Starting phenix.real_space_refine
on Sat Oct 11 10:08:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jzn_36748/10_2025/8jzn_36748.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jzn_36748/10_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_36748/10_2025/8jzn_36748.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jzn_36748/10_2025/8jzn_36748.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jzn_36748/10_2025/8jzn_36748.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jzn_36748/10_2025/8jzn_36748.cif"
  }
  resolution = 2.47
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 3.32, per 1000 atoms: 0.26
  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: 1.24
  Conformation dependent library (CDL) restraints added in 588.9 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  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: 0.52
  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: 2.75

  Time building geometry restraints manager: 1.70 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:             1.760
  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:             0.000
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     14.240
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.030
  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:8.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.740
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.021   0.001   ARG A 791 
 TYR   0.017   0.002   TYR A1804 
 PHE   0.027   0.002   PHE A1657 
 TRP   0.018   0.002   TRP A 493 
 HIS   0.010   0.001   HIS A1195 

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

*********************** 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  : 0.494 
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: 0.6782
  time to fit residues: 123.0289
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  : 0.489 
-------------------------------------------------------------------------------
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 98 optimal weight:   10.0000
   chunk 107 optimal weight:    0.5980
   chunk 10 optimal weight:    0.0030
   chunk 66 optimal weight:    3.9990
   chunk 130 optimal weight:    0.8980
   chunk 124 optimal weight:    0.8980
   chunk 103 optimal weight:    0.5980
   chunk 77 optimal weight:    0.8980
   chunk 122 optimal weight:    7.9990
   chunk 91 optimal weight:    0.9980
   chunk 55 optimal weight:    0.9990
   overall best weight:    0.5990

-------------------------------------------------------------------------------
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
A1688 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.157347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.105508 restraints weight = 14174.978|
|-----------------------------------------------------------------------------|
r_work (start): 0.3255 rms_B_bonded: 2.24
r_work: 0.3112 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2969 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.2969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7422
moved from start:          0.1336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  13207  Z= 0.136
  Angle     :  0.662   9.744  17988  Z= 0.321
  Chirality :  0.042   0.173   2024
  Planarity :  0.005   0.055   2147
  Dihedral  : 16.075 167.524   2984
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 15.20 %
    Favored  : 81.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.30 (0.21), residues: 1461
  helix:  0.04 (0.17), residues: 892
  sheet:  0.46 (0.65), residues: 66
  loop : -0.47 (0.28), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 791 
 TYR   0.015   0.001   TYR A1503 
 PHE   0.015   0.001   PHE A1581 
 TRP   0.015   0.001   TRP A 664 
 HIS   0.010   0.001   HIS A1195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 (13203)
  covalent geometry    : angle       0.66177 (17978)
  SS BOND              : bond        0.00378 (    2)
  SS BOND              : angle       0.51971 (    4)
  hydrogen bonds       : bond        0.05189 (  640)
  hydrogen bonds       : angle       4.87524 ( 1857)
  link_BETA1-4         : bond        0.00090 (    1)
  link_BETA1-4         : angle       1.82650 (    3)
  link_NAG-ASN         : bond        0.00316 (    1)
  link_NAG-ASN         : angle       1.85291 (    3)

*********************** 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
  195 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 158
  time to evaluate  : 0.480 
Fit side-chains
REVERT: A  386 LYS cc_start: 0.8600 (mmmt) cc_final: 0.7776 (mmtt)
REVERT: A  443 ARG cc_start: 0.7784 (mtm180) cc_final: 0.6262 (mtm110)
REVERT: A  518 VAL cc_start: 0.8638 (OUTLIER) cc_final: 0.8388 (m)
REVERT: A  533 TRP cc_start: 0.7155 (t60) cc_final: 0.5500 (m100)
REVERT: A  640 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8093 (mp)
REVERT: A  745 LYS cc_start: 0.7701 (ttmt) cc_final: 0.7177 (mptt)
REVERT: A  791 ARG cc_start: 0.7570 (ptp-110) cc_final: 0.6447 (ptm-80)
REVERT: A  794 THR cc_start: 0.8412 (p) cc_final: 0.8112 (t)
REVERT: A  809 PHE cc_start: 0.7891 (OUTLIER) cc_final: 0.7016 (p90)
REVERT: A  974 GLU cc_start: 0.7439 (pm20) cc_final: 0.7186 (pm20)
REVERT: A  984 GLU cc_start: 0.6932 (tm-30) cc_final: 0.6711 (tm-30)
REVERT: A 1088 HIS cc_start: 0.8134 (OUTLIER) cc_final: 0.7058 (t70)
REVERT: A 1202 THR cc_start: 0.8879 (t) cc_final: 0.8629 (m)
REVERT: A 1269 GLN cc_start: 0.7373 (OUTLIER) cc_final: 0.6248 (mm-40)
REVERT: A 1642 MET cc_start: 0.6565 (tmm) cc_final: 0.6027 (pmm)
REVERT: A 1739 GLU cc_start: 0.7244 (mm-30) cc_final: 0.7041 (tp30)
REVERT: A 1836 VAL cc_start: 0.8052 (m) cc_final: 0.7787 (p)
  outliers start: 37
  outliers final: 7
  residues processed: 182
  average time/residue: 0.5926
  time to fit residues: 117.9540
Evaluate side-chains
  152 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 140
  time to evaluate  : 0.431 
-------------------------------------------------------------------------------
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  610 PHE
Chi-restraints excluded: chain A residue  616 LEU
Chi-restraints excluded: chain A residue  640 LEU
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 1847 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 95 optimal weight:    0.7980
   chunk 107 optimal weight:    0.6980
   chunk 134 optimal weight:    0.9980
   chunk 109 optimal weight:    0.0070
   chunk 66 optimal weight:    0.6980
   chunk 86 optimal weight:    3.9990
   chunk 144 optimal weight:    0.0470
   chunk 4 optimal weight:    1.9990
   chunk 104 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   chunk 73 optimal weight:    2.9990
   overall best weight:    0.4496

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

Flipped N/Q/H residues before XYZ refinement:
A 700 ASN
A 721 ASN
** 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 = 0.3887 r_free = 0.3887 target = 0.158707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.107418 restraints weight = 14358.198|
|-----------------------------------------------------------------------------|
r_work (start): 0.3277 rms_B_bonded: 2.77
r_work: 0.3121 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.2976 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.2976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7384
moved from start:          0.1744

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044  13207  Z= 0.114
  Angle     :  0.584   9.263  17988  Z= 0.284
  Chirality :  0.040   0.158   2024
  Planarity :  0.004   0.052   2147
  Dihedral  : 13.673 170.445   2965
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 15.74 %
    Favored  : 80.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.42 (0.22), residues: 1461
  helix:  0.70 (0.17), residues: 890
  sheet:  0.58 (0.66), residues: 66
  loop : -0.34 (0.29), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 852 
 TYR   0.017   0.001   TYR A1503 
 PHE   0.014   0.001   PHE A1581 
 TRP   0.014   0.001   TRP A 664 
 HIS   0.009   0.001   HIS A1195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 (13203)
  covalent geometry    : angle       0.58299 (17978)
  SS BOND              : bond        0.00381 (    2)
  SS BOND              : angle       0.51400 (    4)
  hydrogen bonds       : bond        0.04503 (  640)
  hydrogen bonds       : angle       4.47895 ( 1857)
  link_BETA1-4         : bond        0.00419 (    1)
  link_BETA1-4         : angle       1.80364 (    3)
  link_NAG-ASN         : bond        0.00233 (    1)
  link_NAG-ASN         : angle       1.76493 (    3)

*********************** 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
  200 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 156
  time to evaluate  : 0.392 
Fit side-chains
   revert: symmetry clash
REVERT: A  386 LYS cc_start: 0.8643 (mmmt) cc_final: 0.7776 (mmtt)
REVERT: A  443 ARG cc_start: 0.7774 (mtm180) cc_final: 0.6246 (mtm110)
REVERT: A  518 VAL cc_start: 0.8613 (OUTLIER) cc_final: 0.8400 (m)
REVERT: A  533 TRP cc_start: 0.7299 (t60) cc_final: 0.5476 (m100)
REVERT: A  719 TRP cc_start: 0.6798 (m100) cc_final: 0.6588 (m100)
REVERT: A  745 LYS cc_start: 0.7581 (ttmt) cc_final: 0.7120 (mptt)
REVERT: A  763 ARG cc_start: 0.7643 (mmt180) cc_final: 0.6726 (mtm-85)
REVERT: A  791 ARG cc_start: 0.7426 (ptp-110) cc_final: 0.6379 (ptm-80)
REVERT: A  794 THR cc_start: 0.8326 (p) cc_final: 0.8073 (t)
REVERT: A  984 GLU cc_start: 0.6974 (tm-30) cc_final: 0.6756 (tm-30)
REVERT: A 1057 GLU cc_start: 0.7447 (tm-30) cc_final: 0.7085 (tm-30)
REVERT: A 1088 HIS cc_start: 0.8104 (OUTLIER) cc_final: 0.6988 (t70)
REVERT: A 1202 THR cc_start: 0.8875 (t) cc_final: 0.8612 (m)
REVERT: A 1268 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.6954 (tt0)
REVERT: A 1694 MET cc_start: 0.5511 (OUTLIER) cc_final: 0.4842 (mpt)
REVERT: A 1770 MET cc_start: 0.6681 (mpt) cc_final: 0.6481 (mpt)
REVERT: A 1836 VAL cc_start: 0.7750 (m) cc_final: 0.7470 (p)
  outliers start: 44
  outliers final: 15
  residues processed: 181
  average time/residue: 0.6220
  time to fit residues: 122.7342
Evaluate side-chains
  162 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 143
  time to evaluate  : 0.462 
-------------------------------------------------------------------------------
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  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  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  761 MET
Chi-restraints excluded: chain A residue 1088 HIS
Chi-restraints excluded: chain A residue 1268 GLU
Chi-restraints excluded: chain A residue 1308 LEU
Chi-restraints excluded: chain A residue 1316 VAL
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 143 optimal weight:    3.9990
   chunk 42 optimal weight:    2.9990
   chunk 43 optimal weight:    0.6980
   chunk 130 optimal weight:    6.9990
   chunk 125 optimal weight:    0.0170
   chunk 146 optimal weight:    5.9990
   chunk 55 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   chunk 136 optimal weight:    0.9990
   chunk 111 optimal weight:    1.9990
   chunk 88 optimal weight:    4.9990
   overall best weight:    1.3424

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

Flipped N/Q/H residues before XYZ refinement:
A 700 ASN
A 721 ASN
** A1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1388 GLN
A1688 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.156185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.104376 restraints weight = 14232.276|
|-----------------------------------------------------------------------------|
r_work (start): 0.3231 rms_B_bonded: 2.82
r_work: 0.3069 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.2923 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.2923
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7413
moved from start:          0.1685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  13207  Z= 0.175
  Angle     :  0.627  11.212  17988  Z= 0.307
  Chirality :  0.042   0.174   2024
  Planarity :  0.004   0.051   2147
  Dihedral  : 12.886 176.736   2965
  Min Nonbonded Distance : 2.372

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 16.04 %
    Favored  : 80.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.52 (0.22), residues: 1461
  helix:  0.86 (0.17), residues: 883
  sheet:  0.52 (0.66), residues: 66
  loop : -0.44 (0.28), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 852 
 TYR   0.018   0.001   TYR A1503 
 PHE   0.014   0.002   PHE A1581 
 TRP   0.014   0.001   TRP A 625 
 HIS   0.007   0.001   HIS A1195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 (13203)
  covalent geometry    : angle       0.62560 (17978)
  SS BOND              : bond        0.00354 (    2)
  SS BOND              : angle       0.48946 (    4)
  hydrogen bonds       : bond        0.04787 (  640)
  hydrogen bonds       : angle       4.46739 ( 1857)
  link_BETA1-4         : bond        0.00228 (    1)
  link_BETA1-4         : angle       2.21950 (    3)
  link_NAG-ASN         : bond        0.00127 (    1)
  link_NAG-ASN         : angle       1.79274 (    3)

*********************** 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
  201 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 153
  time to evaluate  : 0.493 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  230 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.7249 (mt)
REVERT: A  386 LYS cc_start: 0.8560 (mmmt) cc_final: 0.7762 (mmtt)
REVERT: A  443 ARG cc_start: 0.7793 (mtm180) cc_final: 0.6230 (mtm110)
REVERT: A  518 VAL cc_start: 0.8613 (OUTLIER) cc_final: 0.8370 (m)
REVERT: A  533 TRP cc_start: 0.7232 (t60) cc_final: 0.5443 (m100)
REVERT: A  640 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8135 (mp)
REVERT: A  745 LYS cc_start: 0.7545 (ttmt) cc_final: 0.7101 (mptt)
REVERT: A  791 ARG cc_start: 0.7396 (ptp-110) cc_final: 0.6577 (ptt-90)
REVERT: A  794 THR cc_start: 0.8353 (p) cc_final: 0.8023 (t)
REVERT: A  862 ARG cc_start: 0.4542 (OUTLIER) cc_final: 0.3314 (tpm170)
REVERT: A  974 GLU cc_start: 0.7523 (pm20) cc_final: 0.7301 (pm20)
REVERT: A  984 GLU cc_start: 0.6898 (tm-30) cc_final: 0.6619 (tm-30)
REVERT: A 1057 GLU cc_start: 0.7542 (tm-30) cc_final: 0.7221 (tm-30)
REVERT: A 1088 HIS cc_start: 0.8344 (OUTLIER) cc_final: 0.7111 (t70)
REVERT: A 1202 THR cc_start: 0.8828 (t) cc_final: 0.8579 (m)
REVERT: A 1268 GLU cc_start: 0.7434 (mt-10) cc_final: 0.7007 (tt0)
REVERT: A 1269 GLN cc_start: 0.7540 (mt0) cc_final: 0.6111 (mm-40)
REVERT: A 1642 MET cc_start: 0.6221 (OUTLIER) cc_final: 0.5625 (pmm)
REVERT: A 1694 MET cc_start: 0.5456 (OUTLIER) cc_final: 0.4855 (mpt)
REVERT: A 1836 VAL cc_start: 0.7778 (m) cc_final: 0.7474 (p)
  outliers start: 48
  outliers final: 18
  residues processed: 179
  average time/residue: 0.6052
  time to fit residues: 118.3984
Evaluate side-chains
  172 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 147
  time to evaluate  : 0.463 
-------------------------------------------------------------------------------
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  741 GLU
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 1308 LEU
Chi-restraints excluded: chain A residue 1316 VAL
Chi-restraints excluded: chain A residue 1339 VAL
Chi-restraints excluded: chain A residue 1378 LEU
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 106 optimal weight:    2.9990
   chunk 127 optimal weight:    1.9990
   chunk 111 optimal weight:    0.8980
   chunk 47 optimal weight:    5.9990
   chunk 10 optimal weight:    1.9990
   chunk 80 optimal weight:    3.9990
   chunk 57 optimal weight:    0.7980
   chunk 124 optimal weight:    2.9990
   chunk 145 optimal weight:    6.9990
   chunk 141 optimal weight:    0.0060
   chunk 60 optimal weight:    0.3980
   overall best weight:    0.8198

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

Flipped N/Q/H residues before XYZ refinement:
A 700 ASN
** A1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1388 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.157534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.105897 restraints weight = 14252.100|
|-----------------------------------------------------------------------------|
r_work (start): 0.3256 rms_B_bonded: 2.82
r_work: 0.3096 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.2951 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.2951
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7387
moved from start:          0.1898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  13207  Z= 0.128
  Angle     :  0.572   9.280  17988  Z= 0.281
  Chirality :  0.040   0.153   2024
  Planarity :  0.004   0.050   2147
  Dihedral  : 12.165 161.741   2963
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 17.19 %
    Favored  : 79.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.80 (0.22), residues: 1461
  helix:  1.12 (0.17), residues: 882
  sheet:  0.69 (0.67), residues: 66
  loop : -0.40 (0.29), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A 852 
 TYR   0.017   0.001   TYR A1503 
 PHE   0.015   0.001   PHE A1581 
 TRP   0.014   0.001   TRP A 625 
 HIS   0.008   0.001   HIS A1195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 (13203)
  covalent geometry    : angle       0.57132 (17978)
  SS BOND              : bond        0.00339 (    2)
  SS BOND              : angle       0.45395 (    4)
  hydrogen bonds       : bond        0.04272 (  640)
  hydrogen bonds       : angle       4.32758 ( 1857)
  link_BETA1-4         : bond        0.00286 (    1)
  link_BETA1-4         : angle       1.93157 (    3)
  link_NAG-ASN         : bond        0.00175 (    1)
  link_NAG-ASN         : angle       1.72845 (    3)

*********************** 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
  188 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 150
  time to evaluate  : 0.439 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  386 LYS cc_start: 0.8564 (mmmt) cc_final: 0.7743 (mmtt)
REVERT: A  443 ARG cc_start: 0.7784 (mtm180) cc_final: 0.6210 (mtm110)
REVERT: A  518 VAL cc_start: 0.8609 (OUTLIER) cc_final: 0.8383 (m)
REVERT: A  533 TRP cc_start: 0.7288 (t60) cc_final: 0.5450 (m100)
REVERT: A  640 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8084 (mp)
REVERT: A  745 LYS cc_start: 0.7498 (ttmt) cc_final: 0.7046 (mptt)
REVERT: A  791 ARG cc_start: 0.7371 (ptp-110) cc_final: 0.6311 (ptm-80)
REVERT: A  794 THR cc_start: 0.8306 (p) cc_final: 0.8033 (t)
REVERT: A  809 PHE cc_start: 0.7812 (OUTLIER) cc_final: 0.6850 (p90)
REVERT: A  862 ARG cc_start: 0.4530 (OUTLIER) cc_final: 0.3230 (tpm170)
REVERT: A  984 GLU cc_start: 0.6946 (tm-30) cc_final: 0.6643 (tm-30)
REVERT: A 1057 GLU cc_start: 0.7546 (tm-30) cc_final: 0.7221 (tm-30)
REVERT: A 1088 HIS cc_start: 0.8299 (OUTLIER) cc_final: 0.7215 (t70)
REVERT: A 1202 THR cc_start: 0.8890 (t) cc_final: 0.8597 (m)
REVERT: A 1268 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.7000 (tt0)
REVERT: A 1269 GLN cc_start: 0.7468 (mt0) cc_final: 0.6044 (mm-40)
REVERT: A 1504 ARG cc_start: 0.7301 (tmm160) cc_final: 0.7095 (tmm160)
REVERT: A 1694 MET cc_start: 0.5444 (OUTLIER) cc_final: 0.4889 (mpt)
REVERT: A 1770 MET cc_start: 0.6840 (mpt) cc_final: 0.6597 (mpt)
REVERT: A 1836 VAL cc_start: 0.7739 (m) cc_final: 0.7440 (p)
REVERT: A 1848 ASN cc_start: 0.7978 (p0) cc_final: 0.7693 (p0)
  outliers start: 38
  outliers final: 19
  residues processed: 169
  average time/residue: 0.6225
  time to fit residues: 114.8202
Evaluate side-chains
  175 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 149
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
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  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  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 1268 GLU
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 1388 GLN
Chi-restraints excluded: chain A residue 1482 LEU
Chi-restraints excluded: chain A residue 1642 MET
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 90 optimal weight:    3.9990
   chunk 126 optimal weight:    0.6980
   chunk 8 optimal weight:    0.6980
   chunk 21 optimal weight:    3.9990
   chunk 2 optimal weight:    2.9990
   chunk 91 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   chunk 144 optimal weight:    2.9990
   chunk 53 optimal weight:    0.1980
   chunk 6 optimal weight:    1.9990
   chunk 67 optimal weight:    3.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A 700 ASN
A 721 ASN
** A1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1688 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.157356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.106002 restraints weight = 14166.492|
|-----------------------------------------------------------------------------|
r_work (start): 0.3258 rms_B_bonded: 2.79
r_work: 0.3096 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.2952 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.2952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7397
moved from start:          0.1936

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= 0.136
  Angle     :  0.577   9.194  17988  Z= 0.283
  Chirality :  0.040   0.159   2024
  Planarity :  0.004   0.050   2147
  Dihedral  : 11.886 149.989   2963
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 16.96 %
    Favored  : 79.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.89 (0.22), residues: 1461
  helix:  1.19 (0.17), residues: 885
  sheet:  0.67 (0.67), residues: 66
  loop : -0.36 (0.29), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 852 
 TYR   0.018   0.001   TYR A1503 
 PHE   0.014   0.001   PHE A1581 
 TRP   0.014   0.001   TRP A 625 
 HIS   0.007   0.001   HIS A1195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 (13203)
  covalent geometry    : angle       0.57575 (17978)
  SS BOND              : bond        0.00342 (    2)
  SS BOND              : angle       0.43678 (    4)
  hydrogen bonds       : bond        0.04298 (  640)
  hydrogen bonds       : angle       4.28477 ( 1857)
  link_BETA1-4         : bond        0.00054 (    1)
  link_BETA1-4         : angle       1.97097 (    3)
  link_NAG-ASN         : bond        0.00093 (    1)
  link_NAG-ASN         : angle       1.73990 (    3)

*********************** 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
  199 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 153
  time to evaluate  : 0.449 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  386 LYS cc_start: 0.8568 (mmmt) cc_final: 0.7746 (mmtt)
REVERT: A  443 ARG cc_start: 0.7789 (mtm180) cc_final: 0.6207 (mtm110)
REVERT: A  518 VAL cc_start: 0.8618 (OUTLIER) cc_final: 0.8397 (m)
REVERT: A  533 TRP cc_start: 0.7298 (t60) cc_final: 0.5459 (m100)
REVERT: A  640 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8076 (mp)
REVERT: A  745 LYS cc_start: 0.7487 (ttmt) cc_final: 0.7039 (mptt)
REVERT: A  791 ARG cc_start: 0.7469 (ptp-110) cc_final: 0.6361 (ptm-80)
REVERT: A  794 THR cc_start: 0.8311 (p) cc_final: 0.8046 (t)
REVERT: A  809 PHE cc_start: 0.7868 (OUTLIER) cc_final: 0.6910 (p90)
REVERT: A  862 ARG cc_start: 0.4569 (OUTLIER) cc_final: 0.3234 (tpm170)
REVERT: A  984 GLU cc_start: 0.6983 (tm-30) cc_final: 0.6713 (tm-30)
REVERT: A 1057 GLU cc_start: 0.7570 (tm-30) cc_final: 0.7214 (tm-30)
REVERT: A 1088 HIS cc_start: 0.8334 (OUTLIER) cc_final: 0.7242 (t70)
REVERT: A 1202 THR cc_start: 0.8836 (t) cc_final: 0.8592 (m)
REVERT: A 1268 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.6919 (tt0)
REVERT: A 1269 GLN cc_start: 0.7547 (OUTLIER) cc_final: 0.6152 (mm-40)
REVERT: A 1388 GLN cc_start: 0.4848 (OUTLIER) cc_final: 0.4586 (mt0)
REVERT: A 1642 MET cc_start: 0.5519 (tpt) cc_final: 0.5211 (pmm)
REVERT: A 1694 MET cc_start: 0.5420 (OUTLIER) cc_final: 0.4835 (mpt)
REVERT: A 1770 MET cc_start: 0.6815 (mpt) cc_final: 0.6547 (mpt)
REVERT: A 1836 VAL cc_start: 0.7720 (m) cc_final: 0.7445 (p)
REVERT: A 1848 ASN cc_start: 0.7996 (p0) cc_final: 0.7724 (p0)
  outliers start: 46
  outliers final: 22
  residues processed: 179
  average time/residue: 0.6346
  time to fit residues: 124.0087
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  : 0.491 
-------------------------------------------------------------------------------
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  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  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 1083 SER
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 1328 CYS
Chi-restraints excluded: chain A residue 1339 VAL
Chi-restraints excluded: chain A residue 1378 LEU
Chi-restraints excluded: chain A residue 1388 GLN
Chi-restraints excluded: chain A residue 1612 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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 19 optimal weight:    0.9990
   chunk 31 optimal weight:    0.5980
   chunk 36 optimal weight:    3.9990
   chunk 99 optimal weight:    2.9990
   chunk 80 optimal weight:    0.5980
   chunk 142 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9990
   chunk 143 optimal weight:    2.9990
   chunk 25 optimal weight:    0.5980
   chunk 30 optimal weight:    4.9990
   chunk 111 optimal weight:    1.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
A 700 ASN
** A1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1388 GLN
A1688 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.158288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.106665 restraints weight = 14177.187|
|-----------------------------------------------------------------------------|
r_work (start): 0.3267 rms_B_bonded: 2.82
r_work: 0.3106 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work: 0.2961 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.2961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7372
moved from start:          0.2098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  13207  Z= 0.118
  Angle     :  0.553   9.045  17988  Z= 0.273
  Chirality :  0.040   0.154   2024
  Planarity :  0.004   0.050   2147
  Dihedral  : 11.432 136.799   2963
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 17.49 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.08 (0.22), residues: 1461
  helix:  1.35 (0.17), residues: 885
  sheet:  0.75 (0.68), residues: 66
  loop : -0.33 (0.29), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 852 
 TYR   0.015   0.001   TYR A1503 
 PHE   0.014   0.001   PHE A1581 
 TRP   0.013   0.001   TRP A 625 
 HIS   0.008   0.001   HIS A1195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 (13203)
  covalent geometry    : angle       0.55192 (17978)
  SS BOND              : bond        0.00322 (    2)
  SS BOND              : angle       0.42663 (    4)
  hydrogen bonds       : bond        0.04059 (  640)
  hydrogen bonds       : angle       4.19254 ( 1857)
  link_BETA1-4         : bond        0.00185 (    1)
  link_BETA1-4         : angle       1.89136 (    3)
  link_NAG-ASN         : bond        0.00164 (    1)
  link_NAG-ASN         : angle       1.69191 (    3)

*********************** 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
  192 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 152
  time to evaluate  : 0.421 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  371 GLU cc_start: 0.6974 (tp30) cc_final: 0.6493 (pt0)
REVERT: A  386 LYS cc_start: 0.8578 (mmmt) cc_final: 0.7762 (mmtt)
REVERT: A  443 ARG cc_start: 0.7780 (mtm180) cc_final: 0.6197 (mtm110)
REVERT: A  533 TRP cc_start: 0.7332 (t60) cc_final: 0.5334 (m100)
REVERT: A  640 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8081 (mp)
REVERT: A  745 LYS cc_start: 0.7391 (ttmt) cc_final: 0.6909 (mptt)
REVERT: A  791 ARG cc_start: 0.7373 (ptp-110) cc_final: 0.6282 (ptm-80)
REVERT: A  794 THR cc_start: 0.8231 (p) cc_final: 0.7987 (t)
REVERT: A  809 PHE cc_start: 0.7832 (OUTLIER) cc_final: 0.6926 (p90)
REVERT: A  862 ARG cc_start: 0.4539 (OUTLIER) cc_final: 0.3218 (tpm170)
REVERT: A  974 GLU cc_start: 0.7629 (pm20) cc_final: 0.7401 (pm20)
REVERT: A  984 GLU cc_start: 0.6809 (tm-30) cc_final: 0.6120 (tm-30)
REVERT: A  988 ARG cc_start: 0.7106 (mtm-85) cc_final: 0.6700 (mtm-85)
REVERT: A 1057 GLU cc_start: 0.7588 (tm-30) cc_final: 0.7256 (tm-30)
REVERT: A 1088 HIS cc_start: 0.8307 (OUTLIER) cc_final: 0.7218 (t70)
REVERT: A 1202 THR cc_start: 0.8828 (OUTLIER) cc_final: 0.8581 (m)
REVERT: A 1268 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.6928 (tt0)
REVERT: A 1269 GLN cc_start: 0.7519 (OUTLIER) cc_final: 0.6144 (mm-40)
REVERT: A 1694 MET cc_start: 0.5223 (OUTLIER) cc_final: 0.4702 (mpt)
REVERT: A 1770 MET cc_start: 0.6825 (mpt) cc_final: 0.6615 (mpt)
REVERT: A 1836 VAL cc_start: 0.7693 (m) cc_final: 0.7430 (p)
REVERT: A 1848 ASN cc_start: 0.7998 (p0) cc_final: 0.7742 (p0)
  outliers start: 40
  outliers final: 21
  residues processed: 175
  average time/residue: 0.6306
  time to fit residues: 120.2084
Evaluate side-chains
  178 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 149
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
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  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  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 1083 SER
Chi-restraints excluded: chain A residue 1088 HIS
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 1388 GLN
Chi-restraints excluded: chain A residue 1653 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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 37 optimal weight:    7.9990
   chunk 57 optimal weight:    4.9990
   chunk 88 optimal weight:    2.9990
   chunk 110 optimal weight:    0.9980
   chunk 14 optimal weight:    2.9990
   chunk 93 optimal weight:    1.9990
   chunk 64 optimal weight:    4.9990
   chunk 109 optimal weight:    0.9990
   chunk 147 optimal weight:    0.0970
   chunk 31 optimal weight:    0.6980
   chunk 119 optimal weight:    1.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
A 700 ASN
A 721 ASN
A 824 GLN
** A1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1388 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.157667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.106890 restraints weight = 14110.574|
|-----------------------------------------------------------------------------|
r_work (start): 0.3268 rms_B_bonded: 2.64
r_work: 0.3105 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.2961 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.2961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7402
moved from start:          0.2075

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= 0.137
  Angle     :  0.564   9.510  17988  Z= 0.278
  Chirality :  0.040   0.159   2024
  Planarity :  0.004   0.049   2147
  Dihedral  : 11.365 132.354   2963
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 17.80 %
    Favored  : 79.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.09 (0.22), residues: 1461
  helix:  1.37 (0.17), residues: 879
  sheet:  0.74 (0.67), residues: 66
  loop : -0.30 (0.29), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 376 
 TYR   0.018   0.001   TYR A1503 
 PHE   0.014   0.001   PHE A1581 
 TRP   0.013   0.001   TRP A 625 
 HIS   0.008   0.001   HIS A1195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 (13203)
  covalent geometry    : angle       0.56265 (17978)
  SS BOND              : bond        0.00335 (    2)
  SS BOND              : angle       0.45810 (    4)
  hydrogen bonds       : bond        0.04201 (  640)
  hydrogen bonds       : angle       4.21372 ( 1857)
  link_BETA1-4         : bond        0.00067 (    1)
  link_BETA1-4         : angle       1.93609 (    3)
  link_NAG-ASN         : bond        0.00076 (    1)
  link_NAG-ASN         : angle       1.74533 (    3)

*********************** 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
  190 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 152
  time to evaluate  : 0.499 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  371 GLU cc_start: 0.6980 (tp30) cc_final: 0.6503 (pt0)
REVERT: A  386 LYS cc_start: 0.8586 (mmmt) cc_final: 0.7777 (mmtt)
REVERT: A  443 ARG cc_start: 0.7813 (mtm180) cc_final: 0.6220 (mtm110)
REVERT: A  640 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8123 (mp)
REVERT: A  745 LYS cc_start: 0.7429 (ttmt) cc_final: 0.6961 (mptt)
REVERT: A  791 ARG cc_start: 0.7378 (ptp-110) cc_final: 0.6285 (ptm-80)
REVERT: A  794 THR cc_start: 0.8247 (p) cc_final: 0.7994 (t)
REVERT: A  809 PHE cc_start: 0.7914 (OUTLIER) cc_final: 0.6971 (p90)
REVERT: A  862 ARG cc_start: 0.4605 (OUTLIER) cc_final: 0.3333 (tpm170)
REVERT: A  974 GLU cc_start: 0.7629 (pm20) cc_final: 0.7379 (pm20)
REVERT: A  984 GLU cc_start: 0.6876 (tm-30) cc_final: 0.6172 (tm-30)
REVERT: A  988 ARG cc_start: 0.7150 (mtm-85) cc_final: 0.6716 (mtm-85)
REVERT: A 1057 GLU cc_start: 0.7609 (tm-30) cc_final: 0.7277 (tm-30)
REVERT: A 1088 HIS cc_start: 0.8347 (OUTLIER) cc_final: 0.7158 (t70)
REVERT: A 1202 THR cc_start: 0.8843 (OUTLIER) cc_final: 0.8588 (m)
REVERT: A 1269 GLN cc_start: 0.7538 (OUTLIER) cc_final: 0.6141 (mm-40)
REVERT: A 1642 MET cc_start: 0.5905 (mpt) cc_final: 0.5602 (pmm)
REVERT: A 1694 MET cc_start: 0.5285 (OUTLIER) cc_final: 0.4777 (mpt)
REVERT: A 1770 MET cc_start: 0.6819 (mpt) cc_final: 0.6588 (mpt)
REVERT: A 1836 VAL cc_start: 0.7713 (m) cc_final: 0.7450 (p)
REVERT: A 1848 ASN cc_start: 0.8090 (p0) cc_final: 0.7795 (p0)
  outliers start: 38
  outliers final: 24
  residues processed: 174
  average time/residue: 0.6413
  time to fit residues: 121.6324
Evaluate side-chains
  180 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 149
  time to evaluate  : 0.481 
-------------------------------------------------------------------------------
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  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  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 1083 SER
Chi-restraints excluded: chain A residue 1088 HIS
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 1690 MET
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 94 optimal weight:    4.9990
   chunk 28 optimal weight:    0.6980
   chunk 68 optimal weight:    0.1980
   chunk 36 optimal weight:    0.9980
   chunk 32 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9980
   chunk 79 optimal weight:    0.9980
   chunk 40 optimal weight:    1.9990
   chunk 10 optimal weight:    4.9990
   chunk 145 optimal weight:    5.9990
   chunk 85 optimal weight:    3.9990
   overall best weight:    0.7180

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.158392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.107318 restraints weight = 14205.006|
|-----------------------------------------------------------------------------|
r_work (start): 0.3275 rms_B_bonded: 2.68
r_work: 0.3115 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.2970 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.2970
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7395
moved from start:          0.2144

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= 0.120
  Angle     :  0.553  10.371  17988  Z= 0.274
  Chirality :  0.040   0.154   2024
  Planarity :  0.004   0.049   2147
  Dihedral  : 11.227 127.732   2963
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 18.33 %
    Favored  : 79.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.17 (0.22), residues: 1461
  helix:  1.42 (0.18), residues: 882
  sheet:  0.80 (0.68), residues: 66
  loop : -0.26 (0.29), residues: 513

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 (13203)
  covalent geometry    : angle       0.55218 (17978)
  SS BOND              : bond        0.00332 (    2)
  SS BOND              : angle       0.43176 (    4)
  hydrogen bonds       : bond        0.04070 (  640)
  hydrogen bonds       : angle       4.17743 ( 1857)
  link_BETA1-4         : bond        0.00054 (    1)
  link_BETA1-4         : angle       1.86887 (    3)
  link_NAG-ASN         : bond        0.00143 (    1)
  link_NAG-ASN         : angle       1.70848 (    3)

*********************** 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
  180 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 149
  time to evaluate  : 0.499 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  371 GLU cc_start: 0.6983 (tp30) cc_final: 0.6515 (pt0)
REVERT: A  386 LYS cc_start: 0.8586 (mmmt) cc_final: 0.7777 (mmtt)
REVERT: A  443 ARG cc_start: 0.7810 (mtm180) cc_final: 0.6220 (mtm110)
REVERT: A  533 TRP cc_start: 0.7358 (t60) cc_final: 0.5362 (m100)
REVERT: A  745 LYS cc_start: 0.7409 (ttmt) cc_final: 0.6926 (mptt)
REVERT: A  791 ARG cc_start: 0.7386 (ptp-110) cc_final: 0.6300 (ptm-80)
REVERT: A  794 THR cc_start: 0.8239 (p) cc_final: 0.7997 (t)
REVERT: A  862 ARG cc_start: 0.4523 (OUTLIER) cc_final: 0.3279 (tpm170)
REVERT: A  974 GLU cc_start: 0.7667 (pm20) cc_final: 0.7411 (pm20)
REVERT: A  984 GLU cc_start: 0.6933 (tm-30) cc_final: 0.6135 (tm-30)
REVERT: A  988 ARG cc_start: 0.7119 (mtm-85) cc_final: 0.6656 (mtm-85)
REVERT: A 1057 GLU cc_start: 0.7606 (tm-30) cc_final: 0.7269 (tm-30)
REVERT: A 1088 HIS cc_start: 0.8335 (OUTLIER) cc_final: 0.7229 (t70)
REVERT: A 1202 THR cc_start: 0.8849 (OUTLIER) cc_final: 0.8596 (m)
REVERT: A 1269 GLN cc_start: 0.7537 (OUTLIER) cc_final: 0.6147 (mm-40)
REVERT: A 1388 GLN cc_start: 0.4897 (OUTLIER) cc_final: 0.4632 (mt0)
REVERT: A 1642 MET cc_start: 0.5901 (mpt) cc_final: 0.5593 (pmm)
REVERT: A 1694 MET cc_start: 0.5246 (OUTLIER) cc_final: 0.4748 (mpt)
REVERT: A 1770 MET cc_start: 0.6811 (mpt) cc_final: 0.6552 (mpt)
REVERT: A 1836 VAL cc_start: 0.7732 (m) cc_final: 0.7472 (p)
REVERT: A 1848 ASN cc_start: 0.8105 (p0) cc_final: 0.7841 (p0)
  outliers start: 31
  outliers final: 22
  residues processed: 166
  average time/residue: 0.6674
  time to fit residues: 120.3590
Evaluate side-chains
  177 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 149
  time to evaluate  : 0.455 
-------------------------------------------------------------------------------
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  537 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  862 ARG
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 1268 GLU
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 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 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 24 optimal weight:    0.0070
   chunk 134 optimal weight:    2.9990
   chunk 94 optimal weight:    5.9990
   chunk 5 optimal weight:    0.9990
   chunk 26 optimal weight:    0.7980
   chunk 125 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9990
   chunk 119 optimal weight:    2.9990
   chunk 83 optimal weight:    2.9990
   chunk 35 optimal weight:    3.9990
   chunk 30 optimal weight:    0.0870
   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 700 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 = 0.3895 r_free = 0.3895 target = 0.159491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.108972 restraints weight = 14243.698|
|-----------------------------------------------------------------------------|
r_work (start): 0.3297 rms_B_bonded: 2.48
r_work: 0.3138 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.2994 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.2994
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7434
moved from start:          0.2282

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= 0.110
  Angle     :  0.537   8.458  17988  Z= 0.266
  Chirality :  0.039   0.158   2024
  Planarity :  0.004   0.049   2147
  Dihedral  : 10.928 119.283   2962
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 18.56 %
    Favored  : 79.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.30 (0.23), residues: 1461
  helix:  1.51 (0.18), residues: 889
  sheet:  0.40 (0.66), residues: 71
  loop : -0.14 (0.30), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 376 
 TYR   0.016   0.001   TYR A1503 
 PHE   0.015   0.001   PHE A 887 
 TRP   0.014   0.001   TRP A 625 
 HIS   0.009   0.001   HIS A1195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 (13203)
  covalent geometry    : angle       0.53603 (17978)
  SS BOND              : bond        0.00333 (    2)
  SS BOND              : angle       0.41555 (    4)
  hydrogen bonds       : bond        0.03888 (  640)
  hydrogen bonds       : angle       4.11162 ( 1857)
  link_BETA1-4         : bond        0.00135 (    1)
  link_BETA1-4         : angle       1.80677 (    3)
  link_NAG-ASN         : bond        0.00169 (    1)
  link_NAG-ASN         : angle       1.64370 (    3)

********************** 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
  182 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 152
  time to evaluate  : 0.495 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  371 GLU cc_start: 0.7007 (tp30) cc_final: 0.6588 (pt0)
REVERT: A  386 LYS cc_start: 0.8605 (mmmt) cc_final: 0.7803 (mmtt)
REVERT: A  443 ARG cc_start: 0.7833 (mtm180) cc_final: 0.6255 (mtm110)
REVERT: A  533 TRP cc_start: 0.7419 (t60) cc_final: 0.5435 (m100)
REVERT: A  640 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8099 (mp)
REVERT: A  745 LYS cc_start: 0.7431 (ttmt) cc_final: 0.6968 (mptt)
REVERT: A  791 ARG cc_start: 0.7443 (ptp-110) cc_final: 0.6369 (ptm-80)
REVERT: A  794 THR cc_start: 0.8326 (p) cc_final: 0.8075 (t)
REVERT: A  809 PHE cc_start: 0.7513 (OUTLIER) cc_final: 0.7038 (p90)
REVERT: A  862 ARG cc_start: 0.4620 (OUTLIER) cc_final: 0.3481 (tpm170)
REVERT: A  946 ARG cc_start: 0.8080 (mmt180) cc_final: 0.7549 (mpt180)
REVERT: A  974 GLU cc_start: 0.7755 (pm20) cc_final: 0.7505 (pm20)
REVERT: A  984 GLU cc_start: 0.6926 (tm-30) cc_final: 0.6513 (tm-30)
REVERT: A 1057 GLU cc_start: 0.7670 (tm-30) cc_final: 0.7331 (tm-30)
REVERT: A 1088 HIS cc_start: 0.8368 (OUTLIER) cc_final: 0.7254 (t70)
REVERT: A 1202 THR cc_start: 0.8928 (OUTLIER) cc_final: 0.8672 (m)
REVERT: A 1269 GLN cc_start: 0.7575 (OUTLIER) cc_final: 0.6195 (mm-40)
REVERT: A 1642 MET cc_start: 0.6025 (mpt) cc_final: 0.5748 (pmm)
REVERT: A 1694 MET cc_start: 0.5261 (OUTLIER) cc_final: 0.4751 (mpt)
REVERT: A 1770 MET cc_start: 0.6829 (mpt) cc_final: 0.6563 (mpt)
REVERT: A 1836 VAL cc_start: 0.7764 (m) cc_final: 0.7557 (p)
REVERT: A 1848 ASN cc_start: 0.8115 (p0) cc_final: 0.7900 (p0)
  outliers start: 30
  outliers final: 19
  residues processed: 168
  average time/residue: 0.6775
  time to fit residues: 123.4274
Evaluate side-chains
  176 residues out of total 1309 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 150
  time to evaluate  : 0.518 
-------------------------------------------------------------------------------
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  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  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 1083 SER
Chi-restraints excluded: chain A residue 1088 HIS
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 1328 CYS
Chi-restraints excluded: chain A residue 1339 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 59 optimal weight:    4.9990
   chunk 50 optimal weight:    1.9990
   chunk 123 optimal weight:    0.8980
   chunk 74 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 142 optimal weight:    0.2980
   chunk 23 optimal weight:    3.9990
   chunk 41 optimal weight:    2.9990
   chunk 36 optimal weight:    0.7980
   chunk 144 optimal weight:    2.9990
   chunk 117 optimal weight:    0.5980
   overall best weight:    0.9182

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.158164 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.106626 restraints weight = 14155.540|
|-----------------------------------------------------------------------------|
r_work (start): 0.3265 rms_B_bonded: 2.71
r_work: 0.3108 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.2964 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.2964
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7408
moved from start:          0.2226

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= 0.134
  Angle     :  0.558   9.172  17988  Z= 0.277
  Chirality :  0.040   0.159   2024
  Planarity :  0.004   0.048   2147
  Dihedral  : 10.877 115.635   2961
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 18.56 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.24 (0.23), residues: 1461
  helix:  1.46 (0.17), residues: 888
  sheet:  0.41 (0.66), residues: 71
  loop : -0.15 (0.29), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 852 
 TYR   0.015   0.001   TYR A 308 
 PHE   0.016   0.001   PHE A1499 
 TRP   0.013   0.001   TRP A 625 
 HIS   0.007   0.001   HIS A1195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 (13203)
  covalent geometry    : angle       0.55709 (17978)
  SS BOND              : bond        0.00332 (    2)
  SS BOND              : angle       0.43733 (    4)
  hydrogen bonds       : bond        0.04125 (  640)
  hydrogen bonds       : angle       4.14648 ( 1857)
  link_BETA1-4         : bond        0.00089 (    1)
  link_BETA1-4         : angle       1.88901 (    3)
  link_NAG-ASN         : bond        0.00041 (    1)
  link_NAG-ASN         : angle       1.74060 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6032.04 seconds
wall clock time: 103 minutes 17.85 seconds (6197.85 seconds total)