihedral  : 11.288 126.757   2963
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 18.18 %
    Favored  : 78.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.04 (0.22), residues: 1461
  helix:  1.34 (0.17), residues: 882
  sheet:  0.72 (0.67), residues: 66
  loop : -0.36 (0.29), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 625 
 HIS   0.008   0.001   HIS A1195 
 PHE   0.014   0.001   PHE A1581 
 TYR   0.020   0.001   TYR A1503 
 ARG   0.009   0.000   ARG A 852 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00131 (    1)
  link_NAG-ASN         : angle       1.71211 (    3)
  link_BETA1-4         : bond        0.00134 (    1)
  link_BETA1-4         : angle       1.89373 (    3)
  hydrogen bonds       : bond        0.04160 (  640)
  hydrogen bonds       : angle       4.21327 ( 1857)
  SS BOND              : bond        0.00325 (    2)
  SS BOND              : angle       0.44771 (    4)
  covalent geometry    : bond        0.00289 (13203)
  covalent geometry    : angle       0.57050 (17978)

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

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

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 151
  time to evaluate  : 1.844 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  371 GLU cc_start: 0.7015 (tp30) cc_final: 0.6549 (pt0)
REVERT: A  386 LYS cc_start: 0.8598 (mmmt) cc_final: 0.7779 (mmtt)
REVERT: A  443 ARG cc_start: 0.7845 (mtm180) cc_final: 0.6259 (mtm110)
REVERT: A  533 TRP cc_start: 0.7359 (t60) cc_final: 0.5404 (m100)
REVERT: A  640 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8157 (mp)
REVERT: A  725 ARG cc_start: 0.5971 (OUTLIER) cc_final: 0.5586 (mtm180)
REVERT: A  745 LYS cc_start: 0.7459 (ttmt) cc_final: 0.6972 (mptt)
REVERT: A  791 ARG cc_start: 0.7448 (ptp-110) cc_final: 0.6360 (ptm-80)
REVERT: A  794 THR cc_start: 0.8340 (p) cc_final: 0.8062 (t)
REVERT: A  862 ARG cc_start: 0.4596 (OUTLIER) cc_final: 0.3304 (tpm170)
REVERT: A  974 GLU cc_start: 0.7609 (pm20) cc_final: 0.7344 (pm20)
REVERT: A 1088 HIS cc_start: 0.8388 (OUTLIER) cc_final: 0.7281 (t70)
REVERT: A 1202 THR cc_start: 0.8879 (OUTLIER) cc_final: 0.8619 (m)
REVERT: A 1268 GLU cc_start: 0.7500 (mt-10) cc_final: 0.7076 (tt0)
REVERT: A 1269 GLN cc_start: 0.7165 (OUTLIER) cc_final: 0.6176 (mm-40)
REVERT: A 1694 MET cc_start: 0.5323 (OUTLIER) cc_final: 0.4822 (mpt)
REVERT: A 1836 VAL cc_start: 0.7718 (m) cc_final: 0.7458 (p)
REVERT: A 1848 ASN cc_start: 0.8145 (p0) cc_final: 0.7866 (p0)
  outliers start: 41
  outliers final: 26
  residues processed: 176
  average time/residue: 1.2067
  time to fit residues: 234.1482
Evaluate side-chains
  182 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 149
  time to evaluate  : 1.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 ILE
Chi-restraints excluded: chain A residue  198 SER
Chi-restraints excluded: chain A residue  348 MET
Chi-restraints excluded: chain A residue  430 VAL
Chi-restraints excluded: chain A residue  440 LYS
Chi-restraints excluded: chain A residue  473 THR
Chi-restraints excluded: chain A residue  527 HIS
Chi-restraints excluded: chain A residue  537 ILE
Chi-restraints excluded: chain A residue  607 THR
Chi-restraints excluded: chain A residue  610 PHE
Chi-restraints excluded: chain A residue  616 LEU
Chi-restraints excluded: chain A residue  640 LEU
Chi-restraints excluded: chain A residue  667 VAL
Chi-restraints excluded: chain A residue  725 ARG
Chi-restraints excluded: chain A residue  734 ILE
Chi-restraints excluded: chain A residue  741 GLU
Chi-restraints excluded: chain A residue  761 MET
Chi-restraints excluded: chain A residue  862 ARG
Chi-restraints excluded: chain A residue  877 LYS
Chi-restraints excluded: chain A residue 1083 SER
Chi-restraints excluded: chain A residue 1088 HIS
Chi-restraints excluded: chain A residue 1130 VAL
Chi-restraints excluded: chain A residue 1202 THR
Chi-restraints excluded: chain A residue 1269 GLN
Chi-restraints excluded: chain A residue 1308 LEU
Chi-restraints excluded: chain A residue 1328 CYS
Chi-restraints excluded: chain A residue 1339 VAL
Chi-restraints excluded: chain A residue 1612 VAL
Chi-restraints excluded: chain A residue 1653 VAL
Chi-restraints excluded: chain A residue 1694 MET
Chi-restraints excluded: chain A residue 1751 LEU
Chi-restraints excluded: chain A residue 1816 ILE
Chi-restraints excluded: chain A residue 1847 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 145 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 86 optimal weight:    4.9990
   chunk 6 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 126 optimal weight:    0.0670
   chunk 93 optimal weight:    0.7980
   chunk 112 optimal weight:    1.9990
   chunk 104 optimal weight:    0.0980
   chunk 45 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   overall best weight:    0.9922

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

Flipped N/Q/H residues before XYZ refinement:
A 700 ASN
A 824 GLN
** A1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1269 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.157421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.106228 restraints weight = 14192.197|
|-----------------------------------------------------------------------------|
r_work (start): 0.3258 rms_B_bonded: 2.74
r_work: 0.3099 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.2955 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.2955
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7419
moved from start:          0.2111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  13207  Z= 0.141
  Angle     :  0.586  11.127  17988  Z= 0.288
  Chirality :  0.041   0.157   2024
  Planarity :  0.004   0.050   2147
  Dihedral  : 11.185 122.613   2962
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 18.26 %
    Favored  : 78.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.02 (0.22), residues: 1461
  helix:  1.32 (0.17), residues: 882
  sheet:  0.71 (0.67), residues: 66
  loop : -0.35 (0.29), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 625 
 HIS   0.008   0.001   HIS A1195 
 PHE   0.014   0.001   PHE A1499 
 TYR   0.019   0.001   TYR A1503 
 ARG   0.006   0.000   ARG A 988 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00076 (    1)
  link_NAG-ASN         : angle       1.73888 (    3)
  link_BETA1-4         : bond        0.00052 (    1)
  link_BETA1-4         : angle       1.94499 (    3)
  hydrogen bonds       : bond        0.04243 (  640)
  hydrogen bonds       : angle       4.22530 ( 1857)
  SS BOND              : bond        0.00337 (    2)
  SS BOND              : angle       0.47079 (    4)
  covalent geometry    : bond        0.00330 (13203)
  covalent geometry    : angle       0.58563 (17978)

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

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

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 149
  time to evaluate  : 1.413 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  371 GLU cc_start: 0.6963 (tp30) cc_final: 0.6455 (pt0)
REVERT: A  386 LYS cc_start: 0.8583 (mmmt) cc_final: 0.7762 (mmtt)
REVERT: A  443 ARG cc_start: 0.7826 (mtm180) cc_final: 0.6228 (mtm110)
REVERT: A  533 TRP cc_start: 0.7337 (t60) cc_final: 0.5359 (m100)
REVERT: A  640 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8111 (mp)
REVERT: A  725 ARG cc_start: 0.5935 (OUTLIER) cc_final: 0.5551 (mtm180)
REVERT: A  745 LYS cc_start: 0.7418 (ttmt) cc_final: 0.6948 (mptt)
REVERT: A  791 ARG cc_start: 0.7420 (ptp-110) cc_final: 0.6332 (ptm-80)
REVERT: A  794 THR cc_start: 0.8341 (p) cc_final: 0.8060 (t)
REVERT: A  862 ARG cc_start: 0.4519 (OUTLIER) cc_final: 0.3277 (tpm170)
REVERT: A  974 GLU cc_start: 0.7593 (pm20) cc_final: 0.7325 (pm20)
REVERT: A 1088 HIS cc_start: 0.8371 (OUTLIER) cc_final: 0.7183 (t70)
REVERT: A 1202 THR cc_start: 0.8850 (OUTLIER) cc_final: 0.8588 (m)
REVERT: A 1268 GLU cc_start: 0.7464 (mt-10) cc_final: 0.7036 (tt0)
REVERT: A 1269 GLN cc_start: 0.7237 (OUTLIER) cc_final: 0.6251 (mm-40)
REVERT: A 1642 MET cc_start: 0.5579 (tmm) cc_final: 0.5020 (pmm)
REVERT: A 1694 MET cc_start: 0.5294 (OUTLIER) cc_final: 0.4801 (mpt)
REVERT: A 1836 VAL cc_start: 0.7711 (m) cc_final: 0.7450 (p)
REVERT: A 1848 ASN cc_start: 0.8130 (p0) cc_final: 0.7833 (p0)
  outliers start: 37
  outliers final: 25
  residues processed: 171
  average time/residue: 1.2575
  time to fit residues: 234.6454
Evaluate side-chains
  181 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 149
  time to evaluate  : 1.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 ILE
Chi-restraints excluded: chain A residue  198 SER
Chi-restraints excluded: chain A residue  348 MET
Chi-restraints excluded: chain A residue  430 VAL
Chi-restraints excluded: chain A residue  440 LYS
Chi-restraints excluded: chain A residue  527 HIS
Chi-restraints excluded: chain A residue  537 ILE
Chi-restraints excluded: chain A residue  607 THR
Chi-restraints excluded: chain A residue  610 PHE
Chi-restraints excluded: chain A residue  616 LEU
Chi-restraints excluded: chain A residue  640 LEU
Chi-restraints excluded: chain A residue  667 VAL
Chi-restraints excluded: chain A residue  725 ARG
Chi-restraints excluded: chain A residue  734 ILE
Chi-restraints excluded: chain A residue  741 GLU
Chi-restraints excluded: chain A residue  761 MET
Chi-restraints excluded: chain A residue  862 ARG
Chi-restraints excluded: chain A residue  877 LYS
Chi-restraints excluded: chain A residue 1083 SER
Chi-restraints excluded: chain A residue 1088 HIS
Chi-restraints excluded: chain A residue 1130 VAL
Chi-restraints excluded: chain A residue 1202 THR
Chi-restraints excluded: chain A residue 1269 GLN
Chi-restraints excluded: chain A residue 1308 LEU
Chi-restraints excluded: chain A residue 1328 CYS
Chi-restraints excluded: chain A residue 1339 VAL
Chi-restraints excluded: chain A residue 1612 VAL
Chi-restraints excluded: chain A residue 1653 VAL
Chi-restraints excluded: chain A residue 1694 MET
Chi-restraints excluded: chain A residue 1751 LEU
Chi-restraints excluded: chain A residue 1816 ILE
Chi-restraints excluded: chain A residue 1847 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 30 optimal weight:    0.2980
   chunk 116 optimal weight:    0.9980
   chunk 33 optimal weight:    3.9990
   chunk 83 optimal weight:    0.4980
   chunk 77 optimal weight:    2.9990
   chunk 81 optimal weight:    0.3980
   chunk 56 optimal weight:    0.9980
   chunk 10 optimal weight:    0.0970
   chunk 41 optimal weight:    4.9990
   chunk 92 optimal weight:    0.7980
   chunk 117 optimal weight:    1.9990
   overall best weight:    0.4178

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

Flipped N/Q/H residues before XYZ refinement:
A 700 ASN
A 824 GLN
** A1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1269 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.159442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.108891 restraints weight = 14156.133|
|-----------------------------------------------------------------------------|
r_work (start): 0.3296 rms_B_bonded: 2.77
r_work: 0.3136 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.2992 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.2992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7430
moved from start:          0.2266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  13207  Z= 0.107
  Angle     :  0.557  10.181  17988  Z= 0.274
  Chirality :  0.039   0.161   2024
  Planarity :  0.004   0.050   2147
  Dihedral  : 10.885 117.034   2961
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 19.02 %
    Favored  : 78.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.21 (0.23), residues: 1461
  helix:  1.49 (0.18), residues: 882
  sheet:  0.37 (0.66), residues: 71
  loop : -0.26 (0.29), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 625 
 HIS   0.009   0.001   HIS A1195 
 PHE   0.013   0.001   PHE A1581 
 TYR   0.017   0.001   TYR A1503 
 ARG   0.010   0.000   ARG A 852 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00251 (    1)
  link_NAG-ASN         : angle       1.60928 (    3)
  link_BETA1-4         : bond        0.00108 (    1)
  link_BETA1-4         : angle       1.81103 (    3)
  hydrogen bonds       : bond        0.03863 (  640)
  hydrogen bonds       : angle       4.13055 ( 1857)
  SS BOND              : bond        0.00317 (    2)
  SS BOND              : angle       0.38926 (    4)
  covalent geometry    : bond        0.00231 (13203)
  covalent geometry    : angle       0.55630 (17978)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 11192.06 seconds
wall clock time: 192 minutes 52.94 seconds (11572.94 seconds total)