Starting phenix.real_space_refine
on Tue Jun 10 16:55:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vyj_43662/06_2025/8vyj_43662.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vyj_43662/06_2025/8vyj_43662.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vyj_43662/06_2025/8vyj_43662.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vyj_43662/06_2025/8vyj_43662.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vyj_43662/06_2025/8vyj_43662.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vyj_43662/06_2025/8vyj_43662.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   1.000
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      89      5.16       5
     C    7746      2.51       5
     N    1803      2.21       5
     O    2075      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 11715
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 11210
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1395, 11210
          Classifications: {'peptide': 1395}
          Link IDs: {'PTRANS': 49, 'TRANS': 1345}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 70
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 70
          Unusual residues: {'NAG': 5}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
    Chain: "C"
      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: "D"
      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: "E"
      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: 351
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 351
          Unusual residues: {'6OU': 2, 'NAG': 3, 'Y01': 7}
          Classifications: {'undetermined': 12}
          Link IDs: {None: 11}
          Unresolved non-hydrogen bonds: 37
          Unresolved non-hydrogen angles: 42
          Unresolved non-hydrogen dihedrals: 44
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'Y01:plan-2': 1, 'Y01:plan-1': 1}
          Unresolved non-hydrogen planarities: 7
  Time building chain proxies: 8.41, per 1000 atoms: 0.72
  Number of scatterers: 11715
  At special positions: 0
  Unit cell: (139.345, 132.153, 137.547, 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      89     16.00
     P       2     15.00
     O    2075      8.00
     N    1803      7.00
     C    7746      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 280 " - pdb=" SG  CYS A 335 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 326 " - pdb=" SG  CYS A 341 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 683 " - pdb=" SG  CYS A 686 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 906 " - pdb=" SG  CYS A 915 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1176 " - pdb=" SG  CYS A1178 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1363 " - pdb=" SG  CYS A1384 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1728 " - pdb=" SG  CYS A1742 " 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 B   2 " - " NAG B   3 "
      " NAG B   3 " - " NAG B   4 "
      " NAG B   4 " - " NAG B   5 "
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
    NAG-ASN
      " NAG A2109 " - " ASN A 318 "
      " NAG A2110 " - " ASN A 283 "
      " NAG A2111 " - " ASN A 291 "
      " NAG E   1 " - " ASN A1365 "
  Time building additional restraints: 2.97
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2774 Ramachandran restraints generated.
    1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2638

  Finding SS restraints...
    Secondary structure from input PDB file:
      65 helices and 5 sheets defined
      64.9% alpha, 2.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.18
  Creating SS restraints...
    Processing helix  chain 'A' and resid 21 through 29
      removed outlier: 4.190A  pdb=" N   ARG A  27 " --> pdb=" O   ALA A  23 " (cutoff:3.500A)
      removed outlier: 4.269A  pdb=" N   ALA A  29 " --> pdb=" O   GLU A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 89
    Processing helix  chain 'A' and resid 118 through 130
      removed outlier: 3.961A  pdb=" N   ALA A 124 " --> pdb=" O   ILE A 120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 148
      removed outlier: 4.262A  pdb=" N   LEU A 142 " --> pdb=" O   MET A 138 " (cutoff:3.500A)
      removed outlier: 4.408A  pdb=" N   THR A 143 " --> pdb=" O   CYS A 139 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 156 through 180
      removed outlier: 4.094A  pdb=" N   VAL A 160 " --> pdb=" O   TRP A 156 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   TYR A 162 " --> pdb=" O   LYS A 158 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   THR A 163 " --> pdb=" O   TYR A 159 " (cutoff:3.500A)
      removed outlier: 4.781A  pdb=" N   PHE A 170 " --> pdb=" O   ALA A 166 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 207
      removed outlier: 3.972A  pdb=" N   PHE A 198 " --> pdb=" O   ASN A 194 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   SER A 199 " --> pdb=" O   TRP A 195 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   VAL A 200 " --> pdb=" O   LEU A 196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 210
      No H-bonds generated for 'chain 'A' and resid 208 through 210'
    Processing helix  chain 'A' and resid 218 through 222
      removed outlier: 3.880A  pdb=" N   ARG A 222 " --> pdb=" O   ARG A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 224 through 232
    Processing helix  chain 'A' and resid 233 through 245
      removed outlier: 3.937A  pdb=" N   LYS A 237 " --> pdb=" O   ILE A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 270
      removed outlier: 3.541A  pdb=" N   GLN A 270 " --> pdb=" O   LEU A 266 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 310 through 314
      removed outlier: 3.530A  pdb=" N   TYR A 314 " --> pdb=" O   PRO A 311 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 348 through 352
    Processing helix  chain 'A' and resid 357 through 371
    Processing helix  chain 'A' and resid 374 through 386
    Processing helix  chain 'A' and resid 389 through 401
      removed outlier: 3.998A  pdb=" N   PHE A 393 " --> pdb=" O   TYR A 389 " (cutoff:3.500A)
      removed outlier: 4.173A  pdb=" N   PHE A 398 " --> pdb=" O   MET A 394 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   LEU A 399 " --> pdb=" O   LEU A 395 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 402 through 433
      removed outlier: 3.579A  pdb=" N   THR A 427 " --> pdb=" O   THR A 423 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 688 through 695
      removed outlier: 3.821A  pdb=" N   ARG A 693 " --> pdb=" O   ARG A 689 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   TYR A 694 " --> pdb=" O   LEU A 690 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 705 through 714
    Processing helix  chain 'A' and resid 715 through 736
      removed outlier: 5.557A  pdb=" N   LEU A 721 " --> pdb=" O   PRO A 717 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   THR A 722 " --> pdb=" O   PHE A 718 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   ASN A 730 " --> pdb=" O   CYS A 726 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   LEU A 736 " --> pdb=" O   LEU A 732 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 742 through 771
      removed outlier: 3.980A  pdb=" N   GLU A 746 " --> pdb=" O   THR A 742 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 772 through 777
      removed outlier: 4.396A  pdb=" N   PHE A 777 " --> pdb=" O   PRO A 773 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 780 through 798
    Processing helix  chain 'A' and resid 810 through 820
      removed outlier: 3.715A  pdb=" N   ARG A 814 " --> pdb=" O   ARG A 811 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   LEU A 818 " --> pdb=" O   VAL A 815 " (cutoff:3.500A)
      removed outlier: 4.049A  pdb=" N   LYS A 820 " --> pdb=" O   LYS A 817 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 824 through 835
      removed outlier: 3.880A  pdb=" N   LEU A 828 " --> pdb=" O   THR A 824 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 839 through 862
      removed outlier: 4.355A  pdb=" N   THR A 843 " --> pdb=" O   LEU A 839 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   LEU A 844 " --> pdb=" O   GLY A 840 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 863 through 865
      No H-bonds generated for 'chain 'A' and resid 863 through 865'
    Processing helix  chain 'A' and resid 883 through 897
    Processing helix  chain 'A' and resid 899 through 906
    Processing helix  chain 'A' and resid 914 through 943
    Processing helix  chain 'A' and resid 1171 through 1175
      removed outlier: 4.154A  pdb=" N   ARG A1174 " --> pdb=" O   GLY A1171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1185 through 1204
      removed outlier: 4.304A  pdb=" N   TRP A1191 " --> pdb=" O   PRO A1187 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   TRP A1192 " --> pdb=" O   GLY A1188 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   HIS A1204 " --> pdb=" O   HIS A1200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1204 through 1221
      removed outlier: 3.744A  pdb=" N   GLU A1208 " --> pdb=" O   HIS A1204 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1222 through 1225
      removed outlier: 3.927A  pdb=" N   GLU A1225 " --> pdb=" O   LEU A1222 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1222 through 1225'
    Processing helix  chain 'A' and resid 1226 through 1230
      removed outlier: 4.202A  pdb=" N   GLU A1230 " --> pdb=" O   ILE A1227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1235 through 1261
      removed outlier: 3.598A  pdb=" N   THR A1247 " --> pdb=" O   ASP A1243 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1269 through 1291
      removed outlier: 4.206A  pdb=" N   TRP A1273 " --> pdb=" O   ASN A1269 " (cutoff:3.500A)
      removed outlier: 4.383A  pdb=" N   LEU A1274 " --> pdb=" O   ALA A1270 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   ASP A1275 " --> pdb=" O   TRP A1271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1298 through 1305
      removed outlier: 4.088A  pdb=" N   LEU A1302 " --> pdb=" O   PRO A1298 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   ARG A1303 " --> pdb=" O   ILE A1299 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   THR A1304 " --> pdb=" O   LYS A1300 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   LEU A1305 " --> pdb=" O   SER A1301 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1298 through 1305'
    Processing helix  chain 'A' and resid 1306 through 1315
      Proline residue:  A1310  - end of helix
      removed outlier: 4.268A  pdb=" N   SER A1315 " --> pdb=" O   ARG A1312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1319 through 1329
      removed outlier: 4.432A  pdb=" N   VAL A1323 " --> pdb=" O   GLY A1319 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1330 through 1356
      removed outlier: 3.601A  pdb=" N   ILE A1334 " --> pdb=" O   ALA A1330 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   VAL A1340 " --> pdb=" O   ASN A1336 " (cutoff:3.500A)
      removed outlier: 4.131A  pdb=" N   PHE A1348 " --> pdb=" O   PHE A1344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1380 through 1387
      removed outlier: 3.597A  pdb=" N   CYS A1384 " --> pdb=" O   ASN A1380 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1404 through 1417
      removed outlier: 3.540A  pdb=" N   THR A1417 " --> pdb=" O   LEU A1413 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1420 through 1430
      removed outlier: 4.124A  pdb=" N   ILE A1424 " --> pdb=" O   GLY A1420 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1443 through 1445
      No H-bonds generated for 'chain 'A' and resid 1443 through 1445'
    Processing helix  chain 'A' and resid 1446 through 1458
      removed outlier: 4.149A  pdb=" N   PHE A1450 " --> pdb=" O   MET A1446 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   SER A1458 " --> pdb=" O   ILE A1454 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1459 through 1481
    Processing helix  chain 'A' and resid 1488 through 1500
      removed outlier: 3.744A  pdb=" N   LYS A1500 " --> pdb=" O   ASN A1496 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1514 through 1520
      removed outlier: 3.752A  pdb=" N   GLN A1518 " --> pdb=" O   LEU A1514 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1521 through 1527
    Processing helix  chain 'A' and resid 1527 through 1547
      removed outlier: 4.425A  pdb=" N   ASP A1531 " --> pdb=" O   LYS A1527 " (cutoff:3.500A)
      removed outlier: 4.073A  pdb=" N   VAL A1547 " --> pdb=" O   VAL A1543 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1553 through 1577
      removed outlier: 3.921A  pdb=" N   ILE A1557 " --> pdb=" O   SER A1553 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   ILE A1559 " --> pdb=" O   GLU A1555 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1592 through 1611
      removed outlier: 3.975A  pdb=" N   PHE A1596 " --> pdb=" O   ASN A1592 " (cutoff:3.500A)
      removed outlier: 4.297A  pdb=" N   LEU A1601 " --> pdb=" O   VAL A1597 " (cutoff:3.500A)
      removed outlier: 4.183A  pdb=" N   SER A1602 " --> pdb=" O   VAL A1598 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1619 through 1627
      removed outlier: 4.167A  pdb=" N   VAL A1624 " --> pdb=" O   THR A1620 " (cutoff:3.500A)
      removed outlier: 4.920A  pdb=" N   ILE A1625 " --> pdb=" O   LEU A1621 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   ARG A1626 " --> pdb=" O   PHE A1622 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1628 through 1640
      removed outlier: 3.613A  pdb=" N   LEU A1634 " --> pdb=" O   GLY A1631 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   ARG A1635 " --> pdb=" O   ARG A1632 " (cutoff:3.500A)
      removed outlier: 4.201A  pdb=" N   LEU A1636 " --> pdb=" O   ILE A1633 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   ILE A1637 " --> pdb=" O   LEU A1634 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1642 through 1676
      Proline residue:  A1655  - end of helix
      removed outlier: 3.952A  pdb=" N   ASN A1659 " --> pdb=" O   PRO A1655 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   ILE A1660 " --> pdb=" O   ALA A1656 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1696 through 1708
    Processing helix  chain 'A' and resid 1713 through 1718
    Processing helix  chain 'A' and resid 1744 through 1777
      removed outlier: 3.720A  pdb=" N   GLY A1748 " --> pdb=" O   SER A1744 " (cutoff:3.500A)
      removed outlier: 4.491A  pdb=" N   LEU A1750 " --> pdb=" O   ALA A1746 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   TYR A1755 " --> pdb=" O   PHE A1751 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1791 through 1802
    Processing helix  chain 'A' and resid 1810 through 1818
      removed outlier: 4.692A  pdb=" N   ASP A1816 " --> pdb=" O   SER A1812 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1828 through 1834
      removed outlier: 3.782A  pdb=" N   SER A1834 " --> pdb=" O   PRO A1830 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1835 through 1838
      removed outlier: 3.677A  pdb=" N   MET A1838 " --> pdb=" O   LEU A1835 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1835 through 1838'
    Processing helix  chain 'A' and resid 1850 through 1860
    Processing helix  chain 'A' and resid 1868 through 1882
      removed outlier: 3.789A  pdb=" N   LYS A1872 " --> pdb=" O   MET A1868 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   ALA A1882 " --> pdb=" O   LYS A1878 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 95
    Processing sheet with id=AA2, first strand: chain 'A' and resid 278 through 282
    Processing sheet with id=AA3, first strand: chain 'A' and resid 294 through 296
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1362 through 1365
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1808 through 1809
      removed outlier: 4.193A  pdb=" N   VAL A1843 " --> pdb=" O   ARG A1847 " (cutoff:3.500A)

    588 hydrogen bonds defined for protein.
    1665 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.65

  Time building geometry restraints manager: 3.54 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2273
        1.33 -     1.45: 2979
        1.45 -     1.58: 6606
        1.58 -     1.70: 4
        1.70 -     1.83: 145
  Bond restraints: 12007
  Sorted by residual:
  bond pdb=" C   PRO A 684 "
       pdb=" N   PRO A 685 "
    ideal  model  delta    sigma   weight residual
    1.334  1.365 -0.032 2.34e-02 1.83e+03 1.82e+00
  bond pdb=" CG1 ILE A1600 "
       pdb=" CD1 ILE A1600 "
    ideal  model  delta    sigma   weight residual
    1.513  1.466  0.047 3.90e-02 6.57e+02 1.43e+00
  bond pdb=" CB  LYS A1505 "
       pdb=" CG  LYS A1505 "
    ideal  model  delta    sigma   weight residual
    1.520  1.551 -0.031 3.00e-02 1.11e+03 1.09e+00
  bond pdb=" CB  MET A 135 "
       pdb=" CG  MET A 135 "
    ideal  model  delta    sigma   weight residual
    1.520  1.551 -0.031 3.00e-02 1.11e+03 1.08e+00
  bond pdb=" CB  GLU A 346 "
       pdb=" CG  GLU A 346 "
    ideal  model  delta    sigma   weight residual
    1.520  1.549 -0.029 3.00e-02 1.11e+03 9.58e-01
  ... (remaining 12002 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.12: 16071
        2.12 -     4.23: 192
        4.23 -     6.35: 29
        6.35 -     8.47: 8
        8.47 -    10.59: 2
  Bond angle restraints: 16302
  Sorted by residual:
  angle pdb=" CB  MET A 135 "
        pdb=" CG  MET A 135 "
        pdb=" SD  MET A 135 "
      ideal   model   delta    sigma   weight residual
     112.70  123.29  -10.59 3.00e+00 1.11e-01 1.25e+01
  angle pdb=" CA  MET A1498 "
        pdb=" CB  MET A1498 "
        pdb=" CG  MET A1498 "
      ideal   model   delta    sigma   weight residual
     114.10  120.65   -6.55 2.00e+00 2.50e-01 1.07e+01
  angle pdb=" C   ALA A1330 "
        pdb=" N   ILE A1331 "
        pdb=" CA  ILE A1331 "
      ideal   model   delta    sigma   weight residual
     120.33  122.94   -2.61 8.00e-01 1.56e+00 1.07e+01
  angle pdb=" N   ILE A1593 "
        pdb=" CA  ILE A1593 "
        pdb=" C   ILE A1593 "
      ideal   model   delta    sigma   weight residual
     112.35  107.81    4.54 1.41e+00 5.03e-01 1.04e+01
  angle pdb=" CB  LYS A1505 "
        pdb=" CG  LYS A1505 "
        pdb=" CD  LYS A1505 "
      ideal   model   delta    sigma   weight residual
     111.30  118.14   -6.84 2.30e+00 1.89e-01 8.84e+00
  ... (remaining 16297 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.25: 6957
       28.25 -    56.50: 559
       56.50 -    84.74: 79
       84.74 -   112.99: 34
      112.99 -   141.24: 10
  Dihedral angle restraints: 7639
    sinusoidal: 3561
      harmonic: 4078
  Sorted by residual:
  dihedral pdb=" CB  CYS A 280 "
           pdb=" SG  CYS A 280 "
           pdb=" SG  CYS A 335 "
           pdb=" CB  CYS A 335 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -164.36   78.36     1      1.00e+01 1.00e-02 7.66e+01
  dihedral pdb=" CB  CYS A1363 "
           pdb=" SG  CYS A1363 "
           pdb=" SG  CYS A1384 "
           pdb=" CB  CYS A1384 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -155.25   69.25     1      1.00e+01 1.00e-02 6.20e+01
  dihedral pdb=" CB  CYS A1728 "
           pdb=" SG  CYS A1728 "
           pdb=" SG  CYS A1742 "
           pdb=" CB  CYS A1742 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  160.12  -67.12     1      1.00e+01 1.00e-02 5.87e+01
  ... (remaining 7636 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 1173
       0.029 -    0.058: 479
       0.058 -    0.087: 187
       0.087 -    0.116: 52
       0.116 -    0.146: 11
  Chirality restraints: 1902
  Sorted by residual:
  chirality pdb=" C1  NAG A2110 "
            pdb=" ND2 ASN A 283 "
            pdb=" C2  NAG A2110 "
            pdb=" O5  NAG A2110 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.25   -0.15 2.00e-01 2.50e+01 5.29e-01
  chirality pdb=" C2  NAG D   1 "
            pdb=" C1  NAG D   1 "
            pdb=" C3  NAG D   1 "
            pdb=" N2  NAG D   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.36   -0.14 2.00e-01 2.50e+01 4.58e-01
  chirality pdb=" C3  NAG D   1 "
            pdb=" C2  NAG D   1 "
            pdb=" C4  NAG D   1 "
            pdb=" O3  NAG D   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.45    2.31    0.13 2.00e-01 2.50e+01 4.52e-01
  ... (remaining 1899 not shown)

  Planarity restraints: 1965
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A1725 "   -0.031 5.00e-02 4.00e+02   4.65e-02 3.46e+00
        pdb=" N   PRO A1726 "    0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO A1726 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A1726 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 222 "   -0.009 2.00e-02 2.50e+03   1.73e-02 3.01e+00
        pdb=" C   ARG A 222 "    0.030 2.00e-02 2.50e+03
        pdb=" O   ARG A 222 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   VAL A 223 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 403 "    0.012 2.00e-02 2.50e+03   1.17e-02 2.75e+00
        pdb=" CG  TYR A 403 "   -0.025 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 403 "    0.011 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 403 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 403 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 403 "    0.013 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 403 "   -0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR A 403 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 1962 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.71: 373
        2.71 -     3.26: 11812
        3.26 -     3.81: 17249
        3.81 -     4.35: 19458
        4.35 -     4.90: 32854
  Nonbonded interactions: 81746
  Sorted by model distance:
  nonbonded pdb=" O   LYS A1264 "
            pdb=" OG1 THR A1268 "
     model   vdw
     2.169 3.040
  nonbonded pdb=" OG1 THR A1390 "
            pdb=" OE2 GLU A1392 "
     model   vdw
     2.202 3.040
  nonbonded pdb=" N   GLU A 346 "
            pdb=" OE1 GLU A 346 "
     model   vdw
     2.287 3.120
  nonbonded pdb=" O   GLY A 180 "
            pdb=" OG1 THR A 187 "
     model   vdw
     2.320 3.040
  nonbonded pdb=" N   ASP A1714 "
            pdb=" OD1 ASP A1714 "
     model   vdw
     2.324 3.120
  ... (remaining 81741 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
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             6.740
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.490
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     29.600
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7102
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      :  0.003   0.047  12025  Z= 0.141
  Angle     :  0.622  10.586  16349  Z= 0.325
  Chirality :  0.038   0.146   1902
  Planarity :  0.004   0.046   1961
  Dihedral  : 20.756 141.240   4980
  Min Nonbonded Distance : 2.169

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.43 %
    Favored  : 92.57 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  : 29.41 %
    Favored  : 70.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.46 (0.24), residues: 1387
  helix:  0.91 (0.19), residues: 815
  sheet: -1.92 (0.76), residues: 36
  loop : -2.16 (0.27), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A1258 
 HIS   0.004   0.001   HIS A 738 
 PHE   0.022   0.001   PHE A 942 
 TYR   0.025   0.001   TYR A 403 
 ARG   0.006   0.000   ARG A1626 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00335 (    4)
  link_NAG-ASN         : angle       2.66673 (   12)
  link_BETA1-4         : bond        0.00647 (    7)
  link_BETA1-4         : angle       1.25431 (   21)
  hydrogen bonds       : bond        0.16751 (  588)
  hydrogen bonds       : angle       5.79048 ( 1665)
  SS BOND              : bond        0.00274 (    7)
  SS BOND              : angle       1.54480 (   14)
  covalent geometry    : bond        0.00303 (12007)
  covalent geometry    : angle       0.61493 (16302)

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

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

  2774 Ramachandran restraints generated.
    1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2774 Ramachandran restraints generated.
    1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  384 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 382
  time to evaluate  : 1.129 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  305 ASP cc_start: 0.7487 (m-30) cc_final: 0.7250 (m-30)
REVERT: A  790 ILE cc_start: 0.8917 (tp) cc_final: 0.8415 (tp)
REVERT: A  876 LEU cc_start: 0.8887 (tp) cc_final: 0.8652 (mp)
REVERT: A 1222 LEU cc_start: 0.8241 (mt) cc_final: 0.7821 (mp)
REVERT: A 1351 MET cc_start: 0.7812 (tpt) cc_final: 0.7577 (tpt)
REVERT: A 1539 CYS cc_start: 0.8868 (m) cc_final: 0.8657 (p)
REVERT: A 1653 SER cc_start: 0.8426 (m) cc_final: 0.8003 (p)
REVERT: A 1851 MET cc_start: 0.3901 (mtp) cc_final: 0.3494 (mpp)
  outliers start: 2
  outliers final: 0
  residues processed: 383
  average time/residue: 0.2868
  time to fit residues: 155.8629
Evaluate side-chains
  276 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 276
  time to evaluate  : 1.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 117 optimal weight:    0.0970
   chunk 105 optimal weight:    1.9990
   chunk 58 optimal weight:    0.5980
   chunk 35 optimal weight:    0.7980
   chunk 71 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9980
   chunk 108 optimal weight:    0.6980
   chunk 42 optimal weight:    0.9990
   chunk 66 optimal weight:    0.5980
   chunk 81 optimal weight:    0.9990
   chunk 126 optimal weight:    0.8980
   overall best weight:    0.5578

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

Flipped N/Q/H residues before XYZ refinement:
A 740 ASN
A 753 ASN
A1289 ASN
A1564 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.172618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.137405 restraints weight = 26300.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.141013 restraints weight = 12849.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.143308 restraints weight = 7876.041|
|-----------------------------------------------------------------------------|
r_work (final): 0.3856
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7307
moved from start:          0.2487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  12025  Z= 0.172
  Angle     :  0.718   9.131  16349  Z= 0.355
  Chirality :  0.043   0.239   1902
  Planarity :  0.005   0.059   1961
  Dihedral  : 15.700 130.723   2342
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.49 %
    Favored  : 93.51 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 27.21 %
    Favored  : 68.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.46 (0.23), residues: 1387
  helix:  0.97 (0.19), residues: 830
  sheet: -1.83 (0.79), residues: 36
  loop : -2.37 (0.26), residues: 521

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 781 
 HIS   0.006   0.001   HIS A 130 
 PHE   0.026   0.002   PHE A 392 
 TYR   0.021   0.001   TYR A 403 
 ARG   0.014   0.001   ARG A1623 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00521 (    4)
  link_NAG-ASN         : angle       3.25130 (   12)
  link_BETA1-4         : bond        0.00766 (    7)
  link_BETA1-4         : angle       2.63607 (   21)
  hydrogen bonds       : bond        0.05754 (  588)
  hydrogen bonds       : angle       4.26851 ( 1665)
  SS BOND              : bond        0.00258 (    7)
  SS BOND              : angle       1.54777 (   14)
  covalent geometry    : bond        0.00342 (12007)
  covalent geometry    : angle       0.70617 (16302)

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

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

  2774 Ramachandran restraints generated.
    1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2774 Ramachandran restraints generated.
    1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  334 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 287
  time to evaluate  : 1.149 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  194 ASN cc_start: 0.7543 (t0) cc_final: 0.7168 (t0)
REVERT: A  277 ARG cc_start: 0.7709 (mtp180) cc_final: 0.7373 (ttm170)
REVERT: A  744 GLU cc_start: 0.8491 (mp0) cc_final: 0.7487 (tt0)
REVERT: A  790 ILE cc_start: 0.8668 (tp) cc_final: 0.8079 (tp)
REVERT: A  794 MET cc_start: 0.9261 (mmp) cc_final: 0.8778 (mmp)
REVERT: A 1258 TRP cc_start: 0.8828 (t60) cc_final: 0.8574 (t60)
REVERT: A 1309 ARG cc_start: 0.8982 (ttp-170) cc_final: 0.8623 (ttp80)
REVERT: A 1534 ILE cc_start: 0.8598 (mm) cc_final: 0.8225 (mt)
REVERT: A 1539 CYS cc_start: 0.9045 (m) cc_final: 0.8473 (p)
REVERT: A 1653 SER cc_start: 0.8696 (m) cc_final: 0.8411 (p)
REVERT: A 1741 ASP cc_start: 0.7359 (t0) cc_final: 0.7123 (m-30)
REVERT: A 1765 ASN cc_start: 0.9154 (t0) cc_final: 0.8907 (t0)
  outliers start: 47
  outliers final: 31
  residues processed: 313
  average time/residue: 0.2169
  time to fit residues: 99.0963
Evaluate side-chains
  293 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 262
  time to evaluate  : 1.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 TYR
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  300 VAL
Chi-restraints excluded: chain A residue  322 ASP
Chi-restraints excluded: chain A residue  335 CYS
Chi-restraints excluded: chain A residue  365 LEU
Chi-restraints excluded: chain A residue  370 THR
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain A residue  731 THR
Chi-restraints excluded: chain A residue  732 LEU
Chi-restraints excluded: chain A residue  753 ASN
Chi-restraints excluded: chain A residue  754 LEU
Chi-restraints excluded: chain A residue  796 LEU
Chi-restraints excluded: chain A residue  831 ILE
Chi-restraints excluded: chain A residue  850 VAL
Chi-restraints excluded: chain A residue  852 ILE
Chi-restraints excluded: chain A residue 1190 VAL
Chi-restraints excluded: chain A residue 1253 GLU
Chi-restraints excluded: chain A residue 1289 ASN
Chi-restraints excluded: chain A residue 1327 LEU
Chi-restraints excluded: chain A residue 1340 VAL
Chi-restraints excluded: chain A residue 1344 PHE
Chi-restraints excluded: chain A residue 1560 LEU
Chi-restraints excluded: chain A residue 1564 ASN
Chi-restraints excluded: chain A residue 1598 VAL
Chi-restraints excluded: chain A residue 1662 LEU
Chi-restraints excluded: chain A residue 1668 MET
Chi-restraints excluded: chain A residue 1750 LEU
Chi-restraints excluded: chain A residue 1763 VAL
Chi-restraints excluded: chain A residue 1775 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 135 optimal weight:    0.9980
   chunk 120 optimal weight:    0.5980
   chunk 31 optimal weight:    0.2980
   chunk 79 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9990
   chunk 67 optimal weight:    0.0570
   chunk 137 optimal weight:    3.9990
   chunk 136 optimal weight:    4.9990
   chunk 85 optimal weight:    0.9980
   chunk 109 optimal weight:    0.4980
   chunk 34 optimal weight:    0.2980
   overall best weight:    0.3498

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

Flipped N/Q/H residues before XYZ refinement:
** A  73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.172898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.136594 restraints weight = 26629.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.140256 restraints weight = 13001.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.142607 restraints weight = 7972.244|
|-----------------------------------------------------------------------------|
r_work (final): 0.3853
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7329
moved from start:          0.2919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  12025  Z= 0.132
  Angle     :  0.664  12.545  16349  Z= 0.324
  Chirality :  0.040   0.223   1902
  Planarity :  0.005   0.085   1961
  Dihedral  : 14.402 133.117   2342
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.63 %
    Favored  : 93.37 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 28.11 %
    Favored  : 68.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.54 (0.23), residues: 1387
  helix:  0.89 (0.19), residues: 843
  sheet: -1.96 (0.77), residues: 36
  loop : -2.45 (0.27), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 781 
 HIS   0.007   0.001   HIS A1849 
 PHE   0.021   0.001   PHE A 816 
 TYR   0.013   0.001   TYR A 403 
 ARG   0.010   0.001   ARG A1629 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00551 (    4)
  link_NAG-ASN         : angle       3.19011 (   12)
  link_BETA1-4         : bond        0.00620 (    7)
  link_BETA1-4         : angle       2.54589 (   21)
  hydrogen bonds       : bond        0.05234 (  588)
  hydrogen bonds       : angle       4.04219 ( 1665)
  SS BOND              : bond        0.00244 (    7)
  SS BOND              : angle       1.33608 (   14)
  covalent geometry    : bond        0.00276 (12007)
  covalent geometry    : angle       0.65192 (16302)

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

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

  2774 Ramachandran restraints generated.
    1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2774 Ramachandran restraints generated.
    1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  312 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 270
  time to evaluate  : 1.178 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 MET cc_start: 0.5891 (mmt) cc_final: 0.5571 (mmt)
REVERT: A  118 HIS cc_start: 0.4334 (OUTLIER) cc_final: 0.3435 (t-90)
REVERT: A  138 MET cc_start: 0.6057 (tpp) cc_final: 0.5849 (tpp)
REVERT: A  194 ASN cc_start: 0.7501 (m-40) cc_final: 0.7163 (t0)
REVERT: A  431 GLU cc_start: 0.6264 (mm-30) cc_final: 0.5866 (mt-10)
REVERT: A  744 GLU cc_start: 0.8499 (mp0) cc_final: 0.7542 (tt0)
REVERT: A  790 ILE cc_start: 0.8691 (tp) cc_final: 0.8086 (tp)
REVERT: A  794 MET cc_start: 0.9273 (mmp) cc_final: 0.8812 (mmp)
REVERT: A  907 MET cc_start: 0.8416 (mtp) cc_final: 0.8159 (mtp)
REVERT: A 1443 ASN cc_start: 0.8722 (t0) cc_final: 0.8456 (t0)
REVERT: A 1534 ILE cc_start: 0.8599 (mm) cc_final: 0.8206 (mt)
REVERT: A 1539 CYS cc_start: 0.9032 (m) cc_final: 0.8458 (p)
REVERT: A 1653 SER cc_start: 0.8674 (m) cc_final: 0.8356 (p)
REVERT: A 1741 ASP cc_start: 0.7432 (t0) cc_final: 0.7223 (m-30)
REVERT: A 1765 ASN cc_start: 0.9135 (t0) cc_final: 0.8890 (t0)
  outliers start: 42
  outliers final: 22
  residues processed: 295
  average time/residue: 0.2175
  time to fit residues: 95.2171
Evaluate side-chains
  280 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 257
  time to evaluate  : 1.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 TYR
Chi-restraints excluded: chain A residue  118 HIS
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  300 VAL
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  322 ASP
Chi-restraints excluded: chain A residue  335 CYS
Chi-restraints excluded: chain A residue  353 THR
Chi-restraints excluded: chain A residue  365 LEU
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain A residue  700 CYS
Chi-restraints excluded: chain A residue  796 LEU
Chi-restraints excluded: chain A residue  825 LEU
Chi-restraints excluded: chain A residue 1204 HIS
Chi-restraints excluded: chain A residue 1327 LEU
Chi-restraints excluded: chain A residue 1340 VAL
Chi-restraints excluded: chain A residue 1384 CYS
Chi-restraints excluded: chain A residue 1560 LEU
Chi-restraints excluded: chain A residue 1648 PHE
Chi-restraints excluded: chain A residue 1662 LEU
Chi-restraints excluded: chain A residue 1668 MET
Chi-restraints excluded: chain A residue 1750 LEU
Chi-restraints excluded: chain A residue 1775 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 113 optimal weight:    0.5980
   chunk 98 optimal weight:    0.8980
   chunk 72 optimal weight:    0.8980
   chunk 65 optimal weight:    0.2980
   chunk 55 optimal weight:    2.9990
   chunk 64 optimal weight:    1.9990
   chunk 22 optimal weight:    0.2980
   chunk 45 optimal weight:    0.8980
   chunk 97 optimal weight:    0.7980
   chunk 44 optimal weight:    0.0050
   chunk 120 optimal weight:    0.0980
   overall best weight:    0.2594

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

Flipped N/Q/H residues before XYZ refinement:
A  73 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.173472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.137250 restraints weight = 26777.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.141047 restraints weight = 12936.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.143457 restraints weight = 7863.434|
|-----------------------------------------------------------------------------|
r_work (final): 0.3858
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7315
moved from start:          0.3244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  12025  Z= 0.120
  Angle     :  0.650   9.719  16349  Z= 0.317
  Chirality :  0.040   0.250   1902
  Planarity :  0.004   0.055   1961
  Dihedral  : 13.212 142.377   2342
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.85 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 28.68 %
    Favored  : 68.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.45 (0.23), residues: 1387
  helix:  1.06 (0.19), residues: 829
  sheet: -1.77 (0.79), residues: 36
  loop : -2.53 (0.26), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 781 
 HIS   0.002   0.001   HIS A 738 
 PHE   0.021   0.001   PHE A 816 
 TYR   0.013   0.001   TYR A1767 
 ARG   0.011   0.001   ARG A1623 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00544 (    4)
  link_NAG-ASN         : angle       3.03407 (   12)
  link_BETA1-4         : bond        0.00666 (    7)
  link_BETA1-4         : angle       2.70383 (   21)
  hydrogen bonds       : bond        0.04590 (  588)
  hydrogen bonds       : angle       3.93363 ( 1665)
  SS BOND              : bond        0.00244 (    7)
  SS BOND              : angle       1.31525 (   14)
  covalent geometry    : bond        0.00245 (12007)
  covalent geometry    : angle       0.63771 (16302)

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

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

  2774 Ramachandran restraints generated.
    1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2774 Ramachandran restraints generated.
    1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  312 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 274
  time to evaluate  : 1.252 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 MET cc_start: 0.5904 (mmt) cc_final: 0.5610 (mmt)
REVERT: A  118 HIS cc_start: 0.4333 (OUTLIER) cc_final: 0.3438 (t-90)
REVERT: A  138 MET cc_start: 0.6047 (tpp) cc_final: 0.5831 (tpp)
REVERT: A  194 ASN cc_start: 0.7567 (m-40) cc_final: 0.7238 (t0)
REVERT: A  352 TYR cc_start: 0.8774 (m-80) cc_final: 0.8570 (m-80)
REVERT: A  431 GLU cc_start: 0.6259 (mm-30) cc_final: 0.5868 (mt-10)
REVERT: A  744 GLU cc_start: 0.8603 (mp0) cc_final: 0.7696 (tt0)
REVERT: A  790 ILE cc_start: 0.8717 (tp) cc_final: 0.8099 (tp)
REVERT: A  794 MET cc_start: 0.9270 (mmp) cc_final: 0.8773 (mmp)
REVERT: A  907 MET cc_start: 0.8456 (mtp) cc_final: 0.8100 (mtp)
REVERT: A  912 GLN cc_start: 0.7192 (tt0) cc_final: 0.6709 (pm20)
REVERT: A 1253 GLU cc_start: 0.7161 (mt-10) cc_final: 0.6941 (mp0)
REVERT: A 1443 ASN cc_start: 0.8738 (t0) cc_final: 0.8524 (t0)
REVERT: A 1534 ILE cc_start: 0.8599 (mm) cc_final: 0.8217 (mt)
REVERT: A 1539 CYS cc_start: 0.9046 (m) cc_final: 0.8445 (p)
REVERT: A 1546 MET cc_start: 0.8292 (tpt) cc_final: 0.7985 (mmm)
REVERT: A 1653 SER cc_start: 0.8642 (m) cc_final: 0.8289 (p)
REVERT: A 1662 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7489 (tp)
REVERT: A 1741 ASP cc_start: 0.7466 (t0) cc_final: 0.7251 (m-30)
REVERT: A 1765 ASN cc_start: 0.9135 (t0) cc_final: 0.8857 (t0)
  outliers start: 38
  outliers final: 22
  residues processed: 293
  average time/residue: 0.2312
  time to fit residues: 102.0666
Evaluate side-chains
  282 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 258
  time to evaluate  : 1.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 HIS
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  300 VAL
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  353 THR
Chi-restraints excluded: chain A residue  365 LEU
Chi-restraints excluded: chain A residue  700 CYS
Chi-restraints excluded: chain A residue  732 LEU
Chi-restraints excluded: chain A residue  736 LEU
Chi-restraints excluded: chain A residue  796 LEU
Chi-restraints excluded: chain A residue  825 LEU
Chi-restraints excluded: chain A residue 1259 VAL
Chi-restraints excluded: chain A residue 1327 LEU
Chi-restraints excluded: chain A residue 1340 VAL
Chi-restraints excluded: chain A residue 1344 PHE
Chi-restraints excluded: chain A residue 1353 VAL
Chi-restraints excluded: chain A residue 1560 LEU
Chi-restraints excluded: chain A residue 1648 PHE
Chi-restraints excluded: chain A residue 1662 LEU
Chi-restraints excluded: chain A residue 1668 MET
Chi-restraints excluded: chain A residue 1727 TYR
Chi-restraints excluded: chain A residue 1750 LEU
Chi-restraints excluded: chain A residue 1775 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 71 optimal weight:    0.6980
   chunk 103 optimal weight:    1.9990
   chunk 79 optimal weight:    0.8980
   chunk 28 optimal weight:    0.0770
   chunk 132 optimal weight:    9.9990
   chunk 93 optimal weight:    0.6980
   chunk 112 optimal weight:    0.9990
   chunk 60 optimal weight:    0.0270
   chunk 69 optimal weight:    2.9990
   chunk 102 optimal weight:    0.7980
   overall best weight:    0.4596

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

Flipped N/Q/H residues before XYZ refinement:
A1765 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.171191 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.134972 restraints weight = 26570.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.138662 restraints weight = 12979.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.141044 restraints weight = 7923.854|
|-----------------------------------------------------------------------------|
r_work (final): 0.3830
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7358
moved from start:          0.3592

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  12025  Z= 0.131
  Angle     :  0.664   8.852  16349  Z= 0.325
  Chirality :  0.041   0.244   1902
  Planarity :  0.004   0.058   1961
  Dihedral  : 12.576 148.501   2342
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.85 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 28.43 %
    Favored  : 67.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.49 (0.23), residues: 1387
  helix:  0.96 (0.19), residues: 841
  sheet: -1.83 (0.83), residues: 34
  loop : -2.50 (0.26), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 781 
 HIS   0.005   0.001   HIS A 738 
 PHE   0.035   0.001   PHE A1246 
 TYR   0.016   0.001   TYR A 403 
 ARG   0.016   0.001   ARG A1623 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00534 (    4)
  link_NAG-ASN         : angle       3.01365 (   12)
  link_BETA1-4         : bond        0.00625 (    7)
  link_BETA1-4         : angle       2.81038 (   21)
  hydrogen bonds       : bond        0.04576 (  588)
  hydrogen bonds       : angle       3.94135 ( 1665)
  SS BOND              : bond        0.00293 (    7)
  SS BOND              : angle       1.74552 (   14)
  covalent geometry    : bond        0.00284 (12007)
  covalent geometry    : angle       0.65045 (16302)

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

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

  2774 Ramachandran restraints generated.
    1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2774 Ramachandran restraints generated.
    1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  314 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 265
  time to evaluate  : 1.624 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 MET cc_start: 0.5936 (mmt) cc_final: 0.5626 (mmt)
REVERT: A  118 HIS cc_start: 0.4061 (OUTLIER) cc_final: 0.3252 (t-90)
REVERT: A  138 MET cc_start: 0.5954 (tpp) cc_final: 0.5732 (tpp)
REVERT: A  194 ASN cc_start: 0.7599 (m-40) cc_final: 0.7267 (t0)
REVERT: A  431 GLU cc_start: 0.6239 (mm-30) cc_final: 0.5838 (mt-10)
REVERT: A  744 GLU cc_start: 0.8568 (mp0) cc_final: 0.7687 (tt0)
REVERT: A  790 ILE cc_start: 0.8722 (tp) cc_final: 0.8061 (tp)
REVERT: A  794 MET cc_start: 0.9263 (mmp) cc_final: 0.8725 (mmp)
REVERT: A  912 GLN cc_start: 0.7251 (tt0) cc_final: 0.6708 (pm20)
REVERT: A 1253 GLU cc_start: 0.7163 (mt-10) cc_final: 0.6927 (mp0)
REVERT: A 1392 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6924 (pt0)
REVERT: A 1419 LYS cc_start: 0.8508 (mmtm) cc_final: 0.8239 (mmtp)
REVERT: A 1443 ASN cc_start: 0.8788 (t0) cc_final: 0.8444 (t0)
REVERT: A 1534 ILE cc_start: 0.8622 (mm) cc_final: 0.8256 (mt)
REVERT: A 1539 CYS cc_start: 0.9024 (m) cc_final: 0.8391 (p)
REVERT: A 1546 MET cc_start: 0.8378 (tpt) cc_final: 0.8146 (mmm)
REVERT: A 1653 SER cc_start: 0.8753 (m) cc_final: 0.8324 (p)
REVERT: A 1662 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7504 (tp)
REVERT: A 1765 ASN cc_start: 0.9196 (t0) cc_final: 0.8987 (t0)
  outliers start: 49
  outliers final: 33
  residues processed: 295
  average time/residue: 0.2581
  time to fit residues: 117.7109
Evaluate side-chains
  288 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 252
  time to evaluate  : 1.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 HIS
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  322 ASP
Chi-restraints excluded: chain A residue  335 CYS
Chi-restraints excluded: chain A residue  353 THR
Chi-restraints excluded: chain A residue  365 LEU
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain A residue  418 GLU
Chi-restraints excluded: chain A residue  700 CYS
Chi-restraints excluded: chain A residue  732 LEU
Chi-restraints excluded: chain A residue  736 LEU
Chi-restraints excluded: chain A residue  796 LEU
Chi-restraints excluded: chain A residue  825 LEU
Chi-restraints excluded: chain A residue  850 VAL
Chi-restraints excluded: chain A residue  908 GLU
Chi-restraints excluded: chain A residue  939 LEU
Chi-restraints excluded: chain A residue 1204 HIS
Chi-restraints excluded: chain A residue 1218 SER
Chi-restraints excluded: chain A residue 1259 VAL
Chi-restraints excluded: chain A residue 1340 VAL
Chi-restraints excluded: chain A residue 1344 PHE
Chi-restraints excluded: chain A residue 1353 VAL
Chi-restraints excluded: chain A residue 1384 CYS
Chi-restraints excluded: chain A residue 1392 GLU
Chi-restraints excluded: chain A residue 1598 VAL
Chi-restraints excluded: chain A residue 1629 ARG
Chi-restraints excluded: chain A residue 1662 LEU
Chi-restraints excluded: chain A residue 1668 MET
Chi-restraints excluded: chain A residue 1672 SER
Chi-restraints excluded: chain A residue 1727 TYR
Chi-restraints excluded: chain A residue 1750 LEU
Chi-restraints excluded: chain A residue 1775 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 84 optimal weight:    2.9990
   chunk 58 optimal weight:    0.8980
   chunk 22 optimal weight:    0.0980
   chunk 40 optimal weight:    0.8980
   chunk 90 optimal weight:    0.9990
   chunk 56 optimal weight:    1.9990
   chunk 29 optimal weight:    0.0670
   chunk 45 optimal weight:    0.6980
   chunk 83 optimal weight:    0.2980
   chunk 11 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9990
   overall best weight:    0.4118

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

Flipped N/Q/H residues before XYZ refinement:
A  73 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.171031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.135300 restraints weight = 26958.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.138988 restraints weight = 13087.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.141338 restraints weight = 7959.316|
|-----------------------------------------------------------------------------|
r_work (final): 0.3829
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7366
moved from start:          0.3853

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  12025  Z= 0.125
  Angle     :  0.678  11.281  16349  Z= 0.330
  Chirality :  0.041   0.290   1902
  Planarity :  0.004   0.060   1961
  Dihedral  : 11.956 151.849   2342
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.07 %
    Favored  : 92.93 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 29.89 %
    Favored  : 66.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.46 (0.23), residues: 1387
  helix:  1.06 (0.19), residues: 831
  sheet: -1.86 (0.84), residues: 34
  loop : -2.55 (0.26), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 781 
 HIS   0.003   0.001   HIS A 738 
 PHE   0.020   0.001   PHE A 816 
 TYR   0.016   0.001   TYR A 403 
 ARG   0.020   0.001   ARG A1623 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00546 (    4)
  link_NAG-ASN         : angle       3.04175 (   12)
  link_BETA1-4         : bond        0.00611 (    7)
  link_BETA1-4         : angle       2.95036 (   21)
  hydrogen bonds       : bond        0.04429 (  588)
  hydrogen bonds       : angle       3.89028 ( 1665)
  SS BOND              : bond        0.00234 (    7)
  SS BOND              : angle       1.69320 (   14)
  covalent geometry    : bond        0.00268 (12007)
  covalent geometry    : angle       0.66382 (16302)

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

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

  2774 Ramachandran restraints generated.
    1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2774 Ramachandran restraints generated.
    1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  308 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 262
  time to evaluate  : 2.235 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 MET cc_start: 0.5950 (mmt) cc_final: 0.5656 (mmt)
REVERT: A  118 HIS cc_start: 0.4071 (OUTLIER) cc_final: 0.3241 (t-90)
REVERT: A  194 ASN cc_start: 0.7474 (m-40) cc_final: 0.7186 (t0)
REVERT: A  431 GLU cc_start: 0.6174 (mm-30) cc_final: 0.5818 (mt-10)
REVERT: A  744 GLU cc_start: 0.8626 (mp0) cc_final: 0.7606 (tt0)
REVERT: A  790 ILE cc_start: 0.8739 (tp) cc_final: 0.8043 (tp)
REVERT: A  794 MET cc_start: 0.9260 (mmp) cc_final: 0.8676 (mmp)
REVERT: A  912 GLN cc_start: 0.7404 (tt0) cc_final: 0.6689 (pm20)
REVERT: A  932 ASN cc_start: 0.8545 (m110) cc_final: 0.8178 (m-40)
REVERT: A 1253 GLU cc_start: 0.7205 (mt-10) cc_final: 0.6972 (mp0)
REVERT: A 1419 LYS cc_start: 0.8539 (mmtm) cc_final: 0.8267 (mmtm)
REVERT: A 1439 GLN cc_start: 0.7444 (OUTLIER) cc_final: 0.7094 (tm-30)
REVERT: A 1443 ASN cc_start: 0.8786 (t0) cc_final: 0.8460 (t0)
REVERT: A 1534 ILE cc_start: 0.8648 (mm) cc_final: 0.8276 (mt)
REVERT: A 1539 CYS cc_start: 0.9004 (m) cc_final: 0.8774 (t)
REVERT: A 1546 MET cc_start: 0.8420 (tpt) cc_final: 0.8208 (mmm)
REVERT: A 1653 SER cc_start: 0.8763 (m) cc_final: 0.8320 (p)
REVERT: A 1662 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7812 (tp)
REVERT: A 1765 ASN cc_start: 0.9194 (t0) cc_final: 0.8976 (t0)
  outliers start: 46
  outliers final: 34
  residues processed: 291
  average time/residue: 0.2377
  time to fit residues: 106.0853
Evaluate side-chains
  285 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 248
  time to evaluate  : 1.981 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 HIS
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  300 VAL
Chi-restraints excluded: chain A residue  322 ASP
Chi-restraints excluded: chain A residue  335 CYS
Chi-restraints excluded: chain A residue  353 THR
Chi-restraints excluded: chain A residue  365 LEU
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain A residue  418 GLU
Chi-restraints excluded: chain A residue  700 CYS
Chi-restraints excluded: chain A residue  732 LEU
Chi-restraints excluded: chain A residue  753 ASN
Chi-restraints excluded: chain A residue  796 LEU
Chi-restraints excluded: chain A residue  825 LEU
Chi-restraints excluded: chain A residue  852 ILE
Chi-restraints excluded: chain A residue  908 GLU
Chi-restraints excluded: chain A residue  939 LEU
Chi-restraints excluded: chain A residue 1178 CYS
Chi-restraints excluded: chain A residue 1204 HIS
Chi-restraints excluded: chain A residue 1218 SER
Chi-restraints excluded: chain A residue 1259 VAL
Chi-restraints excluded: chain A residue 1327 LEU
Chi-restraints excluded: chain A residue 1340 VAL
Chi-restraints excluded: chain A residue 1344 PHE
Chi-restraints excluded: chain A residue 1347 ILE
Chi-restraints excluded: chain A residue 1353 VAL
Chi-restraints excluded: chain A residue 1384 CYS
Chi-restraints excluded: chain A residue 1439 GLN
Chi-restraints excluded: chain A residue 1564 ASN
Chi-restraints excluded: chain A residue 1629 ARG
Chi-restraints excluded: chain A residue 1648 PHE
Chi-restraints excluded: chain A residue 1662 LEU
Chi-restraints excluded: chain A residue 1668 MET
Chi-restraints excluded: chain A residue 1775 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 57 optimal weight:    0.7980
   chunk 110 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9980
   chunk 8 optimal weight:    2.9990
   chunk 2 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9980
   chunk 39 optimal weight:    0.5980
   chunk 111 optimal weight:    1.9990
   chunk 89 optimal weight:    0.0570
   chunk 28 optimal weight:    0.7980
   chunk 128 optimal weight:    0.4980
   overall best weight:    0.5498

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.169076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.133105 restraints weight = 27324.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.136717 restraints weight = 13346.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.139022 restraints weight = 8132.590|
|-----------------------------------------------------------------------------|
r_work (final): 0.3805
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7418
moved from start:          0.4094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  12025  Z= 0.138
  Angle     :  0.689  15.726  16349  Z= 0.336
  Chirality :  0.041   0.234   1902
  Planarity :  0.004   0.062   1961
  Dihedral  : 11.528 154.948   2342
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.14 %
    Favored  : 92.86 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 30.87 %
    Favored  : 65.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.50 (0.23), residues: 1387
  helix:  1.08 (0.19), residues: 824
  sheet: -1.97 (0.82), residues: 34
  loop : -2.61 (0.25), residues: 529

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 781 
 HIS   0.004   0.001   HIS A 738 
 PHE   0.033   0.001   PHE A1246 
 TYR   0.016   0.001   TYR A 403 
 ARG   0.010   0.001   ARG A1623 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00552 (    4)
  link_NAG-ASN         : angle       3.06951 (   12)
  link_BETA1-4         : bond        0.00550 (    7)
  link_BETA1-4         : angle       2.99831 (   21)
  hydrogen bonds       : bond        0.04604 (  588)
  hydrogen bonds       : angle       3.95160 ( 1665)
  SS BOND              : bond        0.00232 (    7)
  SS BOND              : angle       1.75652 (   14)
  covalent geometry    : bond        0.00304 (12007)
  covalent geometry    : angle       0.67448 (16302)

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

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

  2774 Ramachandran restraints generated.
    1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2774 Ramachandran restraints generated.
    1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  304 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 258
  time to evaluate  : 1.447 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 HIS cc_start: 0.4094 (OUTLIER) cc_final: 0.3235 (t-90)
REVERT: A  194 ASN cc_start: 0.7504 (m-40) cc_final: 0.7228 (t0)
REVERT: A  357 SER cc_start: 0.6821 (p) cc_final: 0.6571 (m)
REVERT: A  431 GLU cc_start: 0.6293 (mm-30) cc_final: 0.5964 (mt-10)
REVERT: A  744 GLU cc_start: 0.8682 (mp0) cc_final: 0.7587 (tt0)
REVERT: A  790 ILE cc_start: 0.8741 (tp) cc_final: 0.8049 (tp)
REVERT: A  794 MET cc_start: 0.9253 (mmp) cc_final: 0.8662 (mmp)
REVERT: A  912 GLN cc_start: 0.7476 (tt0) cc_final: 0.6854 (pm20)
REVERT: A 1253 GLU cc_start: 0.7251 (mt-10) cc_final: 0.7016 (mp0)
REVERT: A 1419 LYS cc_start: 0.8619 (mmtm) cc_final: 0.8362 (mmtm)
REVERT: A 1439 GLN cc_start: 0.7451 (OUTLIER) cc_final: 0.7011 (tm-30)
REVERT: A 1443 ASN cc_start: 0.8866 (t0) cc_final: 0.8616 (t0)
REVERT: A 1539 CYS cc_start: 0.8994 (m) cc_final: 0.8732 (t)
REVERT: A 1653 SER cc_start: 0.8833 (m) cc_final: 0.8380 (p)
REVERT: A 1662 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7798 (tp)
  outliers start: 46
  outliers final: 38
  residues processed: 288
  average time/residue: 0.2470
  time to fit residues: 107.9356
Evaluate side-chains
  289 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 248
  time to evaluate  : 1.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 HIS
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  322 ASP
Chi-restraints excluded: chain A residue  335 CYS
Chi-restraints excluded: chain A residue  365 LEU
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain A residue  396 VAL
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain A residue  418 GLU
Chi-restraints excluded: chain A residue  700 CYS
Chi-restraints excluded: chain A residue  732 LEU
Chi-restraints excluded: chain A residue  753 ASN
Chi-restraints excluded: chain A residue  754 LEU
Chi-restraints excluded: chain A residue  796 LEU
Chi-restraints excluded: chain A residue  825 LEU
Chi-restraints excluded: chain A residue  850 VAL
Chi-restraints excluded: chain A residue  852 ILE
Chi-restraints excluded: chain A residue  908 GLU
Chi-restraints excluded: chain A residue  939 LEU
Chi-restraints excluded: chain A residue 1178 CYS
Chi-restraints excluded: chain A residue 1204 HIS
Chi-restraints excluded: chain A residue 1218 SER
Chi-restraints excluded: chain A residue 1259 VAL
Chi-restraints excluded: chain A residue 1340 VAL
Chi-restraints excluded: chain A residue 1344 PHE
Chi-restraints excluded: chain A residue 1347 ILE
Chi-restraints excluded: chain A residue 1353 VAL
Chi-restraints excluded: chain A residue 1384 CYS
Chi-restraints excluded: chain A residue 1439 GLN
Chi-restraints excluded: chain A residue 1564 ASN
Chi-restraints excluded: chain A residue 1598 VAL
Chi-restraints excluded: chain A residue 1621 LEU
Chi-restraints excluded: chain A residue 1629 ARG
Chi-restraints excluded: chain A residue 1662 LEU
Chi-restraints excluded: chain A residue 1668 MET
Chi-restraints excluded: chain A residue 1670 ILE
Chi-restraints excluded: chain A residue 1672 SER
Chi-restraints excluded: chain A residue 1750 LEU
Chi-restraints excluded: chain A residue 1775 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 1 optimal weight:    0.4980
   chunk 101 optimal weight:    2.9990
   chunk 121 optimal weight:    0.9990
   chunk 23 optimal weight:    0.8980
   chunk 16 optimal weight:    0.0980
   chunk 54 optimal weight:    0.6980
   chunk 75 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9990
   chunk 89 optimal weight:    0.9990
   chunk 31 optimal weight:    0.8980
   chunk 21 optimal weight:    0.0570
   overall best weight:    0.3898

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.169767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.133987 restraints weight = 26736.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.137669 restraints weight = 12910.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.140011 restraints weight = 7833.470|
|-----------------------------------------------------------------------------|
r_work (final): 0.3815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7398
moved from start:          0.4231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  12025  Z= 0.127
  Angle     :  0.719  15.958  16349  Z= 0.345
  Chirality :  0.041   0.294   1902
  Planarity :  0.004   0.064   1961
  Dihedral  : 11.262 156.361   2342
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.99 %
    Favored  : 93.01 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 30.63 %
    Favored  : 65.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.48 (0.23), residues: 1387
  helix:  1.10 (0.19), residues: 824
  sheet: -1.90 (0.83), residues: 34
  loop : -2.63 (0.25), residues: 529

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 781 
 HIS   0.002   0.000   HIS A 738 
 PHE   0.020   0.001   PHE A1267 
 TYR   0.013   0.001   TYR A 378 
 ARG   0.009   0.001   ARG A1623 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00562 (    4)
  link_NAG-ASN         : angle       2.99263 (   12)
  link_BETA1-4         : bond        0.00552 (    7)
  link_BETA1-4         : angle       3.06541 (   21)
  hydrogen bonds       : bond        0.04482 (  588)
  hydrogen bonds       : angle       3.93487 ( 1665)
  SS BOND              : bond        0.00245 (    7)
  SS BOND              : angle       1.45201 (   14)
  covalent geometry    : bond        0.00271 (12007)
  covalent geometry    : angle       0.70585 (16302)

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

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

  2774 Ramachandran restraints generated.
    1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2774 Ramachandran restraints generated.
    1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  307 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 259
  time to evaluate  : 1.636 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 HIS cc_start: 0.4039 (OUTLIER) cc_final: 0.3193 (t-90)
REVERT: A  194 ASN cc_start: 0.7440 (m-40) cc_final: 0.7150 (t0)
REVERT: A  390 MET cc_start: 0.8488 (tmm) cc_final: 0.8243 (tmm)
REVERT: A  431 GLU cc_start: 0.6283 (mm-30) cc_final: 0.5972 (mt-10)
REVERT: A  744 GLU cc_start: 0.8676 (mp0) cc_final: 0.7613 (tt0)
REVERT: A  790 ILE cc_start: 0.8762 (tp) cc_final: 0.8041 (tp)
REVERT: A  794 MET cc_start: 0.9253 (mmp) cc_final: 0.8638 (mmp)
REVERT: A  912 GLN cc_start: 0.7523 (tt0) cc_final: 0.6901 (pm20)
REVERT: A 1247 THR cc_start: 0.6621 (OUTLIER) cc_final: 0.6391 (t)
REVERT: A 1253 GLU cc_start: 0.7257 (mt-10) cc_final: 0.7020 (mp0)
REVERT: A 1258 TRP cc_start: 0.8767 (t60) cc_final: 0.8522 (t60)
REVERT: A 1419 LYS cc_start: 0.8676 (mmtm) cc_final: 0.8455 (mmtp)
REVERT: A 1439 GLN cc_start: 0.7420 (OUTLIER) cc_final: 0.6977 (tm-30)
REVERT: A 1443 ASN cc_start: 0.8831 (t0) cc_final: 0.8462 (t0)
REVERT: A 1496 ASN cc_start: 0.9223 (t0) cc_final: 0.8924 (m-40)
REVERT: A 1539 CYS cc_start: 0.8968 (m) cc_final: 0.8724 (t)
REVERT: A 1626 ARG cc_start: 0.8534 (ptm-80) cc_final: 0.8307 (ttm-80)
REVERT: A 1653 SER cc_start: 0.8760 (m) cc_final: 0.8319 (p)
REVERT: A 1662 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7832 (tp)
REVERT: A 1701 MET cc_start: 0.8813 (tpp) cc_final: 0.8600 (tpp)
  outliers start: 48
  outliers final: 33
  residues processed: 290
  average time/residue: 0.2690
  time to fit residues: 117.5813
Evaluate side-chains
  285 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 248
  time to evaluate  : 2.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 HIS
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  300 VAL
Chi-restraints excluded: chain A residue  335 CYS
Chi-restraints excluded: chain A residue  365 LEU
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain A residue  418 GLU
Chi-restraints excluded: chain A residue  700 CYS
Chi-restraints excluded: chain A residue  732 LEU
Chi-restraints excluded: chain A residue  753 ASN
Chi-restraints excluded: chain A residue  796 LEU
Chi-restraints excluded: chain A residue  812 LEU
Chi-restraints excluded: chain A residue  852 ILE
Chi-restraints excluded: chain A residue  908 GLU
Chi-restraints excluded: chain A residue  939 LEU
Chi-restraints excluded: chain A residue 1178 CYS
Chi-restraints excluded: chain A residue 1204 HIS
Chi-restraints excluded: chain A residue 1218 SER
Chi-restraints excluded: chain A residue 1247 THR
Chi-restraints excluded: chain A residue 1259 VAL
Chi-restraints excluded: chain A residue 1340 VAL
Chi-restraints excluded: chain A residue 1344 PHE
Chi-restraints excluded: chain A residue 1353 VAL
Chi-restraints excluded: chain A residue 1384 CYS
Chi-restraints excluded: chain A residue 1439 GLN
Chi-restraints excluded: chain A residue 1557 ILE
Chi-restraints excluded: chain A residue 1564 ASN
Chi-restraints excluded: chain A residue 1598 VAL
Chi-restraints excluded: chain A residue 1629 ARG
Chi-restraints excluded: chain A residue 1648 PHE
Chi-restraints excluded: chain A residue 1662 LEU
Chi-restraints excluded: chain A residue 1668 MET
Chi-restraints excluded: chain A residue 1672 SER
Chi-restraints excluded: chain A residue 1750 LEU
Chi-restraints excluded: chain A residue 1775 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 4 optimal weight:    3.9990
   chunk 121 optimal weight:    1.9990
   chunk 66 optimal weight:    0.6980
   chunk 98 optimal weight:    1.9990
   chunk 120 optimal weight:    0.9990
   chunk 67 optimal weight:    0.0870
   chunk 56 optimal weight:    1.9990
   chunk 119 optimal weight:    0.9980
   chunk 85 optimal weight:    0.5980
   chunk 97 optimal weight:    0.6980
   chunk 33 optimal weight:    1.9990
   overall best weight:    0.6158

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

Flipped N/Q/H residues before XYZ refinement:
A  73 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.168038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.131930 restraints weight = 27154.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.135502 restraints weight = 13200.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.137795 restraints weight = 8063.186|
|-----------------------------------------------------------------------------|
r_work (final): 0.3789
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7454
moved from start:          0.4460

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  12025  Z= 0.151
  Angle     :  0.744  16.116  16349  Z= 0.363
  Chirality :  0.041   0.236   1902
  Planarity :  0.004   0.066   1961
  Dihedral  : 11.160 157.839   2342
  Min Nonbonded Distance : 2.341

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.57 %
    Favored  : 92.43 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 30.71 %
    Favored  : 65.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.62 (0.23), residues: 1387
  helix:  1.00 (0.19), residues: 822
  sheet: -2.04 (0.80), residues: 34
  loop : -2.69 (0.25), residues: 531

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A1684 
 HIS   0.004   0.001   HIS A 130 
 PHE   0.038   0.001   PHE A1246 
 TYR   0.015   0.001   TYR A 378 
 ARG   0.008   0.001   ARG A1623 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00567 (    4)
  link_NAG-ASN         : angle       3.05726 (   12)
  link_BETA1-4         : bond        0.00544 (    7)
  link_BETA1-4         : angle       3.13565 (   21)
  hydrogen bonds       : bond        0.04760 (  588)
  hydrogen bonds       : angle       4.04967 ( 1665)
  SS BOND              : bond        0.00265 (    7)
  SS BOND              : angle       1.62431 (   14)
  covalent geometry    : bond        0.00336 (12007)
  covalent geometry    : angle       0.73041 (16302)

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

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

  2774 Ramachandran restraints generated.
    1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2774 Ramachandran restraints generated.
    1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  300 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 254
  time to evaluate  : 1.901 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 HIS cc_start: 0.3941 (OUTLIER) cc_final: 0.3095 (t-90)
REVERT: A  194 ASN cc_start: 0.7507 (m-40) cc_final: 0.7218 (t0)
REVERT: A  431 GLU cc_start: 0.6378 (mm-30) cc_final: 0.6065 (mt-10)
REVERT: A  744 GLU cc_start: 0.8601 (mp0) cc_final: 0.7484 (tt0)
REVERT: A  790 ILE cc_start: 0.8748 (tp) cc_final: 0.8032 (tp)
REVERT: A  794 MET cc_start: 0.9268 (mmp) cc_final: 0.8657 (mmp)
REVERT: A 1253 GLU cc_start: 0.7290 (mt-10) cc_final: 0.7054 (mp0)
REVERT: A 1254 MET cc_start: 0.7610 (tmm) cc_final: 0.7406 (tmm)
REVERT: A 1274 LEU cc_start: 0.8732 (tp) cc_final: 0.8524 (tp)
REVERT: A 1419 LYS cc_start: 0.8852 (mmtm) cc_final: 0.8615 (mmtm)
REVERT: A 1439 GLN cc_start: 0.7457 (OUTLIER) cc_final: 0.7011 (tm-30)
REVERT: A 1443 ASN cc_start: 0.8919 (t0) cc_final: 0.8561 (t0)
REVERT: A 1539 CYS cc_start: 0.8972 (m) cc_final: 0.8701 (t)
REVERT: A 1626 ARG cc_start: 0.8554 (ptm-80) cc_final: 0.8324 (ttm-80)
REVERT: A 1653 SER cc_start: 0.8764 (m) cc_final: 0.8375 (p)
REVERT: A 1662 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7598 (tp)
REVERT: A 1701 MET cc_start: 0.8892 (tpp) cc_final: 0.8649 (tpp)
  outliers start: 46
  outliers final: 35
  residues processed: 285
  average time/residue: 0.2209
  time to fit residues: 95.9001
Evaluate side-chains
  289 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 251
  time to evaluate  : 1.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 HIS
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  195 TRP
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  300 VAL
Chi-restraints excluded: chain A residue  335 CYS
Chi-restraints excluded: chain A residue  365 LEU
Chi-restraints excluded: chain A residue  382 LEU
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain A residue  418 GLU
Chi-restraints excluded: chain A residue  700 CYS
Chi-restraints excluded: chain A residue  732 LEU
Chi-restraints excluded: chain A residue  753 ASN
Chi-restraints excluded: chain A residue  796 LEU
Chi-restraints excluded: chain A residue  812 LEU
Chi-restraints excluded: chain A residue  852 ILE
Chi-restraints excluded: chain A residue  939 LEU
Chi-restraints excluded: chain A residue 1178 CYS
Chi-restraints excluded: chain A residue 1204 HIS
Chi-restraints excluded: chain A residue 1218 SER
Chi-restraints excluded: chain A residue 1247 THR
Chi-restraints excluded: chain A residue 1259 VAL
Chi-restraints excluded: chain A residue 1344 PHE
Chi-restraints excluded: chain A residue 1353 VAL
Chi-restraints excluded: chain A residue 1384 CYS
Chi-restraints excluded: chain A residue 1439 GLN
Chi-restraints excluded: chain A residue 1557 ILE
Chi-restraints excluded: chain A residue 1564 ASN
Chi-restraints excluded: chain A residue 1598 VAL
Chi-restraints excluded: chain A residue 1621 LEU
Chi-restraints excluded: chain A residue 1629 ARG
Chi-restraints excluded: chain A residue 1662 LEU
Chi-restraints excluded: chain A residue 1668 MET
Chi-restraints excluded: chain A residue 1670 ILE
Chi-restraints excluded: chain A residue 1672 SER
Chi-restraints excluded: chain A residue 1750 LEU
Chi-restraints excluded: chain A residue 1775 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 56 optimal weight:    1.9990
   chunk 135 optimal weight:    3.9990
   chunk 128 optimal weight:    0.4980
   chunk 41 optimal weight:    4.9990
   chunk 10 optimal weight:    1.9990
   chunk 138 optimal weight:    0.8980
   chunk 55 optimal weight:    0.6980
   chunk 99 optimal weight:    2.9990
   chunk 79 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9990
   chunk 46 optimal weight:    0.0970
   overall best weight:    0.5778

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.167813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.131783 restraints weight = 26584.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.135367 restraints weight = 12947.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.137641 restraints weight = 7891.561|
|-----------------------------------------------------------------------------|
r_work (final): 0.3788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7456
moved from start:          0.4630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12025  Z= 0.146
  Angle     :  0.753  16.298  16349  Z= 0.365
  Chirality :  0.042   0.305   1902
  Planarity :  0.004   0.067   1961
  Dihedral  : 10.929 159.227   2342
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.35 %
    Favored  : 92.65 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 30.95 %
    Favored  : 65.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.73 (0.23), residues: 1387
  helix:  0.92 (0.19), residues: 828
  sheet: -2.07 (0.80), residues: 34
  loop : -2.78 (0.25), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 195 
 HIS   0.003   0.001   HIS A1204 
 PHE   0.021   0.001   PHE A1692 
 TYR   0.015   0.001   TYR A 378 
 ARG   0.007   0.001   ARG A1623 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00561 (    4)
  link_NAG-ASN         : angle       3.04855 (   12)
  link_BETA1-4         : bond        0.00547 (    7)
  link_BETA1-4         : angle       3.14127 (   21)
  hydrogen bonds       : bond        0.04878 (  588)
  hydrogen bonds       : angle       4.08249 ( 1665)
  SS BOND              : bond        0.00270 (    7)
  SS BOND              : angle       1.55833 (   14)
  covalent geometry    : bond        0.00323 (12007)
  covalent geometry    : angle       0.73940 (16302)

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

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

  2774 Ramachandran restraints generated.
    1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2774 Ramachandran restraints generated.
    1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  297 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 256
  time to evaluate  : 1.304 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 HIS cc_start: 0.3956 (OUTLIER) cc_final: 0.3121 (t-90)
REVERT: A  194 ASN cc_start: 0.7375 (m-40) cc_final: 0.7053 (t0)
REVERT: A  390 MET cc_start: 0.8547 (tmm) cc_final: 0.8324 (tmm)
REVERT: A  431 GLU cc_start: 0.6318 (mm-30) cc_final: 0.6030 (mt-10)
REVERT: A  744 GLU cc_start: 0.8555 (mp0) cc_final: 0.7476 (tt0)
REVERT: A  790 ILE cc_start: 0.8750 (tp) cc_final: 0.8010 (tp)
REVERT: A  794 MET cc_start: 0.9291 (mmp) cc_final: 0.8684 (mmp)
REVERT: A 1247 THR cc_start: 0.6605 (OUTLIER) cc_final: 0.6388 (t)
REVERT: A 1253 GLU cc_start: 0.7285 (mt-10) cc_final: 0.7036 (mp0)
REVERT: A 1254 MET cc_start: 0.7637 (tmm) cc_final: 0.7401 (tmm)
REVERT: A 1309 ARG cc_start: 0.9023 (ttt180) cc_final: 0.8763 (ttt180)
REVERT: A 1419 LYS cc_start: 0.8815 (mmtm) cc_final: 0.8559 (mmtm)
REVERT: A 1439 GLN cc_start: 0.7427 (OUTLIER) cc_final: 0.6975 (tm-30)
REVERT: A 1443 ASN cc_start: 0.8939 (t0) cc_final: 0.8660 (t0)
REVERT: A 1539 CYS cc_start: 0.8962 (m) cc_final: 0.8666 (t)
REVERT: A 1626 ARG cc_start: 0.8556 (ptm-80) cc_final: 0.8302 (ttm-80)
REVERT: A 1653 SER cc_start: 0.8686 (m) cc_final: 0.8277 (p)
REVERT: A 1662 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7604 (tp)
REVERT: A 1701 MET cc_start: 0.8905 (tpp) cc_final: 0.8660 (tpp)
  outliers start: 41
  outliers final: 37
  residues processed: 282
  average time/residue: 0.2125
  time to fit residues: 90.2435
Evaluate side-chains
  286 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 245
  time to evaluate  : 1.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 HIS
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  195 TRP
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  300 VAL
Chi-restraints excluded: chain A residue  335 CYS
Chi-restraints excluded: chain A residue  365 LEU
Chi-restraints excluded: chain A residue  382 LEU
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain A residue  418 GLU
Chi-restraints excluded: chain A residue  700 CYS
Chi-restraints excluded: chain A residue  732 LEU
Chi-restraints excluded: chain A residue  753 ASN
Chi-restraints excluded: chain A residue  796 LEU
Chi-restraints excluded: chain A residue  812 LEU
Chi-restraints excluded: chain A residue  852 ILE
Chi-restraints excluded: chain A residue  939 LEU
Chi-restraints excluded: chain A residue 1178 CYS
Chi-restraints excluded: chain A residue 1204 HIS
Chi-restraints excluded: chain A residue 1218 SER
Chi-restraints excluded: chain A residue 1247 THR
Chi-restraints excluded: chain A residue 1259 VAL
Chi-restraints excluded: chain A residue 1344 PHE
Chi-restraints excluded: chain A residue 1347 ILE
Chi-restraints excluded: chain A residue 1353 VAL
Chi-restraints excluded: chain A residue 1384 CYS
Chi-restraints excluded: chain A residue 1439 GLN
Chi-restraints excluded: chain A residue 1553 SER
Chi-restraints excluded: chain A residue 1557 ILE
Chi-restraints excluded: chain A residue 1564 ASN
Chi-restraints excluded: chain A residue 1598 VAL
Chi-restraints excluded: chain A residue 1621 LEU
Chi-restraints excluded: chain A residue 1629 ARG
Chi-restraints excluded: chain A residue 1648 PHE
Chi-restraints excluded: chain A residue 1662 LEU
Chi-restraints excluded: chain A residue 1668 MET
Chi-restraints excluded: chain A residue 1670 ILE
Chi-restraints excluded: chain A residue 1672 SER
Chi-restraints excluded: chain A residue 1750 LEU
Chi-restraints excluded: chain A residue 1775 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 55 optimal weight:    0.7980
   chunk 118 optimal weight:    0.8980
   chunk 123 optimal weight:    0.6980
   chunk 98 optimal weight:    0.9980
   chunk 92 optimal weight:    0.9990
   chunk 96 optimal weight:    0.9980
   chunk 66 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9990
   chunk 8 optimal weight:    1.9990
   chunk 111 optimal weight:    0.5980
   chunk 60 optimal weight:    0.9980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 753 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.166333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.130192 restraints weight = 27038.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.133722 restraints weight = 13233.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.136008 restraints weight = 8104.001|
|-----------------------------------------------------------------------------|
r_work (final): 0.3770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7502
moved from start:          0.4844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  12025  Z= 0.168
  Angle     :  0.773  16.215  16349  Z= 0.379
  Chirality :  0.043   0.309   1902
  Planarity :  0.004   0.068   1961
  Dihedral  : 10.853 160.625   2342
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.00 %
    Favored  : 92.00 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 30.87 %
    Favored  : 65.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.84 (0.23), residues: 1387
  helix:  0.84 (0.19), residues: 829
  sheet: -2.15 (0.79), residues: 34
  loop : -2.86 (0.25), residues: 524

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 195 
 HIS   0.004   0.001   HIS A 738 
 PHE   0.051   0.002   PHE A1246 
 TYR   0.017   0.001   TYR A 378 
 ARG   0.007   0.001   ARG A1623 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00582 (    4)
  link_NAG-ASN         : angle       3.15905 (   12)
  link_BETA1-4         : bond        0.00620 (    7)
  link_BETA1-4         : angle       3.16616 (   21)
  hydrogen bonds       : bond        0.05192 (  588)
  hydrogen bonds       : angle       4.18227 ( 1665)
  SS BOND              : bond        0.00319 (    7)
  SS BOND              : angle       1.58167 (   14)
  covalent geometry    : bond        0.00380 (12007)
  covalent geometry    : angle       0.75994 (16302)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5470.11 seconds
wall clock time: 99 minutes 4.30 seconds (5944.30 seconds total)