Starting phenix.real_space_refine
on Sun May  3 04:16:51 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9p24_71158/05_2026/9p24_71158_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9p24_71158/05_2026/9p24_71158.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.48
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9p24_71158/05_2026/9p24_71158.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9p24_71158/05_2026/9p24_71158.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9p24_71158/05_2026/9p24_71158_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9p24_71158/05_2026/9p24_71158_neut.cif"
  }
  resolution = 3.48
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.022
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
     S      73      5.16       5
     Na      1      4.78       5
     C    6766      2.51       5
     N    1624      2.21       5
     O    1792      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10256
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 10104
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1258, 10104
          Classifications: {'peptide': 1258}
          Link IDs: {'PTRANS': 38, 'TRANS': 1219}
          Chain breaks: 4
    Chain: "A"
      Number of atoms: 152
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 152
          Unusual residues: {' NA': 1, '9Z9': 1, 'NAG': 8}
          Classifications: {'undetermined': 10}
          Link IDs: {None: 9}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 8
  Time building chain proxies: 2.52, per 1000 atoms: 0.25
  Number of scatterers: 10256
  At special positions: 0
  Unit cell: (115.072, 138.446, 134.85, 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      73     16.00
     Na      1     11.00
     O    1792      8.00
     N    1624      7.00
     C    6766      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 280 " - pdb=" SG  CYS A 335 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 326 " - pdb=" SG  CYS A 341 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 906 " - pdb=" SG  CYS A 915 " 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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.17
  Conformation dependent library (CDL) restraints added in 479.0 milliseconds
  

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2370

  Finding SS restraints...
    Secondary structure from input PDB file:
      57 helices and 4 sheets defined
      70.9% alpha, 1.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.35
  Creating SS restraints...
    Processing helix  chain 'A' and resid 17 through 37
      removed outlier: 4.163A  pdb=" N   THR A  37 " --> pdb=" O   ALA A  33 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 90
    Processing helix  chain 'A' and resid 118 through 130
      removed outlier: 3.674A  pdb=" N   ALA A 123 " --> pdb=" O   PRO A 119 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 147
      removed outlier: 3.588A  pdb=" N   MET A 135 " --> pdb=" O   SER A 131 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   PHE A 147 " --> pdb=" O   THR A 143 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 156 through 179
      removed outlier: 4.003A  pdb=" N   VAL A 160 " --> pdb=" O   TRP A 156 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 191
      removed outlier: 3.549A  pdb=" N   ASP A 191 " --> pdb=" O   PHE A 188 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 210
      removed outlier: 4.090A  pdb=" N   LEU A 196 " --> pdb=" O   PRO A 192 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   ASP A 197 " --> pdb=" O   TRP A 193 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 228
      removed outlier: 3.682A  pdb=" N   LEU A 227 " --> pdb=" O   VAL A 223 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 235 through 250
      removed outlier: 3.508A  pdb=" N   ILE A 239 " --> pdb=" O   GLY A 235 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   LEU A 250 " --> pdb=" O   SER A 246 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 253 through 270
      removed outlier: 3.786A  pdb=" N   GLN A 270 " --> pdb=" O   LEU A 266 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 310
    Processing helix  chain 'A' and resid 348 through 352
    Processing helix  chain 'A' and resid 357 through 371
    Processing helix  chain 'A' and resid 373 through 385
      removed outlier: 4.369A  pdb=" N   LEU A 377 " --> pdb=" O   CYS A 373 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 401
      removed outlier: 4.242A  pdb=" N   PHE A 393 " --> pdb=" O   TYR A 389 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   PHE A 398 " --> pdb=" O   MET A 394 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   LEU A 399 " --> pdb=" O   LEU A 395 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   SER A 401 " --> pdb=" O   ILE A 397 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 439
      removed outlier: 3.600A  pdb=" N   ALA A 422 " --> pdb=" O   GLU A 418 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   THR A 423 " --> pdb=" O   GLN A 419 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   GLU A 431 " --> pdb=" O   THR A 427 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   LYS A 432 " --> pdb=" O   GLU A 428 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 703 through 715
    Processing helix  chain 'A' and resid 719 through 735
    Processing helix  chain 'A' and resid 742 through 776
      removed outlier: 3.629A  pdb=" N   LEU A 749 " --> pdb=" O   PHE A 745 " (cutoff:3.500A)
      removed outlier: 4.281A  pdb=" N   LEU A 754 " --> pdb=" O   GLN A 750 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   VAL A 755 " --> pdb=" O   VAL A 751 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   PHE A 756 " --> pdb=" O   GLY A 752 " (cutoff:3.500A)
      Proline residue:  A 773  - end of helix
    Processing helix  chain 'A' and resid 779 through 794
    Processing helix  chain 'A' and resid 804 through 821
      removed outlier: 3.733A  pdb=" N   ARG A 811 " --> pdb=" O   ARG A 808 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   LEU A 813 " --> pdb=" O   PHE A 810 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   VAL A 815 " --> pdb=" O   LEU A 812 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   SER A 821 " --> pdb=" O   LEU A 818 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 822 through 835
    Processing helix  chain 'A' and resid 842 through 861
      removed outlier: 3.583A  pdb=" N   LEU A 846 " --> pdb=" O   LEU A 842 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 862 through 872
      removed outlier: 3.738A  pdb=" N   TYR A 865 " --> pdb=" O   GLY A 862 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   GLU A 867 " --> pdb=" O   ASN A 864 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   ASP A 870 " --> pdb=" O   GLU A 867 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   SER A 871 " --> pdb=" O   LEU A 868 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 883 through 897
    Processing helix  chain 'A' and resid 900 through 911
      removed outlier: 3.775A  pdb=" N   ASP A 905 " --> pdb=" O   GLU A 901 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   VAL A 909 " --> pdb=" O   ASP A 905 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   GLY A 911 " --> pdb=" O   MET A 907 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 912 through 943
      removed outlier: 4.633A  pdb=" N   SER A 943 " --> pdb=" O   LEU A 939 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 958 through 971
    Processing helix  chain 'A' and resid 1189 through 1203
    Processing helix  chain 'A' and resid 1204 through 1221
      removed outlier: 3.657A  pdb=" N   GLU A1208 " --> pdb=" O   HIS A1204 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1222 through 1225
      removed outlier: 3.908A  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 1235 through 1262
      removed outlier: 3.658A  pdb=" N   LYS A1244 " --> pdb=" O   GLU A1240 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1262 through 1267
    Processing helix  chain 'A' and resid 1269 through 1291
      removed outlier: 3.936A  pdb=" N   TRP A1273 " --> pdb=" O   ASN A1269 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   LEU A1291 " --> pdb=" O   VAL A1287 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1296 through 1304
      removed outlier: 3.920A  pdb=" N   LYS A1300 " --> pdb=" O   MET A1296 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   THR A1304 " --> pdb=" O   LYS A1300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1305 through 1315
      Proline residue:  A1310  - end of helix
      removed outlier: 3.527A  pdb=" N   ALA A1313 " --> pdb=" O   PRO A1310 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   SER A1315 " --> pdb=" O   ARG A1312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1317 through 1329
      removed outlier: 3.862A  pdb=" N   VAL A1323 " --> pdb=" O   GLY A1319 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   ASN A1325 " --> pdb=" O   ARG A1321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1331 through 1356
      removed outlier: 4.055A  pdb=" N   ASN A1336 " --> pdb=" O   PRO A1332 " (cutoff:3.500A)
      removed outlier: 4.662A  pdb=" N   VAL A1337 " --> pdb=" O   SER A1333 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   ILE A1347 " --> pdb=" O   ILE A1343 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   PHE A1348 " --> pdb=" O   PHE A1344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1380 through 1387
    Processing helix  chain 'A' and resid 1404 through 1417
      removed outlier: 3.734A  pdb=" N   TYR A1409 " --> pdb=" O   VAL A1405 " (cutoff:3.500A)
      removed outlier: 4.213A  pdb=" N   LEU A1410 " --> pdb=" O   GLY A1406 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1420 through 1430
      removed outlier: 4.087A  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 1457
      removed outlier: 4.117A  pdb=" N   PHE A1450 " --> pdb=" O   MET A1446 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1459 through 1480
      removed outlier: 3.582A  pdb=" N   LYS A1479 " --> pdb=" O   GLN A1475 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1488 through 1503
      removed outlier: 4.115A  pdb=" N   ALA A1497 " --> pdb=" O   LYS A1493 " (cutoff:3.500A)
      removed outlier: 4.202A  pdb=" N   MET A1498 " --> pdb=" O   TYR A1494 " (cutoff:3.500A)
      removed outlier: 4.108A  pdb=" N   LYS A1499 " --> pdb=" O   TYR A1495 " (cutoff:3.500A)
      removed outlier: 5.298A  pdb=" N   LYS A1500 " --> pdb=" O   ASN A1496 " (cutoff:3.500A)
      removed outlier: 4.290A  pdb=" N   SER A1503 " --> pdb=" O   LYS A1499 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1518 through 1526
    Processing helix  chain 'A' and resid 1527 through 1546
      removed outlier: 4.090A  pdb=" N   ASP A1531 " --> pdb=" O   LYS A1527 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1553 through 1582
      removed outlier: 3.507A  pdb=" N   ILE A1557 " --> pdb=" O   SER A1553 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   LEU A1582 " --> pdb=" O   LYS A1578 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1591 through 1616
      removed outlier: 3.547A  pdb=" N   ASP A1595 " --> pdb=" O   TRP A1591 " (cutoff:3.500A)
      removed outlier: 4.602A  pdb=" N   ILE A1611 " --> pdb=" O   VAL A1607 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1618 through 1627
    Processing helix  chain 'A' and resid 1628 through 1631
    Processing helix  chain 'A' and resid 1633 through 1640
      removed outlier: 3.591A  pdb=" N   ARG A1638 " --> pdb=" O   ARG A1635 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1641 through 1654
    Processing helix  chain 'A' and resid 1654 through 1677
      removed outlier: 3.808A  pdb=" N   ASN A1659 " --> pdb=" O   PRO A1655 " (cutoff:3.500A)
      removed outlier: 4.271A  pdb=" N   ILE A1660 " --> pdb=" O   ALA A1656 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   LEU A1663 " --> pdb=" O   ASN A1659 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   LEU A1664 " --> pdb=" O   ILE A1660 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   ALA A1677 " --> pdb=" O   ILE A1673 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1696 through 1708
    Processing helix  chain 'A' and resid 1712 through 1718
      removed outlier: 3.906A  pdb=" N   LEU A1716 " --> pdb=" O   GLY A1712 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1744 through 1778
      removed outlier: 4.036A  pdb=" N   GLY A1748 " --> pdb=" O   SER A1744 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 93
    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 295 through 296
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1361 through 1364
      removed outlier: 3.626A  pdb=" N   ARG A1362 " --> pdb=" O   THR A1396 " (cutoff:3.500A)

    603 hydrogen bonds defined for protein.
    1713 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: 1.56

  Time building geometry restraints manager: 1.40 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1568
        1.31 -     1.44: 2921
        1.44 -     1.57: 5888
        1.57 -     1.70: 0
        1.70 -     1.83: 123
  Bond restraints: 10500
  Sorted by residual:
  bond pdb=" C7  NAG A2102 "
       pdb=" N2  NAG A2102 "
    ideal  model  delta    sigma   weight residual
    1.346  1.453 -0.107 2.00e-02 2.50e+03 2.84e+01
  bond pdb=" C7  NAG A2109 "
       pdb=" N2  NAG A2109 "
    ideal  model  delta    sigma   weight residual
    1.346  1.452 -0.106 2.00e-02 2.50e+03 2.83e+01
  bond pdb=" C7  NAG A2104 "
       pdb=" N2  NAG A2104 "
    ideal  model  delta    sigma   weight residual
    1.346  1.452 -0.106 2.00e-02 2.50e+03 2.82e+01
  bond pdb=" C7  NAG A2103 "
       pdb=" N2  NAG A2103 "
    ideal  model  delta    sigma   weight residual
    1.346  1.452 -0.106 2.00e-02 2.50e+03 2.79e+01
  bond pdb=" C7  NAG A2108 "
       pdb=" N2  NAG A2108 "
    ideal  model  delta    sigma   weight residual
    1.346  1.451 -0.105 2.00e-02 2.50e+03 2.78e+01
  ... (remaining 10495 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.59: 13889
        1.59 -     3.18: 255
        3.18 -     4.78: 60
        4.78 -     6.37: 27
        6.37 -     7.96: 9
  Bond angle restraints: 14240
  Sorted by residual:
  angle pdb=" N   ILE A1334 "
        pdb=" CA  ILE A1334 "
        pdb=" C   ILE A1334 "
      ideal   model   delta    sigma   weight residual
     112.96  108.59    4.37 1.00e+00 1.00e+00 1.91e+01
  angle pdb=" C   LEU A1772 "
        pdb=" N   GLU A1773 "
        pdb=" CA  GLU A1773 "
      ideal   model   delta    sigma   weight residual
     120.44  115.90    4.54 1.36e+00 5.41e-01 1.12e+01
  angle pdb=" N   GLU A1773 "
        pdb=" CA  GLU A1773 "
        pdb=" C   GLU A1773 "
      ideal   model   delta    sigma   weight residual
     111.14  107.62    3.52 1.08e+00 8.57e-01 1.06e+01
  angle pdb=" CA  GLN A1483 "
        pdb=" CB  GLN A1483 "
        pdb=" CG  GLN A1483 "
      ideal   model   delta    sigma   weight residual
     114.10  120.19   -6.09 2.00e+00 2.50e-01 9.27e+00
  angle pdb=" CB  GLN A1483 "
        pdb=" CG  GLN A1483 "
        pdb=" CD  GLN A1483 "
      ideal   model   delta    sigma   weight residual
     112.60  117.52   -4.92 1.70e+00 3.46e-01 8.37e+00
  ... (remaining 14235 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    30.63: 5929
       30.63 -    61.27: 394
       61.27 -    91.90: 26
       91.90 -   122.54: 3
      122.54 -   153.17: 1
  Dihedral angle restraints: 6353
    sinusoidal: 2684
      harmonic: 3669
  Sorted by residual:
  dihedral pdb=" CB  CYS A 326 "
           pdb=" SG  CYS A 326 "
           pdb=" SG  CYS A 341 "
           pdb=" CB  CYS A 341 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  175.14  -82.14     1      1.00e+01 1.00e-02 8.29e+01
  dihedral pdb=" C21 9Z9 A2101 "
           pdb=" C22 9Z9 A2101 "
           pdb=" C23 9Z9 A2101 "
           pdb=" C24 9Z9 A2101 "
      ideal   model   delta sinusoidal    sigma   weight residual
      77.99  -75.18  153.17     1      3.00e+01 1.11e-03 2.02e+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
     -86.00 -122.47   36.47     1      1.00e+01 1.00e-02 1.88e+01
  ... (remaining 6350 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 1062
       0.028 -    0.055: 354
       0.055 -    0.083: 178
       0.083 -    0.111: 54
       0.111 -    0.138: 11
  Chirality restraints: 1659
  Sorted by residual:
  chirality pdb=" CA  PRO A1298 "
            pdb=" N   PRO A1298 "
            pdb=" C   PRO A1298 "
            pdb=" CB  PRO A1298 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 4.79e-01
  chirality pdb=" CA  PRO A1725 "
            pdb=" N   PRO A1725 "
            pdb=" C   PRO A1725 "
            pdb=" CB  PRO A1725 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 4.01e-01
  chirality pdb=" C2  NAG A2103 "
            pdb=" C1  NAG A2103 "
            pdb=" C3  NAG A2103 "
            pdb=" N2  NAG A2103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.62    0.12 2.00e-01 2.50e+01 3.88e-01
  ... (remaining 1656 not shown)

  Planarity restraints: 1732
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A  51 "    0.051 5.00e-02 4.00e+02   7.79e-02 9.70e+00
        pdb=" N   PRO A  52 "   -0.135 5.00e-02 4.00e+02
        pdb=" CA  PRO A  52 "    0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO A  52 "    0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A1597 "   -0.010 2.00e-02 2.50e+03   2.09e-02 4.36e+00
        pdb=" C   VAL A1597 "    0.036 2.00e-02 2.50e+03
        pdb=" O   VAL A1597 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   VAL A1598 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A1600 "   -0.010 2.00e-02 2.50e+03   2.03e-02 4.14e+00
        pdb=" C   ILE A1600 "    0.035 2.00e-02 2.50e+03
        pdb=" O   ILE A1600 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   LEU A1601 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 1729 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.70: 192
        2.70 -     3.25: 10038
        3.25 -     3.80: 15103
        3.80 -     4.35: 17761
        4.35 -     4.90: 30348
  Nonbonded interactions: 73442
  Sorted by model distance:
  nonbonded pdb=" O   PRO A  85 "
            pdb=" OG  SER A  88 "
     model   vdw
     2.144 3.040
  nonbonded pdb=" O   MET A 203 "
            pdb=" OG1 THR A 207 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" OG  SER A 115 "
            pdb=" O   PHE A 117 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" O   ASN A 275 "
            pdb=" OG  SER A 384 "
     model   vdw
     2.287 3.040
  nonbonded pdb=" O   VAL A 806 "
            pdb=" OG  SER A 809 "
     model   vdw
     2.298 3.040
  ... (remaining 73437 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.420
  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:             0.020
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.730
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7870
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      :  0.004   0.107  10506  Z= 0.200
  Angle     :  0.596   7.960  14250  Z= 0.294
  Chirality :  0.037   0.138   1659
  Planarity :  0.004   0.078   1732
  Dihedral  : 18.298 153.170   3968
  Min Nonbonded Distance : 2.144

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  : 31.76 %
    Favored  : 67.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.73 (0.25), residues: 1248
  helix:  1.63 (0.19), residues: 840
  sheet: -2.57 (0.99), residues: 24
  loop : -1.98 (0.30), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1626 
 TYR   0.016   0.001   TYR A1586 
 PHE   0.015   0.001   PHE A1751 
 TRP   0.014   0.001   TRP A 156 
 HIS   0.006   0.001   HIS A 118 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 (10500)
  covalent geometry    : angle       0.59511 (14240)
  SS BOND              : bond        0.00210 (    5)
  SS BOND              : angle       1.31671 (   10)
  hydrogen bonds       : bond        0.12264 (  603)
  hydrogen bonds       : angle       4.41457 ( 1713)
  Misc. bond           : bond        0.02407 (    1)

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 146
  time to evaluate  : 0.394 
Fit side-chains
REVERT: A  774 TYR cc_start: 0.7662 (OUTLIER) cc_final: 0.7277 (t80)
REVERT: A 1595 ASP cc_start: 0.7805 (m-30) cc_final: 0.7169 (m-30)
  outliers start: 3
  outliers final: 0
  residues processed: 148
  average time/residue: 0.0834
  time to fit residues: 18.8436
Evaluate side-chains
  143 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 142
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  774 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 108 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9990
   chunk 97 optimal weight:    6.9990
   chunk 113 optimal weight:    2.9990
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    3.9990
   chunk 123 optimal weight:    0.9980
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:   10.0000
   overall best weight:    1.9586

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

Flipped N/Q/H residues before XYZ refinement:
** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 291 ASN
A 406 ASN
A1354 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.148410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.104536 restraints weight = 16762.028|
|-----------------------------------------------------------------------------|
r_work (start): 0.3278 rms_B_bonded: 3.22
r_work: 0.3144 rms_B_bonded: 3.83 restraints_weight: 0.5000
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
moved from start:          0.0954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  10506  Z= 0.188
  Angle     :  0.571   8.135  14250  Z= 0.299
  Chirality :  0.038   0.146   1659
  Planarity :  0.004   0.062   1732
  Dihedral  :  8.234 145.539   1614
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.69 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 29.77 %
    Favored  : 66.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.82 (0.25), residues: 1248
  helix:  1.76 (0.19), residues: 827
  sheet: -2.94 (0.92), residues: 24
  loop : -1.96 (0.30), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1626 
 TYR   0.018   0.001   TYR A1586 
 PHE   0.022   0.001   PHE A1751 
 TRP   0.015   0.001   TRP A1258 
 HIS   0.003   0.001   HIS A 118 

Details of bonding type rmsd
  covalent geometry    : bond        0.00446 (10500)
  covalent geometry    : angle       0.56895 (14240)
  SS BOND              : bond        0.00401 (    5)
  SS BOND              : angle       1.70240 (   10)
  hydrogen bonds       : bond        0.06317 (  603)
  hydrogen bonds       : angle       3.72048 ( 1713)
  Misc. bond           : bond        0.00091 (    1)

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 146
  time to evaluate  : 0.397 
Fit side-chains
REVERT: A   96 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.7829 (tt)
REVERT: A  346 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8131 (pm20)
REVERT: A  774 TYR cc_start: 0.8070 (OUTLIER) cc_final: 0.7438 (t80)
REVERT: A  858 MET cc_start: 0.9129 (tmm) cc_final: 0.8889 (ttt)
REVERT: A 1494 TYR cc_start: 0.7579 (OUTLIER) cc_final: 0.7339 (t80)
  outliers start: 36
  outliers final: 19
  residues processed: 170
  average time/residue: 0.0803
  time to fit residues: 20.9931
Evaluate side-chains
  158 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 136
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain A residue  101 THR
Chi-restraints excluded: chain A residue  145 CYS
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  215 VAL
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  267 ILE
Chi-restraints excluded: chain A residue  375 GLU
Chi-restraints excluded: chain A residue  390 MET
Chi-restraints excluded: chain A residue  754 LEU
Chi-restraints excluded: chain A residue  759 ILE
Chi-restraints excluded: chain A residue  774 TYR
Chi-restraints excluded: chain A residue  776 TYR
Chi-restraints excluded: chain A residue  793 LEU
Chi-restraints excluded: chain A residue 1251 VAL
Chi-restraints excluded: chain A residue 1343 ILE
Chi-restraints excluded: chain A residue 1374 ASN
Chi-restraints excluded: chain A residue 1494 TYR
Chi-restraints excluded: chain A residue 1544 THR
Chi-restraints excluded: chain A residue 1564 ASN
Chi-restraints excluded: chain A residue 1572 THR
Chi-restraints excluded: chain A residue 1763 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 58 optimal weight:    0.7980
   chunk 17 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 14 optimal weight:    5.9990
   chunk 21 optimal weight:    0.9980
   chunk 46 optimal weight:    0.6980
   chunk 120 optimal weight:    2.9990
   chunk 65 optimal weight:    4.9990
   chunk 90 optimal weight:    0.4980
   chunk 61 optimal weight:    2.9990
   chunk 118 optimal weight:    0.8980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 291 ASN
A 834 ASN
A 864 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.151570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.107996 restraints weight = 16738.107|
|-----------------------------------------------------------------------------|
r_work (start): 0.3323 rms_B_bonded: 3.24
r_work: 0.3189 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7791
moved from start:          0.0989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  10506  Z= 0.114
  Angle     :  0.498   8.842  14250  Z= 0.259
  Chirality :  0.035   0.135   1659
  Planarity :  0.004   0.051   1732
  Dihedral  :  7.510 143.118   1614
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 4.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 30.05 %
    Favored  : 66.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.03 (0.25), residues: 1248
  helix:  1.94 (0.19), residues: 825
  sheet: -3.23 (0.88), residues: 22
  loop : -1.87 (0.30), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1626 
 TYR   0.016   0.001   TYR A1586 
 PHE   0.016   0.001   PHE A1751 
 TRP   0.011   0.001   TRP A 156 
 HIS   0.004   0.001   HIS A 118 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 (10500)
  covalent geometry    : angle       0.49667 (14240)
  SS BOND              : bond        0.00262 (    5)
  SS BOND              : angle       1.20270 (   10)
  hydrogen bonds       : bond        0.04960 (  603)
  hydrogen bonds       : angle       3.42053 ( 1713)
  Misc. bond           : bond        0.00042 (    1)

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 150
  time to evaluate  : 0.367 
Fit side-chains
REVERT: A  101 THR cc_start: 0.7387 (OUTLIER) cc_final: 0.7134 (p)
REVERT: A  774 TYR cc_start: 0.8119 (OUTLIER) cc_final: 0.7414 (t80)
REVERT: A  834 ASN cc_start: 0.8265 (OUTLIER) cc_final: 0.7960 (t0)
REVERT: A  858 MET cc_start: 0.9102 (tmm) cc_final: 0.8849 (ttt)
REVERT: A 1296 MET cc_start: 0.7263 (ptp) cc_final: 0.7062 (ptp)
REVERT: A 1494 TYR cc_start: 0.7580 (OUTLIER) cc_final: 0.7330 (t80)
REVERT: A 1626 ARG cc_start: 0.8211 (ttm-80) cc_final: 0.7885 (ttm110)
  outliers start: 36
  outliers final: 23
  residues processed: 169
  average time/residue: 0.0847
  time to fit residues: 21.5493
Evaluate side-chains
  170 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 143
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 THR
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  267 ILE
Chi-restraints excluded: chain A residue  375 GLU
Chi-restraints excluded: chain A residue  429 GLU
Chi-restraints excluded: chain A residue  749 LEU
Chi-restraints excluded: chain A residue  754 LEU
Chi-restraints excluded: chain A residue  759 ILE
Chi-restraints excluded: chain A residue  774 TYR
Chi-restraints excluded: chain A residue  776 TYR
Chi-restraints excluded: chain A residue  793 LEU
Chi-restraints excluded: chain A residue  827 THR
Chi-restraints excluded: chain A residue  834 ASN
Chi-restraints excluded: chain A residue  916 LEU
Chi-restraints excluded: chain A residue  967 GLN
Chi-restraints excluded: chain A residue 1259 VAL
Chi-restraints excluded: chain A residue 1343 ILE
Chi-restraints excluded: chain A residue 1363 CYS
Chi-restraints excluded: chain A residue 1494 TYR
Chi-restraints excluded: chain A residue 1544 THR
Chi-restraints excluded: chain A residue 1564 ASN
Chi-restraints excluded: chain A residue 1624 VAL
Chi-restraints excluded: chain A residue 1696 THR
Chi-restraints excluded: chain A residue 1708 THR
Chi-restraints excluded: chain A residue 1759 SER
Chi-restraints excluded: chain A residue 1761 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 26 optimal weight:    0.7980
   chunk 6 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   chunk 96 optimal weight:    4.9990
   chunk 53 optimal weight:    0.9980
   chunk 63 optimal weight:    0.9980
   chunk 10 optimal weight:    2.9990
   chunk 88 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9980
   chunk 18 optimal weight:    9.9990
   overall best weight:    1.3582

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

Flipped N/Q/H residues before XYZ refinement:
** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 291 ASN
A 834 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.149439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.105680 restraints weight = 16969.107|
|-----------------------------------------------------------------------------|
r_work (start): 0.3291 rms_B_bonded: 3.24
r_work: 0.3156 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.3156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7834
moved from start:          0.1227

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10506  Z= 0.144
  Angle     :  0.525   8.163  14250  Z= 0.273
  Chirality :  0.036   0.152   1659
  Planarity :  0.004   0.048   1732
  Dihedral  :  7.224 140.355   1614
  Min Nonbonded Distance : 2.350

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.21 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 28.87 %
    Favored  : 66.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.00 (0.25), residues: 1248
  helix:  1.93 (0.19), residues: 827
  sheet: -2.96 (0.92), residues: 24
  loop : -1.94 (0.30), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 965 
 TYR   0.016   0.001   TYR A1586 
 PHE   0.050   0.001   PHE A1587 
 TRP   0.013   0.001   TRP A 156 
 HIS   0.003   0.001   HIS A 118 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 (10500)
  covalent geometry    : angle       0.52382 (14240)
  SS BOND              : bond        0.00324 (    5)
  SS BOND              : angle       1.42690 (   10)
  hydrogen bonds       : bond        0.05403 (  603)
  hydrogen bonds       : angle       3.48900 ( 1713)
  Misc. bond           : bond        0.00032 (    1)

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 148
  time to evaluate  : 0.312 
Fit side-chains
REVERT: A   96 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7846 (tt)
REVERT: A  101 THR cc_start: 0.7379 (OUTLIER) cc_final: 0.7041 (p)
REVERT: A  219 ARG cc_start: 0.8187 (ttt-90) cc_final: 0.7951 (ttp80)
REVERT: A  774 TYR cc_start: 0.8151 (OUTLIER) cc_final: 0.7344 (t80)
REVERT: A  824 THR cc_start: 0.7968 (OUTLIER) cc_final: 0.7734 (m)
REVERT: A  858 MET cc_start: 0.9105 (tmm) cc_final: 0.8895 (ttt)
REVERT: A 1245 MET cc_start: 0.7642 (ttp) cc_final: 0.7028 (tmm)
REVERT: A 1296 MET cc_start: 0.7197 (ptp) cc_final: 0.6995 (ptp)
REVERT: A 1480 LEU cc_start: 0.7733 (tp) cc_final: 0.7282 (tt)
REVERT: A 1494 TYR cc_start: 0.7586 (OUTLIER) cc_final: 0.7351 (t80)
  outliers start: 47
  outliers final: 30
  residues processed: 179
  average time/residue: 0.0808
  time to fit residues: 21.8108
Evaluate side-chains
  176 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 141
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain A residue  101 THR
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  215 VAL
Chi-restraints excluded: chain A residue  267 ILE
Chi-restraints excluded: chain A residue  375 GLU
Chi-restraints excluded: chain A residue  382 LEU
Chi-restraints excluded: chain A residue  429 GLU
Chi-restraints excluded: chain A residue  749 LEU
Chi-restraints excluded: chain A residue  754 LEU
Chi-restraints excluded: chain A residue  759 ILE
Chi-restraints excluded: chain A residue  774 TYR
Chi-restraints excluded: chain A residue  776 TYR
Chi-restraints excluded: chain A residue  793 LEU
Chi-restraints excluded: chain A residue  824 THR
Chi-restraints excluded: chain A residue  827 THR
Chi-restraints excluded: chain A residue  855 VAL
Chi-restraints excluded: chain A residue  916 LEU
Chi-restraints excluded: chain A residue  967 GLN
Chi-restraints excluded: chain A residue 1251 VAL
Chi-restraints excluded: chain A residue 1259 VAL
Chi-restraints excluded: chain A residue 1343 ILE
Chi-restraints excluded: chain A residue 1363 CYS
Chi-restraints excluded: chain A residue 1374 ASN
Chi-restraints excluded: chain A residue 1494 TYR
Chi-restraints excluded: chain A residue 1544 THR
Chi-restraints excluded: chain A residue 1564 ASN
Chi-restraints excluded: chain A residue 1572 THR
Chi-restraints excluded: chain A residue 1624 VAL
Chi-restraints excluded: chain A residue 1651 MET
Chi-restraints excluded: chain A residue 1696 THR
Chi-restraints excluded: chain A residue 1708 THR
Chi-restraints excluded: chain A residue 1759 SER
Chi-restraints excluded: chain A residue 1763 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 67 optimal weight:    0.7980
   chunk 119 optimal weight:    0.0050
   chunk 83 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 77 optimal weight:    9.9990
   chunk 34 optimal weight:    0.8980
   chunk 59 optimal weight:    1.9990
   chunk 4 optimal weight:   10.0000
   chunk 97 optimal weight:    2.9990
   chunk 20 optimal weight:    0.0010
   chunk 47 optimal weight:    1.9990
   overall best weight:    0.7402

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

Flipped N/Q/H residues before XYZ refinement:
** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 214 ASN
A 291 ASN
A1354 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.151737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.108030 restraints weight = 16907.255|
|-----------------------------------------------------------------------------|
r_work (start): 0.3321 rms_B_bonded: 3.25
r_work: 0.3187 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7790
moved from start:          0.1266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  10506  Z= 0.112
  Angle     :  0.502   7.368  14250  Z= 0.260
  Chirality :  0.035   0.138   1659
  Planarity :  0.004   0.046   1732
  Dihedral  :  6.781 130.861   1614
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.33 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 29.41 %
    Favored  : 66.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.11 (0.25), residues: 1248
  helix:  2.00 (0.19), residues: 833
  sheet: -3.31 (0.88), residues: 22
  loop : -1.92 (0.30), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1626 
 TYR   0.014   0.001   TYR A1586 
 PHE   0.015   0.001   PHE A1751 
 TRP   0.012   0.001   TRP A 156 
 HIS   0.004   0.001   HIS A 118 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 (10500)
  covalent geometry    : angle       0.50085 (14240)
  SS BOND              : bond        0.00354 (    5)
  SS BOND              : angle       1.14834 (   10)
  hydrogen bonds       : bond        0.04654 (  603)
  hydrogen bonds       : angle       3.36166 ( 1713)
  Misc. bond           : bond        0.00029 (    1)

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 146
  time to evaluate  : 0.377 
Fit side-chains
REVERT: A   34 ARG cc_start: 0.7300 (OUTLIER) cc_final: 0.7094 (mmp-170)
REVERT: A   96 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7787 (tt)
REVERT: A  101 THR cc_start: 0.7346 (OUTLIER) cc_final: 0.7015 (p)
REVERT: A  718 PHE cc_start: 0.7100 (p90) cc_final: 0.6877 (p90)
REVERT: A  774 TYR cc_start: 0.8103 (OUTLIER) cc_final: 0.7325 (t80)
REVERT: A  824 THR cc_start: 0.7867 (OUTLIER) cc_final: 0.7619 (m)
REVERT: A  858 MET cc_start: 0.9090 (tmm) cc_final: 0.8819 (ttt)
REVERT: A 1253 GLU cc_start: 0.8143 (tt0) cc_final: 0.7713 (tt0)
REVERT: A 1296 MET cc_start: 0.7103 (ptp) cc_final: 0.6368 (ptp)
REVERT: A 1480 LEU cc_start: 0.7758 (tp) cc_final: 0.7300 (tt)
REVERT: A 1494 TYR cc_start: 0.7539 (OUTLIER) cc_final: 0.7322 (t80)
  outliers start: 45
  outliers final: 27
  residues processed: 175
  average time/residue: 0.0833
  time to fit residues: 22.1834
Evaluate side-chains
  176 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 143
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ARG
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain A residue  101 THR
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  145 CYS
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  267 ILE
Chi-restraints excluded: chain A residue  375 GLU
Chi-restraints excluded: chain A residue  382 LEU
Chi-restraints excluded: chain A residue  390 MET
Chi-restraints excluded: chain A residue  749 LEU
Chi-restraints excluded: chain A residue  754 LEU
Chi-restraints excluded: chain A residue  759 ILE
Chi-restraints excluded: chain A residue  774 TYR
Chi-restraints excluded: chain A residue  776 TYR
Chi-restraints excluded: chain A residue  824 THR
Chi-restraints excluded: chain A residue  827 THR
Chi-restraints excluded: chain A residue  916 LEU
Chi-restraints excluded: chain A residue  967 GLN
Chi-restraints excluded: chain A residue 1255 LEU
Chi-restraints excluded: chain A residue 1259 VAL
Chi-restraints excluded: chain A residue 1328 VAL
Chi-restraints excluded: chain A residue 1343 ILE
Chi-restraints excluded: chain A residue 1363 CYS
Chi-restraints excluded: chain A residue 1494 TYR
Chi-restraints excluded: chain A residue 1544 THR
Chi-restraints excluded: chain A residue 1564 ASN
Chi-restraints excluded: chain A residue 1595 ASP
Chi-restraints excluded: chain A residue 1611 ILE
Chi-restraints excluded: chain A residue 1624 VAL
Chi-restraints excluded: chain A residue 1651 MET
Chi-restraints excluded: chain A residue 1696 THR
Chi-restraints excluded: chain A residue 1759 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 50 optimal weight:    9.9990
   chunk 79 optimal weight:    2.9990
   chunk 113 optimal weight:    4.9990
   chunk 47 optimal weight:    2.9990
   chunk 19 optimal weight:    0.7980
   chunk 90 optimal weight:    1.9990
   chunk 69 optimal weight:    0.7980
   chunk 43 optimal weight:    4.9990
   chunk 68 optimal weight:    0.9980
   chunk 98 optimal weight:    0.5980
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 214 ASN
A 291 ASN
A1734 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.150910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.107060 restraints weight = 17102.868|
|-----------------------------------------------------------------------------|
r_work (start): 0.3310 rms_B_bonded: 3.28
r_work: 0.3173 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7809
moved from start:          0.1404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10506  Z= 0.127
  Angle     :  0.526   8.824  14250  Z= 0.272
  Chirality :  0.036   0.136   1659
  Planarity :  0.004   0.047   1732
  Dihedral  :  6.503 112.790   1614
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.81 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 29.05 %
    Favored  : 66.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.09 (0.25), residues: 1248
  helix:  1.99 (0.19), residues: 833
  sheet: -3.39 (0.86), residues: 22
  loop : -1.94 (0.30), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1626 
 TYR   0.015   0.001   TYR A1586 
 PHE   0.016   0.001   PHE A1751 
 TRP   0.012   0.001   TRP A 156 
 HIS   0.003   0.001   HIS A 118 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 (10500)
  covalent geometry    : angle       0.52460 (14240)
  SS BOND              : bond        0.00350 (    5)
  SS BOND              : angle       1.51987 (   10)
  hydrogen bonds       : bond        0.04878 (  603)
  hydrogen bonds       : angle       3.40691 ( 1713)
  Misc. bond           : bond        0.00022 (    1)

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 147
  time to evaluate  : 0.297 
Fit side-chains
REVERT: A  283 ASN cc_start: 0.9036 (OUTLIER) cc_final: 0.8815 (m110)
REVERT: A  718 PHE cc_start: 0.7126 (p90) cc_final: 0.6884 (p90)
REVERT: A  774 TYR cc_start: 0.8072 (OUTLIER) cc_final: 0.7248 (t80)
REVERT: A  824 THR cc_start: 0.7882 (OUTLIER) cc_final: 0.7645 (m)
REVERT: A  858 MET cc_start: 0.9088 (tmm) cc_final: 0.8713 (ttt)
REVERT: A 1245 MET cc_start: 0.7594 (ttp) cc_final: 0.6993 (tmm)
REVERT: A 1253 GLU cc_start: 0.8170 (tt0) cc_final: 0.7745 (tt0)
REVERT: A 1296 MET cc_start: 0.7136 (ptp) cc_final: 0.6464 (ptp)
REVERT: A 1480 LEU cc_start: 0.7687 (tp) cc_final: 0.7205 (tt)
REVERT: A 1494 TYR cc_start: 0.7524 (OUTLIER) cc_final: 0.7323 (t80)
  outliers start: 48
  outliers final: 34
  residues processed: 180
  average time/residue: 0.0792
  time to fit residues: 21.6992
Evaluate side-chains
  179 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 141
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 THR
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  145 CYS
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  215 VAL
Chi-restraints excluded: chain A residue  257 THR
Chi-restraints excluded: chain A residue  267 ILE
Chi-restraints excluded: chain A residue  283 ASN
Chi-restraints excluded: chain A residue  375 GLU
Chi-restraints excluded: chain A residue  382 LEU
Chi-restraints excluded: chain A residue  390 MET
Chi-restraints excluded: chain A residue  749 LEU
Chi-restraints excluded: chain A residue  754 LEU
Chi-restraints excluded: chain A residue  759 ILE
Chi-restraints excluded: chain A residue  774 TYR
Chi-restraints excluded: chain A residue  776 TYR
Chi-restraints excluded: chain A residue  793 LEU
Chi-restraints excluded: chain A residue  824 THR
Chi-restraints excluded: chain A residue  827 THR
Chi-restraints excluded: chain A residue  855 VAL
Chi-restraints excluded: chain A residue  916 LEU
Chi-restraints excluded: chain A residue  967 GLN
Chi-restraints excluded: chain A residue 1255 LEU
Chi-restraints excluded: chain A residue 1259 VAL
Chi-restraints excluded: chain A residue 1328 VAL
Chi-restraints excluded: chain A residue 1343 ILE
Chi-restraints excluded: chain A residue 1363 CYS
Chi-restraints excluded: chain A residue 1374 ASN
Chi-restraints excluded: chain A residue 1494 TYR
Chi-restraints excluded: chain A residue 1544 THR
Chi-restraints excluded: chain A residue 1564 ASN
Chi-restraints excluded: chain A residue 1595 ASP
Chi-restraints excluded: chain A residue 1611 ILE
Chi-restraints excluded: chain A residue 1624 VAL
Chi-restraints excluded: chain A residue 1651 MET
Chi-restraints excluded: chain A residue 1696 THR
Chi-restraints excluded: chain A residue 1759 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 69 optimal weight:    0.9980
   chunk 39 optimal weight:    1.9990
   chunk 7 optimal weight:    3.9990
   chunk 97 optimal weight:    3.9990
   chunk 17 optimal weight:    0.8980
   chunk 22 optimal weight:    0.0060
   chunk 18 optimal weight:    0.9980
   chunk 54 optimal weight:    1.9990
   chunk 124 optimal weight:    0.9990
   chunk 99 optimal weight:    3.9990
   chunk 96 optimal weight:    0.9990
   overall best weight:    0.7798

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

Flipped N/Q/H residues before XYZ refinement:
** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 214 ASN
A1354 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.151916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.108288 restraints weight = 16857.153|
|-----------------------------------------------------------------------------|
r_work (start): 0.3324 rms_B_bonded: 3.22
r_work: 0.3192 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7733
moved from start:          0.1442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  10506  Z= 0.113
  Angle     :  0.525  11.361  14250  Z= 0.267
  Chirality :  0.035   0.147   1659
  Planarity :  0.004   0.046   1732
  Dihedral  :  6.291 102.921   1614
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.73 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 29.77 %
    Favored  : 66.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.21 (0.25), residues: 1248
  helix:  2.10 (0.19), residues: 827
  sheet: -3.42 (0.87), residues: 22
  loop : -1.85 (0.30), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1626 
 TYR   0.013   0.001   TYR A1586 
 PHE   0.015   0.001   PHE A1751 
 TRP   0.015   0.001   TRP A 156 
 HIS   0.003   0.001   HIS A 118 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 (10500)
  covalent geometry    : angle       0.52408 (14240)
  SS BOND              : bond        0.00441 (    5)
  SS BOND              : angle       1.50662 (   10)
  hydrogen bonds       : bond        0.04571 (  603)
  hydrogen bonds       : angle       3.34587 ( 1713)
  Misc. bond           : bond        0.00023 (    1)

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 144
  time to evaluate  : 0.388 
Fit side-chains
REVERT: A  101 THR cc_start: 0.7325 (OUTLIER) cc_final: 0.7085 (p)
REVERT: A  195 TRP cc_start: 0.8094 (m-10) cc_final: 0.7641 (m-10)
REVERT: A  283 ASN cc_start: 0.9114 (OUTLIER) cc_final: 0.8889 (m110)
REVERT: A  774 TYR cc_start: 0.8041 (OUTLIER) cc_final: 0.7252 (t80)
REVERT: A  824 THR cc_start: 0.7828 (OUTLIER) cc_final: 0.7582 (m)
REVERT: A 1253 GLU cc_start: 0.8099 (tt0) cc_final: 0.7669 (tt0)
REVERT: A 1296 MET cc_start: 0.7037 (ptp) cc_final: 0.6297 (ptp)
  outliers start: 42
  outliers final: 31
  residues processed: 169
  average time/residue: 0.0766
  time to fit residues: 20.0382
Evaluate side-chains
  171 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 136
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 THR
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  145 CYS
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  257 THR
Chi-restraints excluded: chain A residue  267 ILE
Chi-restraints excluded: chain A residue  283 ASN
Chi-restraints excluded: chain A residue  375 GLU
Chi-restraints excluded: chain A residue  382 LEU
Chi-restraints excluded: chain A residue  390 MET
Chi-restraints excluded: chain A residue  749 LEU
Chi-restraints excluded: chain A residue  754 LEU
Chi-restraints excluded: chain A residue  759 ILE
Chi-restraints excluded: chain A residue  774 TYR
Chi-restraints excluded: chain A residue  776 TYR
Chi-restraints excluded: chain A residue  793 LEU
Chi-restraints excluded: chain A residue  824 THR
Chi-restraints excluded: chain A residue  827 THR
Chi-restraints excluded: chain A residue  967 GLN
Chi-restraints excluded: chain A residue 1251 VAL
Chi-restraints excluded: chain A residue 1255 LEU
Chi-restraints excluded: chain A residue 1259 VAL
Chi-restraints excluded: chain A residue 1328 VAL
Chi-restraints excluded: chain A residue 1343 ILE
Chi-restraints excluded: chain A residue 1363 CYS
Chi-restraints excluded: chain A residue 1374 ASN
Chi-restraints excluded: chain A residue 1544 THR
Chi-restraints excluded: chain A residue 1564 ASN
Chi-restraints excluded: chain A residue 1611 ILE
Chi-restraints excluded: chain A residue 1624 VAL
Chi-restraints excluded: chain A residue 1651 MET
Chi-restraints excluded: chain A residue 1696 THR
Chi-restraints excluded: chain A residue 1708 THR
Chi-restraints excluded: chain A residue 1759 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 82 optimal weight:    0.5980
   chunk 56 optimal weight:    2.9990
   chunk 115 optimal weight:    2.9990
   chunk 112 optimal weight:    0.6980
   chunk 111 optimal weight:    0.8980
   chunk 68 optimal weight:    0.9990
   chunk 37 optimal weight:    0.6980
   chunk 44 optimal weight:    2.9990
   chunk 29 optimal weight:    3.9990
   chunk 101 optimal weight:    1.9990
   chunk 35 optimal weight:    4.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A 214 ASN
A 291 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.152184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.108594 restraints weight = 16950.705|
|-----------------------------------------------------------------------------|
r_work (start): 0.3327 rms_B_bonded: 3.26
r_work: 0.3192 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7729
moved from start:          0.1541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10506  Z= 0.116
  Angle     :  0.533  10.627  14250  Z= 0.270
  Chirality :  0.036   0.203   1659
  Planarity :  0.004   0.046   1732
  Dihedral  :  6.154  97.775   1614
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.49 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 30.32 %
    Favored  : 66.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.22 (0.25), residues: 1248
  helix:  2.10 (0.19), residues: 827
  sheet: -3.53 (0.89), residues: 22
  loop : -1.81 (0.30), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  53 
 TYR   0.011   0.001   TYR A 378 
 PHE   0.056   0.001   PHE A1587 
 TRP   0.015   0.001   TRP A 156 
 HIS   0.003   0.001   HIS A 118 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 (10500)
  covalent geometry    : angle       0.53249 (14240)
  SS BOND              : bond        0.00331 (    5)
  SS BOND              : angle       1.25987 (   10)
  hydrogen bonds       : bond        0.04499 (  603)
  hydrogen bonds       : angle       3.34062 ( 1713)
  Misc. bond           : bond        0.00022 (    1)

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 139
  time to evaluate  : 0.372 
Fit side-chains
REVERT: A  101 THR cc_start: 0.7310 (OUTLIER) cc_final: 0.7069 (p)
REVERT: A  195 TRP cc_start: 0.8106 (m-10) cc_final: 0.7679 (m-10)
REVERT: A  283 ASN cc_start: 0.9124 (OUTLIER) cc_final: 0.8905 (m110)
REVERT: A  774 TYR cc_start: 0.8036 (OUTLIER) cc_final: 0.7258 (t80)
REVERT: A  824 THR cc_start: 0.7843 (OUTLIER) cc_final: 0.7601 (m)
REVERT: A 1245 MET cc_start: 0.7475 (ttp) cc_final: 0.7048 (tmm)
REVERT: A 1253 GLU cc_start: 0.8095 (tt0) cc_final: 0.7669 (tt0)
REVERT: A 1296 MET cc_start: 0.7030 (ptp) cc_final: 0.6311 (ptp)
REVERT: A 1480 LEU cc_start: 0.7621 (tp) cc_final: 0.7271 (tt)
  outliers start: 38
  outliers final: 31
  residues processed: 163
  average time/residue: 0.0787
  time to fit residues: 19.8839
Evaluate side-chains
  170 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 135
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 THR
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  145 CYS
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  214 ASN
Chi-restraints excluded: chain A residue  257 THR
Chi-restraints excluded: chain A residue  267 ILE
Chi-restraints excluded: chain A residue  283 ASN
Chi-restraints excluded: chain A residue  375 GLU
Chi-restraints excluded: chain A residue  382 LEU
Chi-restraints excluded: chain A residue  390 MET
Chi-restraints excluded: chain A residue  749 LEU
Chi-restraints excluded: chain A residue  754 LEU
Chi-restraints excluded: chain A residue  759 ILE
Chi-restraints excluded: chain A residue  774 TYR
Chi-restraints excluded: chain A residue  776 TYR
Chi-restraints excluded: chain A residue  793 LEU
Chi-restraints excluded: chain A residue  824 THR
Chi-restraints excluded: chain A residue  827 THR
Chi-restraints excluded: chain A residue  916 LEU
Chi-restraints excluded: chain A residue  967 GLN
Chi-restraints excluded: chain A residue 1251 VAL
Chi-restraints excluded: chain A residue 1255 LEU
Chi-restraints excluded: chain A residue 1259 VAL
Chi-restraints excluded: chain A residue 1328 VAL
Chi-restraints excluded: chain A residue 1343 ILE
Chi-restraints excluded: chain A residue 1363 CYS
Chi-restraints excluded: chain A residue 1544 THR
Chi-restraints excluded: chain A residue 1564 ASN
Chi-restraints excluded: chain A residue 1624 VAL
Chi-restraints excluded: chain A residue 1651 MET
Chi-restraints excluded: chain A residue 1696 THR
Chi-restraints excluded: chain A residue 1708 THR
Chi-restraints excluded: chain A residue 1759 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 60 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9980
   chunk 40 optimal weight:    5.9990
   chunk 56 optimal weight:    0.7980
   chunk 122 optimal weight:    3.9990
   chunk 55 optimal weight:    0.6980
   chunk 10 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 35 optimal weight:    0.6980
   chunk 59 optimal weight:    1.9990
   chunk 108 optimal weight:    5.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
A 214 ASN
A1491 GLN
A1659 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.151293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.107515 restraints weight = 16893.391|
|-----------------------------------------------------------------------------|
r_work (start): 0.3315 rms_B_bonded: 3.25
r_work: 0.3179 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7808
moved from start:          0.1608

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  10506  Z= 0.129
  Angle     :  0.554  10.204  14250  Z= 0.281
  Chirality :  0.036   0.179   1659
  Planarity :  0.004   0.046   1732
  Dihedral  :  6.144  95.219   1614
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.97 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 29.95 %
    Favored  : 66.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.10 (0.25), residues: 1248
  helix:  2.00 (0.19), residues: 835
  sheet: -3.57 (0.90), residues: 22
  loop : -1.94 (0.30), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A1626 
 TYR   0.013   0.001   TYR A 378 
 PHE   0.016   0.001   PHE A1751 
 TRP   0.016   0.001   TRP A 156 
 HIS   0.003   0.001   HIS A 118 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 (10500)
  covalent geometry    : angle       0.55285 (14240)
  SS BOND              : bond        0.00344 (    5)
  SS BOND              : angle       1.34417 (   10)
  hydrogen bonds       : bond        0.04758 (  603)
  hydrogen bonds       : angle       3.38828 ( 1713)
  Misc. bond           : bond        0.00018 (    1)

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 134
  time to evaluate  : 0.374 
Fit side-chains
REVERT: A  101 THR cc_start: 0.7351 (OUTLIER) cc_final: 0.7113 (p)
REVERT: A  195 TRP cc_start: 0.8135 (m-10) cc_final: 0.7695 (m-10)
REVERT: A  774 TYR cc_start: 0.8066 (OUTLIER) cc_final: 0.7188 (t80)
REVERT: A  824 THR cc_start: 0.7893 (OUTLIER) cc_final: 0.7651 (m)
REVERT: A  858 MET cc_start: 0.9196 (tmm) cc_final: 0.8967 (ttt)
REVERT: A 1245 MET cc_start: 0.7568 (ttp) cc_final: 0.6976 (tmm)
REVERT: A 1253 GLU cc_start: 0.8122 (tt0) cc_final: 0.7683 (tt0)
REVERT: A 1296 MET cc_start: 0.7070 (ptp) cc_final: 0.6354 (ptp)
REVERT: A 1480 LEU cc_start: 0.7633 (tp) cc_final: 0.7270 (tt)
  outliers start: 42
  outliers final: 33
  residues processed: 164
  average time/residue: 0.0778
  time to fit residues: 19.7947
Evaluate side-chains
  169 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 133
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 THR
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  145 CYS
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  215 VAL
Chi-restraints excluded: chain A residue  257 THR
Chi-restraints excluded: chain A residue  267 ILE
Chi-restraints excluded: chain A residue  375 GLU
Chi-restraints excluded: chain A residue  382 LEU
Chi-restraints excluded: chain A residue  390 MET
Chi-restraints excluded: chain A residue  749 LEU
Chi-restraints excluded: chain A residue  754 LEU
Chi-restraints excluded: chain A residue  759 ILE
Chi-restraints excluded: chain A residue  774 TYR
Chi-restraints excluded: chain A residue  776 TYR
Chi-restraints excluded: chain A residue  793 LEU
Chi-restraints excluded: chain A residue  824 THR
Chi-restraints excluded: chain A residue  827 THR
Chi-restraints excluded: chain A residue  855 VAL
Chi-restraints excluded: chain A residue  916 LEU
Chi-restraints excluded: chain A residue  967 GLN
Chi-restraints excluded: chain A residue 1251 VAL
Chi-restraints excluded: chain A residue 1255 LEU
Chi-restraints excluded: chain A residue 1259 VAL
Chi-restraints excluded: chain A residue 1328 VAL
Chi-restraints excluded: chain A residue 1343 ILE
Chi-restraints excluded: chain A residue 1363 CYS
Chi-restraints excluded: chain A residue 1544 THR
Chi-restraints excluded: chain A residue 1564 ASN
Chi-restraints excluded: chain A residue 1572 THR
Chi-restraints excluded: chain A residue 1624 VAL
Chi-restraints excluded: chain A residue 1651 MET
Chi-restraints excluded: chain A residue 1696 THR
Chi-restraints excluded: chain A residue 1708 THR
Chi-restraints excluded: chain A residue 1759 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 119 optimal weight:    0.0170
   chunk 38 optimal weight:    0.7980
   chunk 59 optimal weight:    0.7980
   chunk 116 optimal weight:    0.7980
   chunk 89 optimal weight:    2.9990
   chunk 99 optimal weight:   20.0000
   chunk 68 optimal weight:    1.9990
   chunk 104 optimal weight:    1.9990
   chunk 67 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9990
   chunk 98 optimal weight:    0.9980
   overall best weight:    0.6818

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

Flipped N/Q/H residues before XYZ refinement:
A 214 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.153006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.109420 restraints weight = 16649.110|
|-----------------------------------------------------------------------------|
r_work (start): 0.3338 rms_B_bonded: 3.20
r_work: 0.3207 rms_B_bonded: 3.83 restraints_weight: 0.5000
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7711
moved from start:          0.1657

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  10506  Z= 0.112
  Angle     :  0.547  10.646  14250  Z= 0.276
  Chirality :  0.036   0.182   1659
  Planarity :  0.004   0.046   1732
  Dihedral  :  6.000  91.367   1614
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.49 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 30.95 %
    Favored  : 66.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.13 (0.25), residues: 1248
  helix:  2.01 (0.19), residues: 837
  sheet: -3.55 (0.93), residues: 22
  loop : -1.91 (0.30), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1626 
 TYR   0.011   0.001   TYR A 378 
 PHE   0.022   0.001   PHE A1587 
 TRP   0.020   0.001   TRP A 156 
 HIS   0.003   0.001   HIS A 118 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 (10500)
  covalent geometry    : angle       0.54626 (14240)
  SS BOND              : bond        0.00315 (    5)
  SS BOND              : angle       1.03960 (   10)
  hydrogen bonds       : bond        0.04323 (  603)
  hydrogen bonds       : angle       3.33722 ( 1713)
  Misc. bond           : bond        0.00026 (    1)

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 137
  time to evaluate  : 0.386 
Fit side-chains
REVERT: A  101 THR cc_start: 0.7273 (OUTLIER) cc_final: 0.7069 (p)
REVERT: A  195 TRP cc_start: 0.8116 (m-10) cc_final: 0.7672 (m-10)
REVERT: A  715 MET cc_start: 0.5245 (tpt) cc_final: 0.4669 (ttp)
REVERT: A  774 TYR cc_start: 0.8016 (OUTLIER) cc_final: 0.7167 (t80)
REVERT: A  824 THR cc_start: 0.7827 (OUTLIER) cc_final: 0.7585 (m)
REVERT: A 1245 MET cc_start: 0.7440 (ttp) cc_final: 0.6988 (tmm)
REVERT: A 1253 GLU cc_start: 0.8090 (tt0) cc_final: 0.7659 (tt0)
REVERT: A 1296 MET cc_start: 0.7101 (ptp) cc_final: 0.6365 (ptp)
REVERT: A 1480 LEU cc_start: 0.7507 (tp) cc_final: 0.7111 (tt)
  outliers start: 33
  outliers final: 27
  residues processed: 156
  average time/residue: 0.0802
  time to fit residues: 19.2078
Evaluate side-chains
  164 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 134
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 THR
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  145 CYS
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  267 ILE
Chi-restraints excluded: chain A residue  375 GLU
Chi-restraints excluded: chain A residue  390 MET
Chi-restraints excluded: chain A residue  749 LEU
Chi-restraints excluded: chain A residue  754 LEU
Chi-restraints excluded: chain A residue  759 ILE
Chi-restraints excluded: chain A residue  774 TYR
Chi-restraints excluded: chain A residue  793 LEU
Chi-restraints excluded: chain A residue  824 THR
Chi-restraints excluded: chain A residue  916 LEU
Chi-restraints excluded: chain A residue  967 GLN
Chi-restraints excluded: chain A residue 1251 VAL
Chi-restraints excluded: chain A residue 1259 VAL
Chi-restraints excluded: chain A residue 1328 VAL
Chi-restraints excluded: chain A residue 1343 ILE
Chi-restraints excluded: chain A residue 1363 CYS
Chi-restraints excluded: chain A residue 1374 ASN
Chi-restraints excluded: chain A residue 1544 THR
Chi-restraints excluded: chain A residue 1564 ASN
Chi-restraints excluded: chain A residue 1572 THR
Chi-restraints excluded: chain A residue 1624 VAL
Chi-restraints excluded: chain A residue 1651 MET
Chi-restraints excluded: chain A residue 1696 THR
Chi-restraints excluded: chain A residue 1708 THR
Chi-restraints excluded: chain A residue 1759 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 36 optimal weight:    0.8980
   chunk 43 optimal weight:    5.9990
   chunk 11 optimal weight:    2.9990
   chunk 115 optimal weight:    1.9990
   chunk 47 optimal weight:    6.9990
   chunk 116 optimal weight:    3.9990
   chunk 55 optimal weight:    1.9990
   chunk 105 optimal weight:    1.9990
   chunk 107 optimal weight:    0.7980
   chunk 67 optimal weight:    2.9990
   chunk 60 optimal weight:    3.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
A 214 ASN
A1507 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.149967 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.106144 restraints weight = 17082.598|
|-----------------------------------------------------------------------------|
r_work (start): 0.3295 rms_B_bonded: 3.24
r_work: 0.3164 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7777
moved from start:          0.1851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  10506  Z= 0.158
  Angle     :  0.597  11.135  14250  Z= 0.303
  Chirality :  0.037   0.178   1659
  Planarity :  0.004   0.048   1732
  Dihedral  :  6.203  89.663   1614
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.61 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 30.41 %
    Favored  : 66.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.95 (0.25), residues: 1248
  helix:  1.88 (0.19), residues: 837
  sheet: -3.32 (0.93), residues: 24
  loop : -2.02 (0.30), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A1626 
 TYR   0.015   0.001   TYR A 378 
 PHE   0.021   0.001   PHE A1751 
 TRP   0.023   0.001   TRP A 156 
 HIS   0.002   0.001   HIS A 118 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 (10500)
  covalent geometry    : angle       0.59543 (14240)
  SS BOND              : bond        0.00379 (    5)
  SS BOND              : angle       1.54827 (   10)
  hydrogen bonds       : bond        0.05642 (  603)
  hydrogen bonds       : angle       3.52933 ( 1713)
  Misc. bond           : bond        0.00008 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2536.07 seconds
wall clock time: 44 minutes 5.40 seconds (2645.40 seconds total)