Starting phenix.real_space_refine
on Wed Mar  4 03:23:41 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7dtd_30851/03_2026/7dtd_30851.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7dtd_30851/03_2026/7dtd_30851.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7dtd_30851/03_2026/7dtd_30851.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7dtd_30851/03_2026/7dtd_30851.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7dtd_30851/03_2026/7dtd_30851.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7dtd_30851/03_2026/7dtd_30851.cif"
  }
  resolution = 3.3
  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=   0.005
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: 4
    Type Number    sf(0)   Gaussians
     S      78      5.16       5
     C    6739      2.51       5
     N    1596      2.21       5
     O    1777      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 63 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10190
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "B"
      Number of atoms: 903
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 111, 881
          Classifications: {'peptide': 111}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 107}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 3
      Conformer: "B"
        Number of residues, atoms: 111, 881
          Classifications: {'peptide': 111}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 107}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 3
          bond proxies already assigned to first conformer: 871
    Chain: "A"
      Number of atoms: 9192
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1138, 9192
          Classifications: {'peptide': 1138}
          Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 1108}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 95
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 95
          Unusual residues: {'9Z9': 1, 'NAG': 4}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
  Time building chain proxies: 2.25, per 1000 atoms: 0.22
  Number of scatterers: 10190
  At special positions: 0
  Unit cell: (137.238, 139.433, 104.301, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      78     16.00
     O    1777      8.00
     N    1596      7.00
     C    6739      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  53 " - pdb=" SG  CYS B 131 " distance=2.10
    Simple disulfide: pdb=" SG  CYS B  58 " - pdb=" SG  CYS A 919 " distance=2.08
    Simple disulfide: pdb=" SG  CYS A 277 " - pdb=" SG  CYS A 345 " distance=2.01
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 351 " distance=2.01
    Simple disulfide: pdb=" SG  CYS A 921 " - pdb=" SG  CYS A 927 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 959 " - pdb=" SG  CYS A 968 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A1376 " - pdb=" SG  CYS A1396 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1741 " - pdb=" SG  CYS A1756 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A2101 " - " ASN A1403 "
      " NAG A2102 " - " ASN A1392 "
      " NAG A2103 " - " ASN A1378 "
      " NAG A2104 " - " ASN A 338 "
  Time building additional restraints: 0.63
  Conformation dependent library (CDL) restraints added in 523.7 milliseconds
  

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2368

  Finding SS restraints...
    Secondary structure from input PDB file:
      53 helices and 4 sheets defined
      68.5% alpha, 5.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.33
  Creating SS restraints...
    Processing helix  chain 'B' and resid 122 through 126
    Processing helix  chain 'B' and resid 136 through 139
    Processing helix  chain 'A' and resid 117 through 126
      removed outlier: 4.094A  pdb=" N   ALA A 121 " --> pdb=" O   LEU A 117 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   VAL A 126 " --> pdb=" O   ILE A 122 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 127 through 146
      removed outlier: 3.645A  pdb=" N   SER A 131 " --> pdb=" O   HIS A 127 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   THR A 146 " --> pdb=" O   CYS A 142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 151 through 177
      removed outlier: 3.629A  pdb=" N   LYS A 155 " --> pdb=" O   PRO A 151 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   ASN A 156 " --> pdb=" O   ASP A 152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 188 through 205
    Processing helix  chain 'A' and resid 214 through 224
      removed outlier: 4.317A  pdb=" N   THR A 217 " --> pdb=" O   ALA A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 225 through 230
      removed outlier: 3.699A  pdb=" N   VAL A 229 " --> pdb=" O   LYS A 225 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 246
      removed outlier: 4.165A  pdb=" N   LYS A 246 " --> pdb=" O   GLN A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 247 through 269
    Processing helix  chain 'A' and resid 271 through 275
    Processing helix  chain 'A' and resid 368 through 380
    Processing helix  chain 'A' and resid 383 through 396
      removed outlier: 4.013A  pdb=" N   LEU A 387 " --> pdb=" O   PHE A 383 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ALA A 394 " --> pdb=" O   LEU A 390 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 399 through 439
      removed outlier: 3.593A  pdb=" N   PHE A 403 " --> pdb=" O   TYR A 399 " (cutoff:3.500A)
      removed outlier: 4.399A  pdb=" N   PHE A 412 " --> pdb=" O   PHE A 408 " (cutoff:3.500A)
      removed outlier: 4.884A  pdb=" N   ILE A 415 " --> pdb=" O   SER A 411 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   GLN A 439 " --> pdb=" O   GLU A 435 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 750 through 763
      removed outlier: 4.246A  pdb=" N   VAL A 760 " --> pdb=" O   LYS A 756 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   VAL A 761 " --> pdb=" O   VAL A 757 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 769 through 787
      removed outlier: 3.740A  pdb=" N   THR A 775 " --> pdb=" O   ASP A 771 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 793 through 819
      removed outlier: 4.638A  pdb=" N   VAL A 799 " --> pdb=" O   HIS A 795 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 831 through 848
      removed outlier: 3.949A  pdb=" N   GLY A 848 " --> pdb=" O   LEU A 844 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 855 through 872
      removed outlier: 4.024A  pdb=" N   LEU A 858 " --> pdb=" O   LEU A 855 " (cutoff:3.500A)
      removed outlier: 4.291A  pdb=" N   ARG A 862 " --> pdb=" O   ARG A 859 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   LEU A 864 " --> pdb=" O   PHE A 861 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   ARG A 865 " --> pdb=" O   ARG A 862 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 873 through 886
      removed outlier: 3.534A  pdb=" N   ASN A 877 " --> pdb=" O   TRP A 873 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 890 through 912
    Processing helix  chain 'A' and resid 914 through 919
    Processing helix  chain 'A' and resid 920 through 923
    Processing helix  chain 'A' and resid 936 through 950
    Processing helix  chain 'A' and resid 953 through 964
      removed outlier: 4.005A  pdb=" N   ASP A 958 " --> pdb=" O   GLU A 954 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   VAL A 962 " --> pdb=" O   ASP A 958 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 964 through 995
      removed outlier: 4.175A  pdb=" N   ASN A 980 " --> pdb=" O   MET A 976 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   SER A 993 " --> pdb=" O   ALA A 989 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   PHE A 995 " --> pdb=" O   LEU A 991 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1203 through 1216
    Processing helix  chain 'A' and resid 1217 through 1234
      removed outlier: 3.860A  pdb=" N   GLU A1221 " --> pdb=" O   HIS A1217 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   THR A1222 " --> pdb=" O   ASN A1218 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1239 through 1245
      removed outlier: 3.560A  pdb=" N   ILE A1242 " --> pdb=" O   ASP A1239 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   ASP A1243 " --> pdb=" O   ILE A1240 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   ARG A1245 " --> pdb=" O   ILE A1242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1248 through 1281
      removed outlier: 3.596A  pdb=" N   LYS A1257 " --> pdb=" O   GLU A1253 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   MET A1267 " --> pdb=" O   PHE A1263 " (cutoff:3.500A)
      removed outlier: 6.954A  pdb=" N   TYR A1276 " --> pdb=" O   VAL A1272 " (cutoff:3.500A)
      removed outlier: 9.602A  pdb=" N   GLN A1277 " --> pdb=" O   ALA A1273 " (cutoff:3.500A)
      removed outlier: 4.229A  pdb=" N   THR A1278 " --> pdb=" O   TYR A1274 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   THR A1281 " --> pdb=" O   GLN A1277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1282 through 1305
      removed outlier: 3.583A  pdb=" N   GLY A1305 " --> pdb=" O   ALA A1301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1311 through 1316
    Processing helix  chain 'A' and resid 1317 through 1327
      Proline residue:  A1323  - end of helix
    Processing helix  chain 'A' and resid 1330 through 1342
      removed outlier: 3.719A  pdb=" N   VAL A1336 " --> pdb=" O   GLY A1332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1343 through 1369
      removed outlier: 3.667A  pdb=" N   ILE A1347 " --> pdb=" O   ALA A1343 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   VAL A1353 " --> pdb=" O   ASN A1349 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   PHE A1361 " --> pdb=" O   PHE A1357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1392 through 1402
    Processing helix  chain 'A' and resid 1417 through 1431
    Processing helix  chain 'A' and resid 1433 through 1443
      removed outlier: 3.816A  pdb=" N   ILE A1437 " --> pdb=" O   GLY A1433 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   ASP A1443 " --> pdb=" O   TYR A1439 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1456 through 1458
      No H-bonds generated for 'chain 'A' and resid 1456 through 1458'
    Processing helix  chain 'A' and resid 1459 through 1470
      removed outlier: 3.656A  pdb=" N   PHE A1463 " --> pdb=" O   MET A1459 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1472 through 1494
      removed outlier: 3.693A  pdb=" N   GLY A1494 " --> pdb=" O   LYS A1490 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1503 through 1515
      removed outlier: 3.537A  pdb=" N   MET A1511 " --> pdb=" O   TYR A1507 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   LYS A1513 " --> pdb=" O   ASN A1509 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1529 through 1540
      removed outlier: 4.002A  pdb=" N   MET A1533 " --> pdb=" O   LYS A1529 " (cutoff:3.500A)
      removed outlier: 4.366A  pdb=" N   ARG A1540 " --> pdb=" O   ASP A1536 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1540 through 1560
      removed outlier: 3.560A  pdb=" N   ASP A1544 " --> pdb=" O   ARG A1540 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   VAL A1560 " --> pdb=" O   VAL A1556 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1566 through 1595
      removed outlier: 3.662A  pdb=" N   ILE A1593 " --> pdb=" O   VAL A1589 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1602 through 1621
      removed outlier: 3.724A  pdb=" N   ILE A1606 " --> pdb=" O   ILE A1602 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1631 through 1639
    Processing helix  chain 'A' and resid 1642 through 1647
      removed outlier: 4.138A  pdb=" N   ILE A1646 " --> pdb=" O   ARG A1642 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1648 through 1652
      removed outlier: 3.954A  pdb=" N   GLY A1652 " --> pdb=" O   LEU A1649 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1655 through 1692
      removed outlier: 3.796A  pdb=" N   LEU A1659 " --> pdb=" O   GLY A1655 " (cutoff:3.500A)
      Proline residue:  A1668  - end of helix
      removed outlier: 4.049A  pdb=" N   ASN A1672 " --> pdb=" O   PRO A1668 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   ILE A1673 " --> pdb=" O   ALA A1669 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1709 through 1722
      removed outlier: 3.522A  pdb=" N   GLN A1719 " --> pdb=" O   ILE A1715 " (cutoff:3.500A)
      removed outlier: 4.109A  pdb=" N   THR A1722 " --> pdb=" O   PHE A1718 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1725 through 1734
      removed outlier: 3.569A  pdb=" N   LEU A1729 " --> pdb=" O   GLY A1725 " (cutoff:3.500A)
      Proline residue:  A1732  - end of helix
    Processing helix  chain 'A' and resid 1758 through 1793
      removed outlier: 4.022A  pdb=" N   GLU A1787 " --> pdb=" O   ALA A1783 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   SER A1790 " --> pdb=" O   LEU A1786 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 40 through 44
      removed outlier: 6.418A  pdb=" N   ILE B  41 " --> pdb=" O   GLN B 150 " (cutoff:3.500A)
      removed outlier: 7.350A  pdb=" N   VAL B 152 " --> pdb=" O   ILE B  41 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   ALA B  43 " --> pdb=" O   VAL B 152 " (cutoff:3.500A)
      removed outlier: 6.765A  pdb=" N   GLU B  62 " --> pdb=" O   ASN B  86 " (cutoff:3.500A)
      removed outlier: 6.423A  pdb=" N   ASN B  86 " --> pdb=" O   GLU B  62 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   ILE B  80 " --> pdb=" O   TRP B  68 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   TYR B  70 " --> pdb=" O   ILE B  78 " (cutoff:3.500A)
      removed outlier: 5.512A  pdb=" N   ILE B  78 " --> pdb=" O   TYR B  70 " (cutoff:3.500A)
      removed outlier: 7.833A  pdb=" N   LEU B  79 " --> pdb=" O   LYS B  96 " (cutoff:3.500A)
      removed outlier: 4.480A  pdb=" N   LYS B  96 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.318A  pdb=" N   GLU B  81 " --> pdb=" O   THR B  94 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 40 through 44
      removed outlier: 6.418A  pdb=" N   ILE B  41 " --> pdb=" O   GLN B 150 " (cutoff:3.500A)
      removed outlier: 7.350A  pdb=" N   VAL B 152 " --> pdb=" O   ILE B  41 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   ALA B  43 " --> pdb=" O   VAL B 152 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 49 through 51
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1375 through 1378

    615 hydrogen bonds defined for protein.
    1725 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: 1.48

  Time building geometry restraints manager: 0.86 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 3072
        1.35 -     1.47: 2763
        1.47 -     1.60: 4484
        1.60 -     1.72: 0
        1.72 -     1.85: 127
  Bond restraints: 10446
  Sorted by residual:
  bond pdb=" C1  NAG A2103 "
       pdb=" O5  NAG A2103 "
    ideal  model  delta    sigma   weight residual
    1.406  1.445 -0.039 2.00e-02 2.50e+03 3.89e+00
  bond pdb=" CA  GLU A 853 "
       pdb=" C   GLU A 853 "
    ideal  model  delta    sigma   weight residual
    1.523  1.502  0.021 1.34e-02 5.57e+03 2.46e+00
  bond pdb=" CA  LYS B  77 "
       pdb=" C   LYS B  77 "
    ideal  model  delta    sigma   weight residual
    1.520  1.502  0.019 1.22e-02 6.72e+03 2.40e+00
  bond pdb=" C04 9Z9 A2105 "
       pdb=" O72 9Z9 A2105 "
    ideal  model  delta    sigma   weight residual
    1.420  1.389  0.031 2.00e-02 2.50e+03 2.34e+00
  bond pdb=" CA  LEU B 149 "
       pdb=" C   LEU B 149 "
    ideal  model  delta    sigma   weight residual
    1.523  1.505  0.019 1.24e-02 6.50e+03 2.29e+00
  ... (remaining 10441 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.95: 13648
        1.95 -     3.90: 452
        3.90 -     5.85: 63
        5.85 -     7.80: 14
        7.80 -     9.75: 1
  Bond angle restraints: 14178
  Sorted by residual:
  angle pdb=" N   ARG A 322 "
        pdb=" CA  ARG A 322 "
        pdb=" C   ARG A 322 "
      ideal   model   delta    sigma   weight residual
     114.31  107.98    6.33 1.29e+00 6.01e-01 2.40e+01
  angle pdb=" N   TYR A 826 "
        pdb=" CA  TYR A 826 "
        pdb=" C   TYR A 826 "
      ideal   model   delta    sigma   weight residual
     113.02  107.43    5.59 1.20e+00 6.94e-01 2.17e+01
  angle pdb=" N   VAL A 765 "
        pdb=" CA  VAL A 765 "
        pdb=" C   VAL A 765 "
      ideal   model   delta    sigma   weight residual
     106.21  111.13   -4.92 1.07e+00 8.73e-01 2.12e+01
  angle pdb=" N   HIS A1597 "
        pdb=" CA  HIS A1597 "
        pdb=" C   HIS A1597 "
      ideal   model   delta    sigma   weight residual
     114.62  109.40    5.22 1.14e+00 7.69e-01 2.10e+01
  angle pdb=" C   GLY A 854 "
        pdb=" N   LEU A 855 "
        pdb=" CA  LEU A 855 "
      ideal   model   delta    sigma   weight residual
     122.95  115.38    7.57 1.66e+00 3.63e-01 2.08e+01
  ... (remaining 14173 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.99: 5770
       22.99 -    45.99: 415
       45.99 -    68.98: 54
       68.98 -    91.97: 7
       91.97 -   114.97: 1
  Dihedral angle restraints: 6247
    sinusoidal: 2581
      harmonic: 3666
  Sorted by residual:
  dihedral pdb=" CA  ARG A1525 "
           pdb=" C   ARG A1525 "
           pdb=" N   PRO A1526 "
           pdb=" CA  PRO A1526 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.56   28.44     0      5.00e+00 4.00e-02 3.24e+01
  dihedral pdb=" CA  VAL A 765 "
           pdb=" C   VAL A 765 "
           pdb=" N   MET A 766 "
           pdb=" CA  MET A 766 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.36   26.64     0      5.00e+00 4.00e-02 2.84e+01
  dihedral pdb=" CA  LEU A 186 "
           pdb=" C   LEU A 186 "
           pdb=" N   ARG A 187 "
           pdb=" CA  ARG A 187 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.34   25.66     0      5.00e+00 4.00e-02 2.63e+01
  ... (remaining 6244 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 1259
       0.051 -    0.103: 324
       0.103 -    0.154: 48
       0.154 -    0.206: 11
       0.206 -    0.257: 7
  Chirality restraints: 1649
  Sorted by residual:
  chirality pdb=" CA AASP B  97 "
            pdb=" N   ASP B  97 "
            pdb=" C   ASP B  97 "
            pdb=" CB AASP B  97 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.66e+00
  chirality pdb=" CG  LEU A 186 "
            pdb=" CB  LEU A 186 "
            pdb=" CD1 LEU A 186 "
            pdb=" CD2 LEU A 186 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.34   -0.25 2.00e-01 2.50e+01 1.52e+00
  chirality pdb=" CA  VAL B  84 "
            pdb=" N   VAL B  84 "
            pdb=" C   VAL B  84 "
            pdb=" CB  VAL B  84 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.68   -0.24 2.00e-01 2.50e+01 1.48e+00
  ... (remaining 1646 not shown)

  Planarity restraints: 1731
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 852 "    0.017 2.00e-02 2.50e+03   3.47e-02 1.21e+01
        pdb=" C   VAL A 852 "   -0.060 2.00e-02 2.50e+03
        pdb=" O   VAL A 852 "    0.023 2.00e-02 2.50e+03
        pdb=" N   GLU A 853 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A1434 "   -0.013 2.00e-02 2.50e+03   1.51e-02 5.70e+00
        pdb=" CG  TRP A1434 "    0.041 2.00e-02 2.50e+03
        pdb=" CD1 TRP A1434 "   -0.020 2.00e-02 2.50e+03
        pdb=" CD2 TRP A1434 "   -0.005 2.00e-02 2.50e+03
        pdb=" NE1 TRP A1434 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A1434 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A1434 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A1434 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A1434 "   -0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP A1434 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 357 "    0.038 5.00e-02 4.00e+02   5.70e-02 5.19e+00
        pdb=" N   PRO A 358 "   -0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO A 358 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 358 "    0.031 5.00e-02 4.00e+02
  ... (remaining 1728 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 178
        2.67 -     3.22: 10295
        3.22 -     3.78: 15220
        3.78 -     4.34: 20747
        4.34 -     4.90: 33384
  Nonbonded interactions: 79824
  Sorted by model distance:
  nonbonded pdb=" O   ILE A 318 "
            pdb=" CG  GLN A 319 "
     model   vdw
     2.107 3.440
  nonbonded pdb=" O   THR A 793 "
            pdb=" N   PHE A 796 "
     model   vdw
     2.279 3.120
  nonbonded pdb=" OD1 ASN A1410 "
            pdb=" N   VAL A1411 "
     model   vdw
     2.291 3.120
  nonbonded pdb=" O   THR A 793 "
            pdb=" N   HIS A 795 "
     model   vdw
     2.334 3.120
  nonbonded pdb=" O   SER A 856 "
            pdb=" OG  SER A 856 "
     model   vdw
     2.341 3.040
  ... (remaining 79819 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.26 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:             0.500
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.750
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.570
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7057
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   0.071  10458  Z= 0.231
  Angle     :  1.123  68.312  14206  Z= 0.641
  Chirality :  0.049   0.257   1649
  Planarity :  0.004   0.057   1727
  Dihedral  : 15.192 114.968   3855
  Min Nonbonded Distance : 2.107

Molprobity Statistics.
  All-atom Clashscore : 13.89
  Ramachandran Plot:
    Outliers :  0.89 %
    Allowed  :  7.76 %
    Favored  : 91.35 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  :  7.06 %
    Favored  : 90.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.18 (0.21), residues: 1242
  helix: -1.36 (0.16), residues: 765
  sheet: -1.22 (0.56), residues: 75
  loop : -3.64 (0.26), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 100 
 TYR   0.020   0.001   TYR A 388 
 PHE   0.015   0.001   PHE A 383 
 TRP   0.041   0.002   TRP A1434 
 HIS   0.007   0.001   HIS B 144 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 (10446)
  covalent geometry    : angle       0.84523 (14178)
  SS BOND              : bond        0.03136 (    8)
  SS BOND              : angle      21.78797 (   16)
  hydrogen bonds       : bond        0.15957 (  611)
  hydrogen bonds       : angle       6.10764 ( 1725)
  link_NAG-ASN         : bond        0.03166 (    4)
  link_NAG-ASN         : angle       3.91528 (   12)

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

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

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 229
  time to evaluate  : 0.231 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  135 MET cc_start: 0.8143 (ttp) cc_final: 0.7909 (ttm)
REVERT: A  409 LEU cc_start: 0.8754 (mm) cc_final: 0.8445 (mm)
REVERT: A  424 MET cc_start: 0.8268 (tpt) cc_final: 0.7466 (mtm)
REVERT: A  815 MET cc_start: 0.8228 (tpp) cc_final: 0.8006 (tpp)
REVERT: A  839 ILE cc_start: 0.8471 (mm) cc_final: 0.8263 (mm)
REVERT: A  853 GLU cc_start: 0.0716 (OUTLIER) cc_final: 0.0280 (tm-30)
REVERT: A 1214 ILE cc_start: 0.8713 (mm) cc_final: 0.8496 (mm)
REVERT: A 1219 TRP cc_start: 0.7457 (m-10) cc_final: 0.6982 (m-90)
REVERT: A 1226 PHE cc_start: 0.8248 (t80) cc_final: 0.7956 (t80)
REVERT: A 1267 MET cc_start: 0.8252 (ttp) cc_final: 0.7622 (tmm)
REVERT: A 1277 GLN cc_start: 0.8293 (tp40) cc_final: 0.7265 (mt0)
REVERT: A 1608 ASP cc_start: 0.7872 (t70) cc_final: 0.7460 (t70)
REVERT: A 1665 MET cc_start: 0.6995 (mmt) cc_final: 0.6411 (mmt)
  outliers start: 25
  outliers final: 12
  residues processed: 253
  average time/residue: 0.0882
  time to fit residues: 32.2061
Evaluate side-chains
  181 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 168
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   40 ASP
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  205 GLU
Chi-restraints excluded: chain A residue  319 GLN
Chi-restraints excluded: chain A residue  320 ASP
Chi-restraints excluded: chain A residue  321 SER
Chi-restraints excluded: chain A residue  777 CYS
Chi-restraints excluded: chain A residue  793 THR
Chi-restraints excluded: chain A residue  853 GLU
Chi-restraints excluded: chain A residue  918 ASP
Chi-restraints excluded: chain A residue 1378 ASN
Chi-restraints excluded: chain A residue 1405 THR
Chi-restraints excluded: chain A residue 1751 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 108 optimal weight:    0.7980
   chunk 49 optimal weight:    7.9990
   chunk 97 optimal weight:    9.9990
   chunk 113 optimal weight:    0.7980
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:   30.0000
   chunk 33 optimal weight:    5.9990
   chunk 123 optimal weight:    2.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    4.9990
   overall best weight:    2.7186

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

Flipped N/Q/H residues before XYZ refinement:
B 140 ASN
** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 319 GLN
A 381 GLN
A 416 ASN
A 429 GLN
A 789 HIS
A 933 HIS
A1217 HIS
A1367 ASN
A1375 HIS
A1554 ASN
A1735 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.162465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.124538 restraints weight = 45913.650|
|-----------------------------------------------------------------------------|
r_work (start): 0.3685 rms_B_bonded: 4.20
r_work: 0.3435 rms_B_bonded: 4.57 restraints_weight: 0.5000
r_work (final): 0.3435
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3437
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3437 r_free = 0.3437    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3437 r_free = 0.3437    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|
r_final: 0.3437
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
moved from start:          0.1668

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050  10458  Z= 0.200
  Angle     :  0.735  11.548  14206  Z= 0.375
  Chirality :  0.044   0.189   1649
  Planarity :  0.005   0.047   1727
  Dihedral  :  7.974  65.331   1544
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 10.11
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  8.16 %
    Favored  : 91.51 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 13.67 %
    Favored  : 83.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -1.38 (0.23), residues: 1242
  helix:  0.08 (0.18), residues: 763
  sheet: -1.05 (0.53), residues: 87
  loop : -2.84 (0.30), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 216 
 TYR   0.020   0.002   TYR A 825 
 PHE   0.018   0.002   PHE A 256 
 TRP   0.024   0.002   TRP A1434 
 HIS   0.005   0.001   HIS A1393 

Details of bonding type rmsd
  covalent geometry    : bond        0.00451 (10446)
  covalent geometry    : angle       0.72237 (14178)
  SS BOND              : bond        0.00548 (    8)
  SS BOND              : angle       2.46480 (   16)
  hydrogen bonds       : bond        0.04412 (  611)
  hydrogen bonds       : angle       4.54650 ( 1725)
  link_NAG-ASN         : bond        0.00437 (    4)
  link_NAG-ASN         : angle       3.89600 (   12)

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

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

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 179
  time to evaluate  : 0.393 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   61 PHE cc_start: 0.5933 (p90) cc_final: 0.5681 (p90)
REVERT: A  253 LEU cc_start: 0.8387 (tt) cc_final: 0.7830 (tp)
REVERT: A  377 ARG cc_start: 0.8863 (OUTLIER) cc_final: 0.8443 (ttt180)
REVERT: A  424 MET cc_start: 0.8748 (OUTLIER) cc_final: 0.7665 (mtm)
REVERT: A  787 MET cc_start: 0.8969 (mtp) cc_final: 0.8695 (mtp)
REVERT: A  918 ASP cc_start: 0.8196 (OUTLIER) cc_final: 0.7813 (t0)
REVERT: A 1214 ILE cc_start: 0.8725 (mm) cc_final: 0.8519 (mm)
REVERT: A 1219 TRP cc_start: 0.7682 (m-10) cc_final: 0.7100 (m-90)
REVERT: A 1226 PHE cc_start: 0.8514 (t80) cc_final: 0.8236 (t80)
REVERT: A 1277 GLN cc_start: 0.8377 (tp40) cc_final: 0.7187 (mt0)
REVERT: A 1435 MET cc_start: 0.8359 (mmm) cc_final: 0.8108 (mmp)
REVERT: A 1548 MET cc_start: 0.7744 (mtt) cc_final: 0.7111 (tpp)
REVERT: A 1608 ASP cc_start: 0.8447 (t70) cc_final: 0.8168 (t70)
  outliers start: 37
  outliers final: 24
  residues processed: 200
  average time/residue: 0.0895
  time to fit residues: 26.2036
Evaluate side-chains
  183 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 156
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  169 SER
Chi-restraints excluded: chain A residue  202 TYR
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  205 GLU
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  217 THR
Chi-restraints excluded: chain A residue  236 ILE
Chi-restraints excluded: chain A residue  320 ASP
Chi-restraints excluded: chain A residue  321 SER
Chi-restraints excluded: chain A residue  377 ARG
Chi-restraints excluded: chain A residue  385 GLU
Chi-restraints excluded: chain A residue  424 MET
Chi-restraints excluded: chain A residue  428 GLU
Chi-restraints excluded: chain A residue  767 ASP
Chi-restraints excluded: chain A residue  775 THR
Chi-restraints excluded: chain A residue  785 MET
Chi-restraints excluded: chain A residue  808 THR
Chi-restraints excluded: chain A residue  918 ASP
Chi-restraints excluded: chain A residue 1292 VAL
Chi-restraints excluded: chain A residue 1321 LEU
Chi-restraints excluded: chain A residue 1405 THR
Chi-restraints excluded: chain A residue 1616 ILE
Chi-restraints excluded: chain A residue 1621 LEU
Chi-restraints excluded: chain A residue 1663 LEU
Chi-restraints excluded: chain A residue 1701 ILE
Chi-restraints excluded: chain A residue 1780 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 29 optimal weight:    6.9990
   chunk 71 optimal weight:    2.9990
   chunk 95 optimal weight:    9.9990
   chunk 31 optimal weight:    0.6980
   chunk 62 optimal weight:    1.9990
   chunk 96 optimal weight:    8.9990
   chunk 91 optimal weight:    0.9990
   chunk 111 optimal weight:    3.9990
   chunk 94 optimal weight:   10.0000
   chunk 61 optimal weight:    0.8980
   chunk 122 optimal weight:    0.9980
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
A 191 ASN
** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 759 HIS
A1450 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.165176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.125527 restraints weight = 40677.195|
|-----------------------------------------------------------------------------|
r_work (start): 0.3694 rms_B_bonded: 3.97
r_work: 0.3487 rms_B_bonded: 4.44 restraints_weight: 0.5000
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3491
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3491 r_free = 0.3491    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3491 r_free = 0.3491    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|
r_final: 0.3491
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
moved from start:          0.2143

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10458  Z= 0.131
  Angle     :  0.643   9.502  14206  Z= 0.330
  Chirality :  0.041   0.183   1649
  Planarity :  0.004   0.050   1727
  Dihedral  :  7.023  63.827   1531
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  7.36 %
    Favored  : 92.40 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 16.53 %
    Favored  : 80.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -0.57 (0.24), residues: 1242
  helix:  0.73 (0.19), residues: 770
  sheet: -0.83 (0.53), residues: 87
  loop : -2.56 (0.32), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1402 
 TYR   0.015   0.002   TYR A 388 
 PHE   0.024   0.001   PHE A1774 
 TRP   0.014   0.001   TRP A1408 
 HIS   0.016   0.001   HIS A 759 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 (10446)
  covalent geometry    : angle       0.63366 (14178)
  SS BOND              : bond        0.00466 (    8)
  SS BOND              : angle       1.73227 (   16)
  hydrogen bonds       : bond        0.03754 (  611)
  hydrogen bonds       : angle       4.19594 ( 1725)
  link_NAG-ASN         : bond        0.00338 (    4)
  link_NAG-ASN         : angle       3.33961 (   12)

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

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

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 179
  time to evaluate  : 0.258 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   61 PHE cc_start: 0.6348 (p90) cc_final: 0.5973 (p90)
REVERT: A  424 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.7701 (mtm)
REVERT: A  766 MET cc_start: 0.6492 (tpt) cc_final: 0.6183 (tpt)
REVERT: A  787 MET cc_start: 0.8833 (mtp) cc_final: 0.8593 (mtp)
REVERT: A  794 ASP cc_start: 0.8131 (OUTLIER) cc_final: 0.7886 (t0)
REVERT: A  918 ASP cc_start: 0.7929 (OUTLIER) cc_final: 0.7674 (t0)
REVERT: A 1214 ILE cc_start: 0.8682 (mm) cc_final: 0.8443 (mm)
REVERT: A 1219 TRP cc_start: 0.7620 (m-10) cc_final: 0.7024 (m-90)
REVERT: A 1266 GLU cc_start: 0.8440 (pp20) cc_final: 0.8091 (pp20)
REVERT: A 1267 MET cc_start: 0.8524 (tmm) cc_final: 0.8087 (tmm)
REVERT: A 1268 LEU cc_start: 0.8753 (mm) cc_final: 0.8004 (mm)
REVERT: A 1277 GLN cc_start: 0.8346 (tp40) cc_final: 0.7164 (mt0)
REVERT: A 1500 MET cc_start: 0.7769 (mtt) cc_final: 0.7355 (mtp)
REVERT: A 1548 MET cc_start: 0.7732 (mtt) cc_final: 0.7126 (tpp)
REVERT: A 1608 ASP cc_start: 0.8463 (t70) cc_final: 0.8183 (t70)
REVERT: A 1780 MET cc_start: 0.8222 (OUTLIER) cc_final: 0.7558 (mtp)
  outliers start: 37
  outliers final: 22
  residues processed: 202
  average time/residue: 0.0770
  time to fit residues: 23.7648
Evaluate side-chains
  186 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 160
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   90 ASP
Chi-restraints excluded: chain B residue  130 THR
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  202 TYR
Chi-restraints excluded: chain A residue  205 GLU
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  217 THR
Chi-restraints excluded: chain A residue  320 ASP
Chi-restraints excluded: chain A residue  385 GLU
Chi-restraints excluded: chain A residue  424 MET
Chi-restraints excluded: chain A residue  767 ASP
Chi-restraints excluded: chain A residue  794 ASP
Chi-restraints excluded: chain A residue  863 LEU
Chi-restraints excluded: chain A residue  909 MET
Chi-restraints excluded: chain A residue  918 ASP
Chi-restraints excluded: chain A residue  936 ASP
Chi-restraints excluded: chain A residue 1228 ILE
Chi-restraints excluded: chain A residue 1292 VAL
Chi-restraints excluded: chain A residue 1304 LEU
Chi-restraints excluded: chain A residue 1321 LEU
Chi-restraints excluded: chain A residue 1379 THR
Chi-restraints excluded: chain A residue 1397 LEU
Chi-restraints excluded: chain A residue 1621 LEU
Chi-restraints excluded: chain A residue 1663 LEU
Chi-restraints excluded: chain A residue 1780 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 42 optimal weight:    7.9990
   chunk 82 optimal weight:    4.9990
   chunk 49 optimal weight:    5.9990
   chunk 8 optimal weight:    9.9990
   chunk 40 optimal weight:   20.0000
   chunk 19 optimal weight:    4.9990
   chunk 17 optimal weight:    9.9990
   chunk 83 optimal weight:    0.9990
   chunk 73 optimal weight:    2.9990
   chunk 87 optimal weight:    0.5980
   chunk 111 optimal weight:    5.9990
   overall best weight:    2.9188

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

Flipped N/Q/H residues before XYZ refinement:
B 140 ASN
A 272 ASN
A 359 ASN
A 759 HIS
A1605 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.161746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.124544 restraints weight = 53181.603|
|-----------------------------------------------------------------------------|
r_work (start): 0.3681 rms_B_bonded: 5.18
r_work (final): 0.3681
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3682
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3682 r_free = 0.3682    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3682 r_free = 0.3682    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|
r_final: 0.3682
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7658
moved from start:          0.2375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  10458  Z= 0.195
  Angle     :  0.684   9.320  14206  Z= 0.351
  Chirality :  0.043   0.190   1649
  Planarity :  0.004   0.057   1727
  Dihedral  :  6.998  61.015   1528
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  8.16 %
    Favored  : 91.51 %
  Rotamer:
    Outliers :  4.92 %
    Allowed  : 17.78 %
    Favored  : 77.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -0.48 (0.24), residues: 1242
  helix:  0.78 (0.19), residues: 770
  sheet: -0.62 (0.54), residues: 87
  loop : -2.51 (0.32), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A1402 
 TYR   0.024   0.002   TYR A 388 
 PHE   0.025   0.002   PHE A1466 
 TRP   0.015   0.002   TRP A1408 
 HIS   0.005   0.001   HIS A1393 

Details of bonding type rmsd
  covalent geometry    : bond        0.00451 (10446)
  covalent geometry    : angle       0.67332 (14178)
  SS BOND              : bond        0.00540 (    8)
  SS BOND              : angle       1.91257 (   16)
  hydrogen bonds       : bond        0.04020 (  611)
  hydrogen bonds       : angle       4.26192 ( 1725)
  link_NAG-ASN         : bond        0.00334 (    4)
  link_NAG-ASN         : angle       3.68178 (   12)

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

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

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 164
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 MET cc_start: 0.8092 (mmt) cc_final: 0.7846 (mmm)
REVERT: A  253 LEU cc_start: 0.8361 (tt) cc_final: 0.7981 (tt)
REVERT: A  278 ILE cc_start: 0.8251 (OUTLIER) cc_final: 0.7936 (mp)
REVERT: A  424 MET cc_start: 0.7879 (OUTLIER) cc_final: 0.7364 (mtm)
REVERT: A  766 MET cc_start: 0.6760 (tpt) cc_final: 0.6481 (tpt)
REVERT: A  787 MET cc_start: 0.8406 (mtp) cc_final: 0.8180 (mtp)
REVERT: A  976 MET cc_start: 0.8126 (ttp) cc_final: 0.7812 (ttp)
REVERT: A 1214 ILE cc_start: 0.8668 (mm) cc_final: 0.8429 (mm)
REVERT: A 1219 TRP cc_start: 0.7648 (m-10) cc_final: 0.7007 (m-90)
REVERT: A 1266 GLU cc_start: 0.8111 (pp20) cc_final: 0.7852 (pp20)
REVERT: A 1277 GLN cc_start: 0.8341 (tp40) cc_final: 0.7153 (mt0)
REVERT: A 1500 MET cc_start: 0.6931 (mtt) cc_final: 0.6633 (mtp)
REVERT: A 1548 MET cc_start: 0.7410 (mtt) cc_final: 0.7100 (tpp)
REVERT: A 1608 ASP cc_start: 0.8176 (t70) cc_final: 0.7885 (t70)
REVERT: A 1628 TYR cc_start: 0.4752 (m-80) cc_final: 0.4510 (m-10)
  outliers start: 54
  outliers final: 33
  residues processed: 200
  average time/residue: 0.0812
  time to fit residues: 24.1976
Evaluate side-chains
  190 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 155
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   55 PHE
Chi-restraints excluded: chain B residue   90 ASP
Chi-restraints excluded: chain B residue  130 THR
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  138 ILE
Chi-restraints excluded: chain A residue  202 TYR
Chi-restraints excluded: chain A residue  205 GLU
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  217 THR
Chi-restraints excluded: chain A residue  236 ILE
Chi-restraints excluded: chain A residue  278 ILE
Chi-restraints excluded: chain A residue  320 ASP
Chi-restraints excluded: chain A residue  332 ASP
Chi-restraints excluded: chain A residue  377 ARG
Chi-restraints excluded: chain A residue  424 MET
Chi-restraints excluded: chain A residue  767 ASP
Chi-restraints excluded: chain A residue  770 VAL
Chi-restraints excluded: chain A residue  775 THR
Chi-restraints excluded: chain A residue  793 THR
Chi-restraints excluded: chain A residue  808 THR
Chi-restraints excluded: chain A residue  863 LEU
Chi-restraints excluded: chain A residue  899 ILE
Chi-restraints excluded: chain A residue  909 MET
Chi-restraints excluded: chain A residue  936 ASP
Chi-restraints excluded: chain A residue 1224 ILE
Chi-restraints excluded: chain A residue 1228 ILE
Chi-restraints excluded: chain A residue 1292 VAL
Chi-restraints excluded: chain A residue 1321 LEU
Chi-restraints excluded: chain A residue 1379 THR
Chi-restraints excluded: chain A residue 1384 ARG
Chi-restraints excluded: chain A residue 1397 LEU
Chi-restraints excluded: chain A residue 1621 LEU
Chi-restraints excluded: chain A residue 1663 LEU
Chi-restraints excluded: chain A residue 1701 ILE
Chi-restraints excluded: chain A residue 1780 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 114 optimal weight:    6.9990
   chunk 87 optimal weight:    3.9990
   chunk 94 optimal weight:   20.0000
   chunk 80 optimal weight:    3.9990
   chunk 120 optimal weight:    5.9990
   chunk 68 optimal weight:    1.9990
   chunk 79 optimal weight:    0.5980
   chunk 108 optimal weight:    8.9990
   chunk 83 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9990
   chunk 50 optimal weight:    0.0020
   overall best weight:    1.5194

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

Flipped N/Q/H residues before XYZ refinement:
B 140 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.163852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.121563 restraints weight = 55490.248|
|-----------------------------------------------------------------------------|
r_work (start): 0.3613 rms_B_bonded: 5.17
r_work: 0.3427 rms_B_bonded: 5.11 restraints_weight: 2.0000
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3430
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3430 r_free = 0.3430    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3430 r_free = 0.3430    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|
r_final: 0.3430
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7836
moved from start:          0.2554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10458  Z= 0.138
  Angle     :  0.648  11.432  14206  Z= 0.329
  Chirality :  0.041   0.172   1649
  Planarity :  0.004   0.064   1727
  Dihedral  :  6.561  60.649   1526
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  7.28 %
    Favored  : 92.40 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 19.30 %
    Favored  : 76.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -0.12 (0.25), residues: 1242
  helix:  1.08 (0.19), residues: 770
  sheet: -0.40 (0.60), residues: 77
  loop : -2.39 (0.32), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A1402 
 TYR   0.018   0.002   TYR A 388 
 PHE   0.021   0.001   PHE A1466 
 TRP   0.015   0.001   TRP A1408 
 HIS   0.004   0.001   HIS A1393 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 (10446)
  covalent geometry    : angle       0.63833 (14178)
  SS BOND              : bond        0.00489 (    8)
  SS BOND              : angle       1.69231 (   16)
  hydrogen bonds       : bond        0.03657 (  611)
  hydrogen bonds       : angle       4.07424 ( 1725)
  link_NAG-ASN         : bond        0.00306 (    4)
  link_NAG-ASN         : angle       3.43698 (   12)

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

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

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 171
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 MET cc_start: 0.8194 (mmt) cc_final: 0.7770 (mmm)
REVERT: A  409 LEU cc_start: 0.8933 (mm) cc_final: 0.8672 (mm)
REVERT: A  424 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.7659 (mtm)
REVERT: A  766 MET cc_start: 0.6817 (tpt) cc_final: 0.6564 (tpt)
REVERT: A  787 MET cc_start: 0.8993 (mtp) cc_final: 0.8770 (mtp)
REVERT: A  816 PHE cc_start: 0.7075 (m-80) cc_final: 0.6821 (m-80)
REVERT: A 1214 ILE cc_start: 0.8705 (mm) cc_final: 0.8454 (mm)
REVERT: A 1219 TRP cc_start: 0.7625 (m-10) cc_final: 0.6968 (m-90)
REVERT: A 1266 GLU cc_start: 0.8511 (pp20) cc_final: 0.8182 (pp20)
REVERT: A 1267 MET cc_start: 0.8615 (tmm) cc_final: 0.8127 (tmm)
REVERT: A 1268 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8013 (mm)
REVERT: A 1277 GLN cc_start: 0.8348 (tp40) cc_final: 0.7164 (mt0)
REVERT: A 1500 MET cc_start: 0.7772 (mtt) cc_final: 0.7371 (mtp)
REVERT: A 1548 MET cc_start: 0.7743 (mtt) cc_final: 0.7125 (tpp)
REVERT: A 1608 ASP cc_start: 0.8536 (t70) cc_final: 0.8215 (t70)
REVERT: A 1628 TYR cc_start: 0.4768 (m-80) cc_final: 0.4504 (m-10)
REVERT: A 1708 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8112 (mp0)
REVERT: A 1780 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.7667 (mtp)
  outliers start: 47
  outliers final: 33
  residues processed: 197
  average time/residue: 0.0783
  time to fit residues: 23.5544
Evaluate side-chains
  193 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 157
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   55 PHE
Chi-restraints excluded: chain B residue   90 ASP
Chi-restraints excluded: chain B residue  130 THR
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  169 SER
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  202 TYR
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  205 GLU
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  217 THR
Chi-restraints excluded: chain A residue  332 ASP
Chi-restraints excluded: chain A residue  377 ARG
Chi-restraints excluded: chain A residue  424 MET
Chi-restraints excluded: chain A residue  767 ASP
Chi-restraints excluded: chain A residue  770 VAL
Chi-restraints excluded: chain A residue  793 THR
Chi-restraints excluded: chain A residue  805 LEU
Chi-restraints excluded: chain A residue  863 LEU
Chi-restraints excluded: chain A residue  909 MET
Chi-restraints excluded: chain A residue  936 ASP
Chi-restraints excluded: chain A residue 1224 ILE
Chi-restraints excluded: chain A residue 1228 ILE
Chi-restraints excluded: chain A residue 1265 LEU
Chi-restraints excluded: chain A residue 1268 LEU
Chi-restraints excluded: chain A residue 1292 VAL
Chi-restraints excluded: chain A residue 1304 LEU
Chi-restraints excluded: chain A residue 1321 LEU
Chi-restraints excluded: chain A residue 1344 ILE
Chi-restraints excluded: chain A residue 1379 THR
Chi-restraints excluded: chain A residue 1397 LEU
Chi-restraints excluded: chain A residue 1405 THR
Chi-restraints excluded: chain A residue 1621 LEU
Chi-restraints excluded: chain A residue 1663 LEU
Chi-restraints excluded: chain A residue 1717 LEU
Chi-restraints excluded: chain A residue 1780 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 82 optimal weight:    4.9990
   chunk 2 optimal weight:    9.9990
   chunk 119 optimal weight:    0.8980
   chunk 21 optimal weight:    6.9990
   chunk 32 optimal weight:    0.0980
   chunk 108 optimal weight:    2.9990
   chunk 8 optimal weight:    7.9990
   chunk 39 optimal weight:    9.9990
   chunk 120 optimal weight:    0.9990
   chunk 90 optimal weight:    4.9990
   chunk 11 optimal weight:    5.9990
   overall best weight:    1.9986

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

Flipped N/Q/H residues before XYZ refinement:
B 140 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.163100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.126390 restraints weight = 45235.732|
|-----------------------------------------------------------------------------|
r_work (start): 0.3702 rms_B_bonded: 4.42
r_work: 0.3447 rms_B_bonded: 4.49 restraints_weight: 0.5000
r_work (final): 0.3447
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3451
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3451 r_free = 0.3451    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3451 r_free = 0.3451    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|
r_final: 0.3451
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7836
moved from start:          0.2729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  10458  Z= 0.155
  Angle     :  0.656  13.833  14206  Z= 0.334
  Chirality :  0.042   0.183   1649
  Planarity :  0.004   0.046   1727
  Dihedral  :  6.237  59.644   1524
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  7.68 %
    Favored  : 92.00 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 19.30 %
    Favored  : 75.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -0.05 (0.25), residues: 1242
  helix:  1.13 (0.19), residues: 772
  sheet: -0.33 (0.60), residues: 77
  loop : -2.37 (0.32), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A1402 
 TYR   0.021   0.002   TYR A 388 
 PHE   0.027   0.001   PHE A 200 
 TRP   0.024   0.001   TRP A1408 
 HIS   0.005   0.001   HIS A1393 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 (10446)
  covalent geometry    : angle       0.64702 (14178)
  SS BOND              : bond        0.00591 (    8)
  SS BOND              : angle       1.43303 (   16)
  hydrogen bonds       : bond        0.03738 (  611)
  hydrogen bonds       : angle       4.06327 ( 1725)
  link_NAG-ASN         : bond        0.00344 (    4)
  link_NAG-ASN         : angle       3.40814 (   12)

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

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

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 171
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 MET cc_start: 0.8281 (mmt) cc_final: 0.7821 (mmm)
REVERT: A  278 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.8001 (mp)
REVERT: A  350 MET cc_start: 0.7234 (ptm) cc_final: 0.6830 (ptp)
REVERT: A  424 MET cc_start: 0.8622 (OUTLIER) cc_final: 0.7652 (mtm)
REVERT: A  759 HIS cc_start: 0.7455 (m90) cc_final: 0.7219 (m90)
REVERT: A  766 MET cc_start: 0.6658 (tpt) cc_final: 0.6409 (tpt)
REVERT: A  787 MET cc_start: 0.8929 (mtp) cc_final: 0.8707 (mtp)
REVERT: A  816 PHE cc_start: 0.7117 (m-80) cc_final: 0.6865 (m-80)
REVERT: A  862 ARG cc_start: 0.8036 (ptm-80) cc_final: 0.7699 (ptm-80)
REVERT: A  918 ASP cc_start: 0.8056 (OUTLIER) cc_final: 0.7762 (t0)
REVERT: A 1214 ILE cc_start: 0.8684 (mm) cc_final: 0.8425 (mm)
REVERT: A 1219 TRP cc_start: 0.7618 (m-10) cc_final: 0.6954 (m-90)
REVERT: A 1266 GLU cc_start: 0.8450 (pp20) cc_final: 0.8149 (pp20)
REVERT: A 1267 MET cc_start: 0.8573 (tmm) cc_final: 0.8117 (tmm)
REVERT: A 1277 GLN cc_start: 0.8339 (tp40) cc_final: 0.7124 (mt0)
REVERT: A 1500 MET cc_start: 0.7613 (mtt) cc_final: 0.7230 (mtp)
REVERT: A 1548 MET cc_start: 0.7751 (mtt) cc_final: 0.7135 (tpp)
REVERT: A 1608 ASP cc_start: 0.8454 (t70) cc_final: 0.8114 (t70)
REVERT: A 1708 GLU cc_start: 0.8534 (mt-10) cc_final: 0.8000 (mp0)
  outliers start: 55
  outliers final: 34
  residues processed: 203
  average time/residue: 0.0687
  time to fit residues: 21.6816
Evaluate side-chains
  198 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 161
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   90 ASP
Chi-restraints excluded: chain B residue  130 THR
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  169 SER
Chi-restraints excluded: chain A residue  202 TYR
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  205 GLU
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  217 THR
Chi-restraints excluded: chain A residue  278 ILE
Chi-restraints excluded: chain A residue  320 ASP
Chi-restraints excluded: chain A residue  377 ARG
Chi-restraints excluded: chain A residue  424 MET
Chi-restraints excluded: chain A residue  767 ASP
Chi-restraints excluded: chain A residue  770 VAL
Chi-restraints excluded: chain A residue  793 THR
Chi-restraints excluded: chain A residue  805 LEU
Chi-restraints excluded: chain A residue  863 LEU
Chi-restraints excluded: chain A residue  899 ILE
Chi-restraints excluded: chain A residue  909 MET
Chi-restraints excluded: chain A residue  918 ASP
Chi-restraints excluded: chain A residue  936 ASP
Chi-restraints excluded: chain A residue 1224 ILE
Chi-restraints excluded: chain A residue 1228 ILE
Chi-restraints excluded: chain A residue 1265 LEU
Chi-restraints excluded: chain A residue 1292 VAL
Chi-restraints excluded: chain A residue 1304 LEU
Chi-restraints excluded: chain A residue 1321 LEU
Chi-restraints excluded: chain A residue 1344 ILE
Chi-restraints excluded: chain A residue 1379 THR
Chi-restraints excluded: chain A residue 1397 LEU
Chi-restraints excluded: chain A residue 1405 THR
Chi-restraints excluded: chain A residue 1621 LEU
Chi-restraints excluded: chain A residue 1663 LEU
Chi-restraints excluded: chain A residue 1717 LEU
Chi-restraints excluded: chain A residue 1780 MET
Chi-restraints excluded: chain A residue 1786 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 106 optimal weight:    8.9990
   chunk 77 optimal weight:    7.9990
   chunk 100 optimal weight:    2.9990
   chunk 123 optimal weight:    0.9990
   chunk 55 optimal weight:    3.9990
   chunk 53 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9980
   chunk 67 optimal weight:    0.9980
   chunk 32 optimal weight:    5.9990
   chunk 72 optimal weight:    4.9990
   chunk 12 optimal weight:    2.9990
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
B 140 ASN
B 144 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4212 r_free = 0.4212 target = 0.164429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.123178 restraints weight = 43155.604|
|-----------------------------------------------------------------------------|
r_work (start): 0.3644 rms_B_bonded: 4.30
r_work: 0.3459 rms_B_bonded: 4.72 restraints_weight: 0.5000
r_work (final): 0.3459
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3464
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3464 r_free = 0.3464    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3464 r_free = 0.3464    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|
r_final: 0.3464
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7814
moved from start:          0.2908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.112  10458  Z= 0.140
  Angle     :  0.670  15.160  14206  Z= 0.335
  Chirality :  0.041   0.179   1649
  Planarity :  0.004   0.046   1727
  Dihedral  :  6.077  58.085   1524
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  7.19 %
    Favored  : 92.48 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 20.29 %
    Favored  : 75.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  0.14 (0.25), residues: 1242
  helix:  1.22 (0.19), residues: 777
  sheet: -0.24 (0.61), residues: 77
  loop : -2.22 (0.32), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1402 
 TYR   0.018   0.001   TYR A 388 
 PHE   0.018   0.001   PHE A1466 
 TRP   0.014   0.001   TRP A1408 
 HIS   0.005   0.001   HIS A1393 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 (10446)
  covalent geometry    : angle       0.65626 (14178)
  SS BOND              : bond        0.00644 (    8)
  SS BOND              : angle       2.83826 (   16)
  hydrogen bonds       : bond        0.03512 (  611)
  hydrogen bonds       : angle       3.95550 ( 1725)
  link_NAG-ASN         : bond        0.00318 (    4)
  link_NAG-ASN         : angle       3.39225 (   12)

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

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

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 163
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 MET cc_start: 0.8157 (mmt) cc_final: 0.7722 (mmm)
REVERT: A  169 SER cc_start: 0.8816 (OUTLIER) cc_final: 0.8297 (p)
REVERT: A  278 ILE cc_start: 0.8374 (OUTLIER) cc_final: 0.7919 (mp)
REVERT: A  424 MET cc_start: 0.8631 (tpt) cc_final: 0.7736 (mtm)
REVERT: A  787 MET cc_start: 0.8918 (mtp) cc_final: 0.8692 (mtt)
REVERT: A  862 ARG cc_start: 0.8017 (ptm-80) cc_final: 0.7714 (ptm-80)
REVERT: A  918 ASP cc_start: 0.7954 (OUTLIER) cc_final: 0.7678 (t0)
REVERT: A 1214 ILE cc_start: 0.8674 (mm) cc_final: 0.8411 (mm)
REVERT: A 1219 TRP cc_start: 0.7611 (m-10) cc_final: 0.6945 (m-90)
REVERT: A 1266 GLU cc_start: 0.8489 (pp20) cc_final: 0.8163 (pp20)
REVERT: A 1267 MET cc_start: 0.8554 (tmm) cc_final: 0.8044 (tmm)
REVERT: A 1277 GLN cc_start: 0.8302 (tp40) cc_final: 0.7048 (mt0)
REVERT: A 1483 ILE cc_start: 0.7590 (tp) cc_final: 0.7322 (tp)
REVERT: A 1500 MET cc_start: 0.7584 (mtt) cc_final: 0.7171 (mtm)
REVERT: A 1548 MET cc_start: 0.7796 (mtt) cc_final: 0.7221 (tpp)
REVERT: A 1608 ASP cc_start: 0.8477 (t70) cc_final: 0.8139 (t70)
REVERT: A 1708 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8072 (mp0)
  outliers start: 47
  outliers final: 28
  residues processed: 193
  average time/residue: 0.0754
  time to fit residues: 22.2666
Evaluate side-chains
  186 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 155
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   90 ASP
Chi-restraints excluded: chain B residue  130 THR
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  169 SER
Chi-restraints excluded: chain A residue  202 TYR
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  217 THR
Chi-restraints excluded: chain A residue  278 ILE
Chi-restraints excluded: chain A residue  332 ASP
Chi-restraints excluded: chain A residue  377 ARG
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain A residue  770 VAL
Chi-restraints excluded: chain A residue  793 THR
Chi-restraints excluded: chain A residue  863 LEU
Chi-restraints excluded: chain A residue  899 ILE
Chi-restraints excluded: chain A residue  918 ASP
Chi-restraints excluded: chain A residue  936 ASP
Chi-restraints excluded: chain A residue  969 LEU
Chi-restraints excluded: chain A residue 1228 ILE
Chi-restraints excluded: chain A residue 1265 LEU
Chi-restraints excluded: chain A residue 1292 VAL
Chi-restraints excluded: chain A residue 1304 LEU
Chi-restraints excluded: chain A residue 1321 LEU
Chi-restraints excluded: chain A residue 1344 ILE
Chi-restraints excluded: chain A residue 1379 THR
Chi-restraints excluded: chain A residue 1397 LEU
Chi-restraints excluded: chain A residue 1405 THR
Chi-restraints excluded: chain A residue 1563 ASP
Chi-restraints excluded: chain A residue 1621 LEU
Chi-restraints excluded: chain A residue 1663 LEU
Chi-restraints excluded: chain A residue 1717 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 111 optimal weight:    7.9990
   chunk 14 optimal weight:    1.9990
   chunk 11 optimal weight:    6.9990
   chunk 103 optimal weight:    9.9990
   chunk 2 optimal weight:   20.0000
   chunk 33 optimal weight:    5.9990
   chunk 105 optimal weight:    7.9990
   chunk 81 optimal weight:    5.9990
   chunk 43 optimal weight:    2.9990
   chunk 47 optimal weight:   10.0000
   chunk 45 optimal weight:    0.8980
   overall best weight:    3.5788

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

Flipped N/Q/H residues before XYZ refinement:
B 140 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.160798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.118857 restraints weight = 54777.221|
|-----------------------------------------------------------------------------|
r_work (start): 0.3579 rms_B_bonded: 4.86
r_work: 0.3388 rms_B_bonded: 4.96 restraints_weight: 0.5000
r_work (final): 0.3388
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3393
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3393 r_free = 0.3393    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3393 r_free = 0.3393    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|
r_final: 0.3393
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7904
moved from start:          0.2954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.108  10458  Z= 0.228
  Angle     :  0.740  14.216  14206  Z= 0.372
  Chirality :  0.045   0.198   1649
  Planarity :  0.004   0.045   1727
  Dihedral  :  6.234  58.952   1521
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  7.84 %
    Favored  : 91.84 %
  Rotamer:
    Outliers :  4.92 %
    Allowed  : 19.93 %
    Favored  : 75.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -0.13 (0.24), residues: 1242
  helix:  0.98 (0.18), residues: 781
  sheet: -0.36 (0.60), residues: 77
  loop : -2.28 (0.32), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 222 
 TYR   0.026   0.002   TYR A 388 
 PHE   0.023   0.002   PHE A1466 
 TRP   0.017   0.002   TRP A1408 
 HIS   0.008   0.001   HIS A1393 

Details of bonding type rmsd
  covalent geometry    : bond        0.00537 (10446)
  covalent geometry    : angle       0.72672 (14178)
  SS BOND              : bond        0.00694 (    8)
  SS BOND              : angle       2.85956 (   16)
  hydrogen bonds       : bond        0.03972 (  611)
  hydrogen bonds       : angle       4.16207 ( 1725)
  link_NAG-ASN         : bond        0.00381 (    4)
  link_NAG-ASN         : angle       3.63170 (   12)

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

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

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 153
  time to evaluate  : 0.410 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 MET cc_start: 0.8327 (mmt) cc_final: 0.7858 (mmm)
REVERT: A  278 ILE cc_start: 0.8443 (OUTLIER) cc_final: 0.7927 (mp)
REVERT: A  424 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.7762 (mtm)
REVERT: A  787 MET cc_start: 0.9001 (mtp) cc_final: 0.8796 (mtp)
REVERT: A  862 ARG cc_start: 0.8108 (ptm-80) cc_final: 0.7741 (ptm-80)
REVERT: A 1214 ILE cc_start: 0.8752 (mm) cc_final: 0.8498 (mm)
REVERT: A 1219 TRP cc_start: 0.7680 (m-10) cc_final: 0.6989 (m-90)
REVERT: A 1266 GLU cc_start: 0.8560 (pp20) cc_final: 0.8272 (pp20)
REVERT: A 1267 MET cc_start: 0.8575 (tmm) cc_final: 0.8114 (tmm)
REVERT: A 1277 GLN cc_start: 0.8322 (tp40) cc_final: 0.7995 (tp40)
REVERT: A 1400 ILE cc_start: 0.7269 (OUTLIER) cc_final: 0.6610 (mt)
REVERT: A 1483 ILE cc_start: 0.7464 (tp) cc_final: 0.7097 (tp)
REVERT: A 1500 MET cc_start: 0.7707 (mtt) cc_final: 0.7298 (mtp)
REVERT: A 1608 ASP cc_start: 0.8441 (t70) cc_final: 0.8115 (t70)
REVERT: A 1708 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8269 (mt-10)
  outliers start: 54
  outliers final: 35
  residues processed: 192
  average time/residue: 0.0777
  time to fit residues: 22.6916
Evaluate side-chains
  191 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 153
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   55 PHE
Chi-restraints excluded: chain B residue   90 ASP
Chi-restraints excluded: chain B residue  130 THR
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  138 ILE
Chi-restraints excluded: chain A residue  169 SER
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  217 THR
Chi-restraints excluded: chain A residue  278 ILE
Chi-restraints excluded: chain A residue  332 ASP
Chi-restraints excluded: chain A residue  377 ARG
Chi-restraints excluded: chain A residue  385 GLU
Chi-restraints excluded: chain A residue  424 MET
Chi-restraints excluded: chain A residue  760 VAL
Chi-restraints excluded: chain A residue  767 ASP
Chi-restraints excluded: chain A residue  770 VAL
Chi-restraints excluded: chain A residue  775 THR
Chi-restraints excluded: chain A residue  793 THR
Chi-restraints excluded: chain A residue  863 LEU
Chi-restraints excluded: chain A residue  899 ILE
Chi-restraints excluded: chain A residue  918 ASP
Chi-restraints excluded: chain A residue  936 ASP
Chi-restraints excluded: chain A residue 1228 ILE
Chi-restraints excluded: chain A residue 1265 LEU
Chi-restraints excluded: chain A residue 1304 LEU
Chi-restraints excluded: chain A residue 1321 LEU
Chi-restraints excluded: chain A residue 1344 ILE
Chi-restraints excluded: chain A residue 1379 THR
Chi-restraints excluded: chain A residue 1384 ARG
Chi-restraints excluded: chain A residue 1397 LEU
Chi-restraints excluded: chain A residue 1400 ILE
Chi-restraints excluded: chain A residue 1405 THR
Chi-restraints excluded: chain A residue 1563 ASP
Chi-restraints excluded: chain A residue 1621 LEU
Chi-restraints excluded: chain A residue 1663 LEU
Chi-restraints excluded: chain A residue 1717 LEU
Chi-restraints excluded: chain A residue 1760 SER
Chi-restraints excluded: chain A residue 1780 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 54 optimal weight:    7.9990
   chunk 95 optimal weight:    0.0870
   chunk 11 optimal weight:    9.9990
   chunk 64 optimal weight:    3.9990
   chunk 65 optimal weight:    3.9990
   chunk 79 optimal weight:    0.9980
   chunk 109 optimal weight:    0.0980
   chunk 15 optimal weight:    2.9990
   chunk 60 optimal weight:    0.7980
   chunk 82 optimal weight:    0.8980
   chunk 7 optimal weight:    9.9990
   overall best weight:    0.5758

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

Flipped N/Q/H residues before XYZ refinement:
B 140 ASN
A 267 GLN
A 272 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.166554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.129264 restraints weight = 48949.026|
|-----------------------------------------------------------------------------|
r_work (start): 0.3744 rms_B_bonded: 4.74
r_work (final): 0.3744
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3744
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3744 r_free = 0.3744    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3745 r_free = 0.3745    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|
r_final: 0.3745
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7578
moved from start:          0.3203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067  10458  Z= 0.123
  Angle     :  0.665  14.800  14206  Z= 0.330
  Chirality :  0.041   0.196   1649
  Planarity :  0.004   0.046   1727
  Dihedral  :  5.732  56.411   1521
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  6.79 %
    Favored  : 92.97 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 21.45 %
    Favored  : 75.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  0.33 (0.25), residues: 1242
  helix:  1.37 (0.19), residues: 778
  sheet:  0.43 (0.65), residues: 65
  loop : -2.21 (0.31), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1402 
 TYR   0.016   0.001   TYR A1628 
 PHE   0.021   0.001   PHE A1774 
 TRP   0.019   0.001   TRP A1434 
 HIS   0.003   0.001   HIS A1393 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 (10446)
  covalent geometry    : angle       0.65613 (14178)
  SS BOND              : bond        0.00498 (    8)
  SS BOND              : angle       1.92029 (   16)
  hydrogen bonds       : bond        0.03363 (  611)
  hydrogen bonds       : angle       3.93360 ( 1725)
  link_NAG-ASN         : bond        0.00323 (    4)
  link_NAG-ASN         : angle       3.26430 (   12)

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

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

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 174
  time to evaluate  : 0.299 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 MET cc_start: 0.8266 (mmt) cc_final: 0.7833 (mmm)
REVERT: A  169 SER cc_start: 0.8862 (OUTLIER) cc_final: 0.8431 (p)
REVERT: A  424 MET cc_start: 0.7809 (OUTLIER) cc_final: 0.7432 (mtm)
REVERT: A  767 ASP cc_start: 0.2400 (OUTLIER) cc_final: 0.0578 (t0)
REVERT: A  808 THR cc_start: 0.8993 (t) cc_final: 0.8747 (t)
REVERT: A 1214 ILE cc_start: 0.8656 (mm) cc_final: 0.8396 (mm)
REVERT: A 1219 TRP cc_start: 0.7647 (m-10) cc_final: 0.6951 (m-90)
REVERT: A 1266 GLU cc_start: 0.8105 (pp20) cc_final: 0.7843 (pp20)
REVERT: A 1267 MET cc_start: 0.8125 (tmm) cc_final: 0.7727 (tmm)
REVERT: A 1277 GLN cc_start: 0.8173 (tp40) cc_final: 0.7821 (tp40)
REVERT: A 1500 MET cc_start: 0.6642 (mtt) cc_final: 0.6360 (mtm)
REVERT: A 1608 ASP cc_start: 0.8115 (t70) cc_final: 0.7866 (t70)
REVERT: A 1708 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7445 (mp0)
  outliers start: 36
  outliers final: 16
  residues processed: 195
  average time/residue: 0.0717
  time to fit residues: 21.3373
Evaluate side-chains
  176 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 157
  time to evaluate  : 0.553 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   90 ASP
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  169 SER
Chi-restraints excluded: chain A residue  217 THR
Chi-restraints excluded: chain A residue  424 MET
Chi-restraints excluded: chain A residue  767 ASP
Chi-restraints excluded: chain A residue  770 VAL
Chi-restraints excluded: chain A residue  793 THR
Chi-restraints excluded: chain A residue  805 LEU
Chi-restraints excluded: chain A residue  918 ASP
Chi-restraints excluded: chain A residue  936 ASP
Chi-restraints excluded: chain A residue 1228 ILE
Chi-restraints excluded: chain A residue 1321 LEU
Chi-restraints excluded: chain A residue 1344 ILE
Chi-restraints excluded: chain A residue 1397 LEU
Chi-restraints excluded: chain A residue 1405 THR
Chi-restraints excluded: chain A residue 1621 LEU
Chi-restraints excluded: chain A residue 1663 LEU
Chi-restraints excluded: chain A residue 1717 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 97 optimal weight:    0.0030
   chunk 62 optimal weight:    6.9990
   chunk 70 optimal weight:    9.9990
   chunk 89 optimal weight:    5.9990
   chunk 28 optimal weight:    0.0000
   chunk 22 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9990
   chunk 101 optimal weight:    4.9990
   chunk 24 optimal weight:    9.9990
   chunk 119 optimal weight:    0.0010
   chunk 109 optimal weight:    0.9990
   overall best weight:    0.4004

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

Flipped N/Q/H residues before XYZ refinement:
B 140 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.168044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.130425 restraints weight = 51187.936|
|-----------------------------------------------------------------------------|
r_work (start): 0.3763 rms_B_bonded: 4.96
r_work (final): 0.3763
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3764
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3764 r_free = 0.3764    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3764 r_free = 0.3764    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|
r_final: 0.3764
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7565
moved from start:          0.3395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.071  10458  Z= 0.124
  Angle     :  0.680  16.179  14206  Z= 0.333
  Chirality :  0.041   0.194   1649
  Planarity :  0.004   0.044   1727
  Dihedral  :  5.605  56.194   1521
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  7.03 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 22.97 %
    Favored  : 74.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  0.63 (0.25), residues: 1242
  helix:  1.56 (0.19), residues: 760
  sheet:  0.52 (0.64), residues: 69
  loop : -1.84 (0.33), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 862 
 TYR   0.014   0.001   TYR A 388 
 PHE   0.018   0.001   PHE A1486 
 TRP   0.015   0.001   TRP A1408 
 HIS   0.003   0.000   HIS A1393 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 (10446)
  covalent geometry    : angle       0.67029 (14178)
  SS BOND              : bond        0.00486 (    8)
  SS BOND              : angle       2.13740 (   16)
  hydrogen bonds       : bond        0.03336 (  611)
  hydrogen bonds       : angle       3.84845 ( 1725)
  link_NAG-ASN         : bond        0.00358 (    4)
  link_NAG-ASN         : angle       3.13770 (   12)

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

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

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 174
  time to evaluate  : 0.394 
Fit side-chains
   revert: symmetry clash
REVERT: A  132 MET cc_start: 0.8283 (mmt) cc_final: 0.7847 (mmm)
REVERT: A  169 SER cc_start: 0.9008 (t) cc_final: 0.8708 (p)
REVERT: A  424 MET cc_start: 0.7805 (OUTLIER) cc_final: 0.7473 (mtm)
REVERT: A  766 MET cc_start: 0.6395 (tpt) cc_final: 0.6080 (tpp)
REVERT: A  767 ASP cc_start: 0.2518 (OUTLIER) cc_final: 0.0663 (t0)
REVERT: A  804 ASN cc_start: 0.7787 (OUTLIER) cc_final: 0.7076 (t0)
REVERT: A  822 MET cc_start: 0.7485 (pmm) cc_final: 0.6527 (ptm)
REVERT: A 1214 ILE cc_start: 0.8649 (mm) cc_final: 0.8390 (mm)
REVERT: A 1219 TRP cc_start: 0.7633 (m-10) cc_final: 0.6929 (m-90)
REVERT: A 1266 GLU cc_start: 0.8100 (pp20) cc_final: 0.7698 (pp20)
REVERT: A 1267 MET cc_start: 0.8134 (tmm) cc_final: 0.7799 (tmm)
REVERT: A 1277 GLN cc_start: 0.8166 (tp40) cc_final: 0.6885 (mt0)
REVERT: A 1500 MET cc_start: 0.6676 (mtt) cc_final: 0.6389 (mtm)
REVERT: A 1608 ASP cc_start: 0.8181 (t70) cc_final: 0.7941 (t70)
REVERT: A 1708 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7598 (mp0)
  outliers start: 28
  outliers final: 16
  residues processed: 187
  average time/residue: 0.0632
  time to fit residues: 18.7621
Evaluate side-chains
  182 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 163
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   90 ASP
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  217 THR
Chi-restraints excluded: chain A residue  424 MET
Chi-restraints excluded: chain A residue  760 VAL
Chi-restraints excluded: chain A residue  767 ASP
Chi-restraints excluded: chain A residue  770 VAL
Chi-restraints excluded: chain A residue  804 ASN
Chi-restraints excluded: chain A residue  936 ASP
Chi-restraints excluded: chain A residue 1228 ILE
Chi-restraints excluded: chain A residue 1292 VAL
Chi-restraints excluded: chain A residue 1321 LEU
Chi-restraints excluded: chain A residue 1344 ILE
Chi-restraints excluded: chain A residue 1397 LEU
Chi-restraints excluded: chain A residue 1405 THR
Chi-restraints excluded: chain A residue 1621 LEU
Chi-restraints excluded: chain A residue 1663 LEU
Chi-restraints excluded: chain A residue 1717 LEU
Chi-restraints excluded: chain A residue 1780 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 14 optimal weight:    8.9990
   chunk 45 optimal weight:    0.2980
   chunk 108 optimal weight:    6.9990
   chunk 26 optimal weight:    1.9990
   chunk 109 optimal weight:    4.9990
   chunk 48 optimal weight:    3.9990
   chunk 97 optimal weight:    0.2980
   chunk 17 optimal weight:    0.0170
   chunk 99 optimal weight:   10.0000
   chunk 13 optimal weight:    0.9980
   chunk 115 optimal weight:   10.0000
   overall best weight:    0.7220

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

Flipped N/Q/H residues before XYZ refinement:
B 140 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.167672 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.130739 restraints weight = 41955.297|
|-----------------------------------------------------------------------------|
r_work (start): 0.3762 rms_B_bonded: 4.10
r_work: 0.3536 rms_B_bonded: 4.43 restraints_weight: 0.5000
r_work (final): 0.3536
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3538
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3538 r_free = 0.3538    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3538 r_free = 0.3538    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|
r_final: 0.3538
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7752
moved from start:          0.3530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10458  Z= 0.122
  Angle     :  0.665  16.072  14206  Z= 0.328
  Chirality :  0.042   0.198   1649
  Planarity :  0.004   0.045   1727
  Dihedral  :  5.496  56.501   1521
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  7.03 %
    Favored  : 92.89 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 23.41 %
    Favored  : 74.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  0.58 (0.25), residues: 1242
  helix:  1.53 (0.19), residues: 767
  sheet:  0.58 (0.65), residues: 69
  loop : -1.95 (0.32), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 862 
 TYR   0.016   0.001   TYR A 388 
 PHE   0.029   0.001   PHE A1774 
 TRP   0.017   0.001   TRP A1271 
 HIS   0.003   0.001   HIS A1393 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 (10446)
  covalent geometry    : angle       0.65792 (14178)
  SS BOND              : bond        0.00441 (    8)
  SS BOND              : angle       1.35196 (   16)
  hydrogen bonds       : bond        0.03355 (  611)
  hydrogen bonds       : angle       3.85032 ( 1725)
  link_NAG-ASN         : bond        0.00317 (    4)
  link_NAG-ASN         : angle       3.07484 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2605.54 seconds
wall clock time: 45 minutes 12.25 seconds (2712.25 seconds total)