Starting phenix.real_space_refine
on Wed Mar  4 09:07:16 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7dsh_30833/03_2026/7dsh_30833.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7dsh_30833/03_2026/7dsh_30833.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.67
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7dsh_30833/03_2026/7dsh_30833.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7dsh_30833/03_2026/7dsh_30833.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7dsh_30833/03_2026/7dsh_30833.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7dsh_30833/03_2026/7dsh_30833.map"
  }
  resolution = 3.67
  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=   0.000 sd=   0.002
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: 6
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     Mg      1      5.21       5
     S      57      5.16       5
     C    7764      2.51       5
     N    2004      2.21       5
     O    2242      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 45 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: 12071
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 9066
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1138, 9066
          Classifications: {'peptide': 1138}
          Link IDs: {'PTRANS': 35, 'TRANS': 1102}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2934
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 362, 2934
          Classifications: {'peptide': 362}
          Link IDs: {'PTRANS': 19, 'TRANS': 342}
    Chain: "C"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ACP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 2.55, per 1000 atoms: 0.21
  Number of scatterers: 12071
  At special positions: 0
  Unit cell: (148.755, 108.665, 130.82, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      57     16.00
     P       3     15.00
     Mg      1     11.99
     O    2242      8.00
     N    2004      7.00
     C    7764      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 110 " - pdb=" SG  CYS B 159 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 216 " - pdb=" SG  CYS B 231 " 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=2, symmetry=0
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG C   2 " - " BMA C   3 "
    NAG-ASN
      " NAG C   1 " - " ASN B 240 "
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.70
  Conformation dependent library (CDL) restraints added in 516.7 milliseconds
  

  2988 Ramachandran restraints generated.
    1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2804

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 12 sheets defined
      34.3% alpha, 7.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.32
  Creating SS restraints...
    Processing helix  chain 'A' and resid 205 through 215
      removed outlier: 3.874A  pdb=" N   LYS A 209 " --> pdb=" O   THR A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 220 through 229
    Processing helix  chain 'A' and resid 239 through 243
      removed outlier: 3.671A  pdb=" N   SER A 243 " --> pdb=" O   PRO A 240 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 244 through 268
      removed outlier: 4.255A  pdb=" N   ILE A 250 " --> pdb=" O   PRO A 246 " (cutoff:3.500A)
      removed outlier: 4.459A  pdb=" N   ARG A 265 " --> pdb=" O   GLU A 261 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   LEU A 268 " --> pdb=" O   ARG A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 461 through 465
      removed outlier: 3.534A  pdb=" N   ARG A 464 " --> pdb=" O   ASP A 461 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   THR A 465 " --> pdb=" O   ILE A 462 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 461 through 465'
    Processing helix  chain 'A' and resid 549 through 571
      removed outlier: 3.807A  pdb=" N   VAL A 554 " --> pdb=" O   ASN A 550 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 573 through 577
      removed outlier: 3.745A  pdb=" N   ASP A 576 " --> pdb=" O   VAL A 573 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 599 through 609
      removed outlier: 3.528A  pdb=" N   TRP A 603 " --> pdb=" O   PHE A 599 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   ALA A 605 " --> pdb=" O   SER A 601 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 619 through 634
      removed outlier: 3.657A  pdb=" N   THR A 626 " --> pdb=" O   GLU A 622 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 651 through 655
      removed outlier: 4.120A  pdb=" N   ILE A 654 " --> pdb=" O   SER A 651 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   SER A 655 " --> pdb=" O   TRP A 652 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 651 through 655'
    Processing helix  chain 'A' and resid 656 through 659
    Processing helix  chain 'A' and resid 696 through 700
      removed outlier: 4.278A  pdb=" N   GLY A 699 " --> pdb=" O   ALA A 696 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 708 through 726
      removed outlier: 3.614A  pdb=" N   GLU A 715 " --> pdb=" O   GLU A 711 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   ALA A 720 " --> pdb=" O   LYS A 716 " (cutoff:3.500A)
      removed outlier: 4.088A  pdb=" N   ARG A 723 " --> pdb=" O   ILE A 719 " (cutoff:3.500A)
      removed outlier: 4.755A  pdb=" N   ASP A 724 " --> pdb=" O   ALA A 720 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   THR A 725 " --> pdb=" O   LYS A 721 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 761 through 775
      removed outlier: 3.605A  pdb=" N   ARG A 765 " --> pdb=" O   GLU A 761 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 798 through 812
      removed outlier: 3.807A  pdb=" N   ALA A 803 " --> pdb=" O   PRO A 799 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   LEU A 804 " --> pdb=" O   ASP A 800 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   VAL A 805 " --> pdb=" O   GLU A 801 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ASP A 810 " --> pdb=" O   ALA A 806 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 892 through 903
    Processing helix  chain 'A' and resid 922 through 936
      removed outlier: 3.791A  pdb=" N   TRP A 926 " --> pdb=" O   GLU A 922 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 946 through 951
      removed outlier: 3.723A  pdb=" N   SER A 950 " --> pdb=" O   VAL A 946 " (cutoff:3.500A)
      removed outlier: 4.539A  pdb=" N   ILE A 951 " --> pdb=" O   VAL A 947 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 946 through 951'
    Processing helix  chain 'A' and resid 971 through 977
      removed outlier: 3.968A  pdb=" N   GLU A 976 " --> pdb=" O   PRO A 972 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 992 through 1001
    Processing helix  chain 'A' and resid 1034 through 1044
      removed outlier: 3.539A  pdb=" N   SER A1038 " --> pdb=" O   ASP A1034 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   TYR A1040 " --> pdb=" O   LEU A1036 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   LYS A1042 " --> pdb=" O   SER A1038 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1074 through 1079
    Processing helix  chain 'A' and resid 1087 through 1092
    Processing helix  chain 'A' and resid 1107 through 1120
      removed outlier: 3.560A  pdb=" N   VAL A1114 " --> pdb=" O   LYS A1110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1134 through 1139
    Processing helix  chain 'A' and resid 1165 through 1167
      No H-bonds generated for 'chain 'A' and resid 1165 through 1167'
    Processing helix  chain 'A' and resid 1168 through 1175
    Processing helix  chain 'A' and resid 1178 through 1183
    Processing helix  chain 'A' and resid 1183 through 1197
      removed outlier: 3.548A  pdb=" N   ILE A1188 " --> pdb=" O   LEU A1184 " (cutoff:3.500A)
      Proline residue:  A1189  - end of helix
      removed outlier: 3.567A  pdb=" N   PHE A1192 " --> pdb=" O   ILE A1188 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   MET A1196 " --> pdb=" O   PHE A1192 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1231 through 1239
      removed outlier: 3.847A  pdb=" N   ILE A1235 " --> pdb=" O   SER A1231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1247 through 1252
    Processing helix  chain 'A' and resid 1253 through 1255
      No H-bonds generated for 'chain 'A' and resid 1253 through 1255'
    Processing helix  chain 'A' and resid 1256 through 1261
      removed outlier: 3.578A  pdb=" N   LEU A1261 " --> pdb=" O   ARG A1257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1266 through 1293
      removed outlier: 4.046A  pdb=" N   TRP A1272 " --> pdb=" O   ARG A1268 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   ILE A1282 " --> pdb=" O   LEU A1278 " (cutoff:3.500A)
      Proline residue:  A1288  - end of helix
      removed outlier: 3.784A  pdb=" N   VAL A1291 " --> pdb=" O   PHE A1287 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   TYR A1292 " --> pdb=" O   PRO A1288 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1311 through 1329
      removed outlier: 3.653A  pdb=" N   ILE A1318 " --> pdb=" O   TYR A1314 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   CYS A1323 " --> pdb=" O   ALA A1319 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   TYR A1326 " --> pdb=" O   SER A1322 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1339 through 1347
      removed outlier: 3.601A  pdb=" N   ALA A1343 " --> pdb=" O   GLY A1339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1348 through 1356
      removed outlier: 3.536A  pdb=" N   THR A1353 " --> pdb=" O   VAL A1349 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   GLY A1354 " --> pdb=" O   PHE A1350 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1367 through 1374
      removed outlier: 3.861A  pdb=" N   ARG A1371 " --> pdb=" O   LYS A1367 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   TYR A1373 " --> pdb=" O   ALA A1369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1375 through 1386
      removed outlier: 4.161A  pdb=" N   TRP A1379 " --> pdb=" O   ALA A1375 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   PHE A1383 " --> pdb=" O   TRP A1379 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   VAL A1384 " --> pdb=" O   ALA A1380 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1386 through 1404
      Proline residue:  A1392  - end of helix
      removed outlier: 4.033A  pdb=" N   LYS A1401 " --> pdb=" O   ASP A1397 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   PHE A1403 " --> pdb=" O   PHE A1399 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1406 through 1416
      removed outlier: 3.566A  pdb=" N   GLN A1416 " --> pdb=" O   ARG A1412 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 74 through 86
    Processing helix  chain 'B' and resid 88 through 98
    Processing helix  chain 'B' and resid 186 through 191
      removed outlier: 3.618A  pdb=" N   VAL B 190 " --> pdb=" O   HIS B 186 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   LEU B 191 " --> pdb=" O   ARG B 187 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 186 through 191'
    Processing helix  chain 'B' and resid 194 through 199
    Processing helix  chain 'B' and resid 232 through 237
    Processing helix  chain 'B' and resid 266 through 270
    Processing helix  chain 'B' and resid 308 through 313
    Processing helix  chain 'B' and resid 372 through 395
      removed outlier: 3.920A  pdb=" N   TYR B 378 " --> pdb=" O   LEU B 374 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   CYS B 385 " --> pdb=" O   GLY B 381 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 406 through 409
      removed outlier: 3.631A  pdb=" N   GLY A 520 " --> pdb=" O   VAL A 407 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   VAL A 521 " --> pdb=" O   ILE A 420 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 447 through 448
      removed outlier: 4.102A  pdb=" N   TYR A 432 " --> pdb=" O   ARG A 513 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 485 through 488
      removed outlier: 4.146A  pdb=" N   MET A 485 " --> pdb=" O   GLU A 498 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   TRP A 487 " --> pdb=" O   ARG A 496 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   ARG A 496 " --> pdb=" O   TRP A 487 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1099 through 1100
      removed outlier: 6.939A  pdb=" N   LEU A 985 " --> pdb=" O   VAL A1100 " (cutoff:3.500A)
      removed outlier: 6.807A  pdb=" N   GLU A 662 " --> pdb=" O   LYS A 984 " (cutoff:3.500A)
      removed outlier: 7.286A  pdb=" N   TRP A 986 " --> pdb=" O   GLU A 662 " (cutoff:3.500A)
      removed outlier: 6.294A  pdb=" N   ILE A 664 " --> pdb=" O   TRP A 986 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 687 through 689
      removed outlier: 4.883A  pdb=" N   LEU A 957 " --> pdb=" O   GLN A 915 " (cutoff:3.500A)
      removed outlier: 6.071A  pdb=" N   GLN A 915 " --> pdb=" O   LEU A 957 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 781 through 783
      removed outlier: 3.555A  pdb=" N   ASP A 793 " --> pdb=" O   GLU A 783 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 813 through 818
      removed outlier: 3.655A  pdb=" N   SER A 814 " --> pdb=" O   GLU A 826 " (cutoff:3.500A)
      removed outlier: 7.557A  pdb=" N   ILE A 824 " --> pdb=" O   VAL A 816 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   ILE A 830 " --> pdb=" O   MET A 827 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 839 through 840
      removed outlier: 3.782A  pdb=" N   SER A 850 " --> pdb=" O   LEU A 840 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   CYS A 851 " --> pdb=" O   ILE A 869 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 127 through 129
      removed outlier: 6.512A  pdb=" N   TYR B 177 " --> pdb=" O   LEU B 326 " (cutoff:3.500A)
      removed outlier: 6.250A  pdb=" N   LEU B 326 " --> pdb=" O   TYR B 177 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 141 through 144
      removed outlier: 3.557A  pdb=" N   ARG B 143 " --> pdb=" O   GLN B 160 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 227 through 228
      removed outlier: 6.794A  pdb=" N   ILE B 227 " --> pdb=" O   ALA B 284 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'B' and resid 246 through 247

    327 hydrogen bonds defined for protein.
    912 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: 1.95

  Time building geometry restraints manager: 0.94 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1984
        1.32 -     1.44: 3402
        1.44 -     1.57: 6875
        1.57 -     1.69: 6
        1.69 -     1.82: 86
  Bond restraints: 12353
  Sorted by residual:
  bond pdb=" O3A ACP A1601 "
       pdb=" PB  ACP A1601 "
    ideal  model  delta    sigma   weight residual
    1.698  1.599  0.099 2.00e-02 2.50e+03 2.47e+01
  bond pdb=" O2B ACP A1601 "
       pdb=" PB  ACP A1601 "
    ideal  model  delta    sigma   weight residual
    1.507  1.606 -0.099 2.00e-02 2.50e+03 2.46e+01
  bond pdb=" N   ILE B 214 "
       pdb=" CA  ILE B 214 "
    ideal  model  delta    sigma   weight residual
    1.460  1.406  0.054 1.10e-02 8.26e+03 2.40e+01
  bond pdb=" C   GLU A1028 "
       pdb=" N   PRO A1029 "
    ideal  model  delta    sigma   weight residual
    1.337  1.391 -0.054 1.24e-02 6.50e+03 1.92e+01
  bond pdb=" C   ILE B 214 "
       pdb=" O   ILE B 214 "
    ideal  model  delta    sigma   weight residual
    1.236  1.192  0.044 1.03e-02 9.43e+03 1.81e+01
  ... (remaining 12348 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.75: 16289
        2.75 -     5.49: 382
        5.49 -     8.24: 64
        8.24 -    10.98: 22
       10.98 -    13.73: 4
  Bond angle restraints: 16761
  Sorted by residual:
  angle pdb=" C   ILE B 214 "
        pdb=" CA  ILE B 214 "
        pdb=" CB  ILE B 214 "
      ideal   model   delta    sigma   weight residual
     111.08  103.81    7.27 1.17e+00 7.31e-01 3.86e+01
  angle pdb=" N   VAL A1311 "
        pdb=" CA  VAL A1311 "
        pdb=" C   VAL A1311 "
      ideal   model   delta    sigma   weight residual
     111.81  106.77    5.04 8.60e-01 1.35e+00 3.43e+01
  angle pdb=" C   MET A1187 "
        pdb=" N   ILE A1188 "
        pdb=" CA  ILE A1188 "
      ideal   model   delta    sigma   weight residual
     120.24  123.75   -3.51 6.30e-01 2.52e+00 3.10e+01
  angle pdb=" C   LYS A 668 "
        pdb=" N   THR A 669 "
        pdb=" CA  THR A 669 "
      ideal   model   delta    sigma   weight residual
     121.54  132.09  -10.55 1.91e+00 2.74e-01 3.05e+01
  angle pdb=" C   CYS A1102 "
        pdb=" N   CYS A1103 "
        pdb=" CA  CYS A1103 "
      ideal   model   delta    sigma   weight residual
     123.47  131.75   -8.28 1.53e+00 4.27e-01 2.93e+01
  ... (remaining 16756 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.24: 7279
       35.24 -    70.48: 82
       70.48 -   105.72: 13
      105.72 -   140.96: 0
      140.96 -   176.20: 1
  Dihedral angle restraints: 7375
    sinusoidal: 3002
      harmonic: 4373
  Sorted by residual:
  dihedral pdb=" CA  LEU A1101 "
           pdb=" C   LEU A1101 "
           pdb=" N   CYS A1102 "
           pdb=" CA  CYS A1102 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -136.42  -43.58     0      5.00e+00 4.00e-02 7.60e+01
  dihedral pdb=" CB  CYS B 110 "
           pdb=" SG  CYS B 110 "
           pdb=" SG  CYS B 159 "
           pdb=" CB  CYS B 159 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -28.45  -57.55     1      1.00e+01 1.00e-02 4.45e+01
  dihedral pdb=" CA  PHE B 398 "
           pdb=" C   PHE B 398 "
           pdb=" N   GLY B 399 "
           pdb=" CA  GLY B 399 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  148.68   31.32     0      5.00e+00 4.00e-02 3.92e+01
  ... (remaining 7372 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.064: 1399
       0.064 -    0.128: 390
       0.128 -    0.192: 52
       0.192 -    0.256: 18
       0.256 -    0.320: 6
  Chirality restraints: 1865
  Sorted by residual:
  chirality pdb=" CB  ILE A 836 "
            pdb=" CA  ILE A 836 "
            pdb=" CG1 ILE A 836 "
            pdb=" CG2 ILE A 836 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.32    0.32 2.00e-01 2.50e+01 2.56e+00
  chirality pdb=" CA  ASN A 675 "
            pdb=" N   ASN A 675 "
            pdb=" C   ASN A 675 "
            pdb=" CB  ASN A 675 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.29e+00
  chirality pdb=" CB  ILE A1072 "
            pdb=" CA  ILE A1072 "
            pdb=" CG1 ILE A1072 "
            pdb=" CG2 ILE A1072 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.35    0.30 2.00e-01 2.50e+01 2.18e+00
  ... (remaining 1862 not shown)

  Planarity restraints: 2124
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A1408 "    0.031 2.00e-02 2.50e+03   5.98e-02 3.58e+01
        pdb=" C   VAL A1408 "   -0.104 2.00e-02 2.50e+03
        pdb=" O   VAL A1408 "    0.038 2.00e-02 2.50e+03
        pdb=" N   GLU A1409 "    0.034 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE B 398 "    0.029 2.00e-02 2.50e+03   5.71e-02 3.26e+01
        pdb=" C   PHE B 398 "   -0.099 2.00e-02 2.50e+03
        pdb=" O   PHE B 398 "    0.037 2.00e-02 2.50e+03
        pdb=" N   GLY B 399 "    0.033 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 986 "   -0.023 2.00e-02 2.50e+03   2.07e-02 1.07e+01
        pdb=" CG  TRP A 986 "    0.052 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 986 "   -0.030 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 986 "    0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 986 "    0.011 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 986 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 986 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 986 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 986 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 986 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 2121 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 223
        2.66 -     3.22: 10909
        3.22 -     3.78: 18638
        3.78 -     4.34: 25981
        4.34 -     4.90: 41468
  Nonbonded interactions: 97219
  Sorted by model distance:
  nonbonded pdb=" NE2 HIS B 209 "
            pdb=" OG  SER B 220 "
     model   vdw
     2.099 3.120
  nonbonded pdb=" N   ASP B 210 "
            pdb=" OD1 ASP B 210 "
     model   vdw
     2.215 3.120
  nonbonded pdb=" OH  TYR A1193 "
            pdb=" OE1 GLN A1280 "
     model   vdw
     2.243 3.040
  nonbonded pdb=" O   THR A1353 "
            pdb=" OG  SER A1357 "
     model   vdw
     2.250 3.040
  nonbonded pdb=" O3G ACP A1601 "
            pdb="MG    MG A1602 "
     model   vdw
     2.254 2.170
  ... (remaining 97214 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.950
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     10.820
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  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:1.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.170
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7419
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      :  0.007   0.099  12360  Z= 0.322
  Angle     :  1.099  16.034  16774  Z= 0.588
  Chirality :  0.063   0.320   1865
  Planarity :  0.007   0.070   2123
  Dihedral  : 12.541 176.197   4565
  Min Nonbonded Distance : 2.099

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  9.50 %
    Favored  : 90.36 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  :  3.61 %
    Favored  : 95.93 %
  Cbeta Deviations :  0.07 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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: -6.04 (0.14), residues: 1494
  helix: -4.69 (0.09), residues: 536
  sheet: -3.88 (0.36), residues: 128
  loop : -3.64 (0.16), residues: 830

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 272 
 TYR   0.030   0.003   TYR A1217 
 PHE   0.030   0.003   PHE A1287 
 TRP   0.054   0.004   TRP B 308 
 HIS   0.013   0.002   HIS A 216 

Details of bonding type rmsd
  covalent geometry    : bond        0.00662 (12353)
  covalent geometry    : angle       1.08499 (16761)
  SS BOND              : bond        0.00394 (    2)
  SS BOND              : angle       1.11105 (    4)
  hydrogen bonds       : bond        0.30506 (  327)
  hydrogen bonds       : angle      11.93959 (  912)
  Misc. bond           : bond        0.00348 (    2)
  link_BETA1-4         : bond        0.01280 (    2)
  link_BETA1-4         : angle       7.08138 (    6)
  link_NAG-ASN         : bond        0.00867 (    1)
  link_NAG-ASN         : angle       8.40935 (    3)

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

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

  2988 Ramachandran restraints generated.
    1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2988 Ramachandran restraints generated.
    1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 191
  time to evaluate  : 0.386 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  477 ASN cc_start: 0.7842 (t0) cc_final: 0.7468 (t0)
REVERT: A  740 TYR cc_start: 0.6855 (p90) cc_final: 0.6138 (p90)
REVERT: A  945 GLU cc_start: 0.7323 (tt0) cc_final: 0.6957 (tt0)
REVERT: A 1097 CYS cc_start: 0.7329 (p) cc_final: 0.7069 (p)
REVERT: A 1139 GLN cc_start: 0.6897 (mt0) cc_final: 0.6677 (pt0)
REVERT: A 1296 MET cc_start: 0.8377 (mmm) cc_final: 0.8060 (mmt)
REVERT: A 1306 ASP cc_start: 0.7188 (p0) cc_final: 0.6944 (t0)
REVERT: A 1321 ILE cc_start: 0.7929 (OUTLIER) cc_final: 0.7448 (mp)
  outliers start: 6
  outliers final: 3
  residues processed: 197
  average time/residue: 0.1132
  time to fit residues: 31.8880
Evaluate side-chains
  110 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 106
  time to evaluate  : 0.517 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  613 VAL
Chi-restraints excluded: chain A residue  911 LEU
Chi-restraints excluded: chain A residue 1321 ILE
Chi-restraints excluded: chain B residue  212 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 98 optimal weight:    0.5980
   chunk 107 optimal weight:    0.9990
   chunk 10 optimal weight:    5.9990
   chunk 66 optimal weight:    2.9990
   chunk 130 optimal weight:    1.9990
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    0.8980
   chunk 122 optimal weight:    2.9990
   chunk 91 optimal weight:    0.9980
   chunk 55 optimal weight:    1.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
A 216 HIS
A 475 HIS
A 484 ASN
A 550 ASN
A 736 ASN
A 778 HIS
A 831 GLN
A 968 GLN
A1176 HIS
A1307 HIS
B 155 GLN
B 172 ASN
B 256 ASN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.130560 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.097905 restraints weight = 20248.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.096206 restraints weight = 18196.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.097270 restraints weight = 15704.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.097853 restraints weight = 12070.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.098288 restraints weight = 10359.373|
|-----------------------------------------------------------------------------|
r_work (final): 0.3467
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7494
moved from start:          0.1716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  12360  Z= 0.186
  Angle     :  0.746  10.104  16774  Z= 0.388
  Chirality :  0.048   0.222   1865
  Planarity :  0.005   0.043   2123
  Dihedral  : 10.713 173.746   1738
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 9.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.17 %
    Favored  : 91.83 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  :  7.22 %
    Favored  : 90.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -4.90 (0.17), residues: 1494
  helix: -3.22 (0.16), residues: 541
  sheet: -3.50 (0.36), residues: 144
  loop : -3.28 (0.18), residues: 809

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 765 
 TYR   0.022   0.002   TYR A1040 
 PHE   0.039   0.002   PHE A 679 
 TRP   0.030   0.002   TRP B 308 
 HIS   0.005   0.001   HIS A1307 

Details of bonding type rmsd
  covalent geometry    : bond        0.00424 (12353)
  covalent geometry    : angle       0.73759 (16761)
  SS BOND              : bond        0.00263 (    2)
  SS BOND              : angle       1.09427 (    4)
  hydrogen bonds       : bond        0.04805 (  327)
  hydrogen bonds       : angle       6.63554 (  912)
  Misc. bond           : bond        0.00207 (    2)
  link_BETA1-4         : bond        0.00684 (    2)
  link_BETA1-4         : angle       4.42383 (    6)
  link_NAG-ASN         : bond        0.00863 (    1)
  link_NAG-ASN         : angle       5.91169 (    3)

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

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

  2988 Ramachandran restraints generated.
    1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2988 Ramachandran restraints generated.
    1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 109
  time to evaluate  : 0.428 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  477 ASN cc_start: 0.7679 (t0) cc_final: 0.7074 (t0)
REVERT: A  827 MET cc_start: 0.8408 (ppp) cc_final: 0.8120 (ppp)
REVERT: A 1006 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8220 (pp)
REVERT: A 1139 GLN cc_start: 0.7097 (mt0) cc_final: 0.6842 (pt0)
  outliers start: 28
  outliers final: 19
  residues processed: 126
  average time/residue: 0.0953
  time to fit residues: 18.0777
Evaluate side-chains
  114 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 94
  time to evaluate  : 0.510 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  501 THR
Chi-restraints excluded: chain A residue  613 VAL
Chi-restraints excluded: chain A residue  730 LEU
Chi-restraints excluded: chain A residue  776 LEU
Chi-restraints excluded: chain A residue  811 VAL
Chi-restraints excluded: chain A residue  836 ILE
Chi-restraints excluded: chain A residue  911 LEU
Chi-restraints excluded: chain A residue  963 ILE
Chi-restraints excluded: chain A residue 1006 LEU
Chi-restraints excluded: chain A residue 1013 LEU
Chi-restraints excluded: chain A residue 1223 MET
Chi-restraints excluded: chain A residue 1381 VAL
Chi-restraints excluded: chain A residue 1433 ASN
Chi-restraints excluded: chain B residue   67 ASN
Chi-restraints excluded: chain B residue   69 VAL
Chi-restraints excluded: chain B residue  141 GLN
Chi-restraints excluded: chain B residue  280 TYR
Chi-restraints excluded: chain B residue  351 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 7 optimal weight:    9.9990
   chunk 95 optimal weight:    0.8980
   chunk 71 optimal weight:    2.9990
   chunk 107 optimal weight:    1.9990
   chunk 148 optimal weight:    0.0030
   chunk 59 optimal weight:    2.9990
   chunk 99 optimal weight:    0.1980
   chunk 56 optimal weight:    1.9990
   chunk 147 optimal weight:    0.9990
   chunk 17 optimal weight:    0.0070
   chunk 25 optimal weight:    1.9990
   overall best weight:    0.4210

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

Flipped N/Q/H residues before XYZ refinement:
A 210 ASN
A 660 GLN
A 704 GLN
A 927 ASN
A 998 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.133289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.100236 restraints weight = 20097.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.099873 restraints weight = 16363.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.100978 restraints weight = 15269.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.101220 restraints weight = 10546.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.101331 restraints weight = 9557.941|
|-----------------------------------------------------------------------------|
r_work (final): 0.3517
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7426
moved from start:          0.2110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  12360  Z= 0.123
  Angle     :  0.647   8.171  16774  Z= 0.336
  Chirality :  0.045   0.195   1865
  Planarity :  0.004   0.041   2123
  Dihedral  :  9.384 175.055   1735
  Min Nonbonded Distance : 2.162

Molprobity Statistics.
  All-atom Clashscore : 10.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.97 %
    Favored  : 92.03 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  :  8.99 %
    Favored  : 88.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -4.14 (0.19), residues: 1494
  helix: -2.23 (0.20), residues: 535
  sheet: -3.29 (0.37), residues: 145
  loop : -3.09 (0.19), residues: 814

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 765 
 TYR   0.026   0.002   TYR A1040 
 PHE   0.018   0.001   PHE A 679 
 TRP   0.017   0.002   TRP B 308 
 HIS   0.005   0.001   HIS A 899 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 (12353)
  covalent geometry    : angle       0.63780 (16761)
  SS BOND              : bond        0.00298 (    2)
  SS BOND              : angle       1.09587 (    4)
  hydrogen bonds       : bond        0.03489 (  327)
  hydrogen bonds       : angle       5.77834 (  912)
  Misc. bond           : bond        0.00142 (    2)
  link_BETA1-4         : bond        0.00466 (    2)
  link_BETA1-4         : angle       4.01551 (    6)
  link_NAG-ASN         : bond        0.00600 (    1)
  link_NAG-ASN         : angle       5.89430 (    3)

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

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

  2988 Ramachandran restraints generated.
    1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2988 Ramachandran restraints generated.
    1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 107
  time to evaluate  : 0.458 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  200 LYS cc_start: 0.4803 (pttm) cc_final: 0.4603 (mtpt)
REVERT: A  224 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7426 (tp)
REVERT: A  267 VAL cc_start: 0.7337 (OUTLIER) cc_final: 0.7065 (t)
REVERT: A  477 ASN cc_start: 0.7703 (t0) cc_final: 0.7160 (t0)
REVERT: A  482 GLN cc_start: 0.6532 (pm20) cc_final: 0.6187 (mp10)
REVERT: A  804 LEU cc_start: 0.7949 (mm) cc_final: 0.7630 (mm)
REVERT: A  827 MET cc_start: 0.8392 (ppp) cc_final: 0.8094 (ppp)
REVERT: A  852 ILE cc_start: 0.7436 (OUTLIER) cc_final: 0.6786 (mt)
REVERT: A  942 ASP cc_start: 0.8402 (OUTLIER) cc_final: 0.8110 (t0)
REVERT: A 1263 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.7793 (tmtt)
  outliers start: 31
  outliers final: 16
  residues processed: 130
  average time/residue: 0.0966
  time to fit residues: 18.6470
Evaluate side-chains
  109 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 88
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  267 VAL
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  501 THR
Chi-restraints excluded: chain A residue  604 VAL
Chi-restraints excluded: chain A residue  613 VAL
Chi-restraints excluded: chain A residue  807 THR
Chi-restraints excluded: chain A residue  836 ILE
Chi-restraints excluded: chain A residue  852 ILE
Chi-restraints excluded: chain A residue  911 LEU
Chi-restraints excluded: chain A residue  942 ASP
Chi-restraints excluded: chain A residue  968 GLN
Chi-restraints excluded: chain A residue 1013 LEU
Chi-restraints excluded: chain A residue 1077 LEU
Chi-restraints excluded: chain A residue 1263 LYS
Chi-restraints excluded: chain A residue 1433 ASN
Chi-restraints excluded: chain B residue  141 GLN
Chi-restraints excluded: chain B residue  212 THR
Chi-restraints excluded: chain B residue  280 TYR
Chi-restraints excluded: chain B residue  351 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 60 optimal weight:    4.9990
   chunk 105 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9980
   chunk 40 optimal weight:    0.0470
   chunk 99 optimal weight:    0.8980
   chunk 59 optimal weight:    0.8980
   chunk 57 optimal weight:    0.7980
   chunk 130 optimal weight:    3.9990
   chunk 4 optimal weight:    2.9990
   chunk 124 optimal weight:    5.9990
   chunk 90 optimal weight:    0.8980
   overall best weight:    0.6878

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

Flipped N/Q/H residues before XYZ refinement:
** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.132425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.099228 restraints weight = 20214.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.099026 restraints weight = 16773.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.099907 restraints weight = 15247.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.100456 restraints weight = 10736.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.100580 restraints weight = 10135.411|
|-----------------------------------------------------------------------------|
r_work (final): 0.3503
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7447
moved from start:          0.2432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  12360  Z= 0.133
  Angle     :  0.632   7.601  16774  Z= 0.326
  Chirality :  0.045   0.190   1865
  Planarity :  0.004   0.041   2123
  Dihedral  :  8.841 175.029   1735
  Min Nonbonded Distance : 2.161

Molprobity Statistics.
  All-atom Clashscore : 10.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.10 %
    Favored  : 91.90 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  :  9.83 %
    Favored  : 87.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -3.66 (0.20), residues: 1494
  helix: -1.69 (0.21), residues: 527
  sheet: -2.92 (0.40), residues: 142
  loop : -2.93 (0.19), residues: 825

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 765 
 TYR   0.024   0.002   TYR A1040 
 PHE   0.019   0.002   PHE A1399 
 TRP   0.014   0.002   TRP A 986 
 HIS   0.005   0.001   HIS A 899 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 (12353)
  covalent geometry    : angle       0.62346 (16761)
  SS BOND              : bond        0.00171 (    2)
  SS BOND              : angle       1.59347 (    4)
  hydrogen bonds       : bond        0.03073 (  327)
  hydrogen bonds       : angle       5.37871 (  912)
  Misc. bond           : bond        0.00136 (    2)
  link_BETA1-4         : bond        0.00563 (    2)
  link_BETA1-4         : angle       3.95776 (    6)
  link_NAG-ASN         : bond        0.00806 (    1)
  link_NAG-ASN         : angle       5.45983 (    3)

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

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

  2988 Ramachandran restraints generated.
    1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2988 Ramachandran restraints generated.
    1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 99
  time to evaluate  : 0.435 
Fit side-chains
   revert: symmetry clash
REVERT: A  200 LYS cc_start: 0.4882 (pttm) cc_final: 0.4628 (mtpt)
REVERT: A  224 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7524 (tp)
REVERT: A  267 VAL cc_start: 0.7354 (OUTLIER) cc_final: 0.7049 (t)
REVERT: A  477 ASN cc_start: 0.7648 (t0) cc_final: 0.7098 (t0)
REVERT: A  482 GLN cc_start: 0.6509 (pm20) cc_final: 0.6193 (mp10)
REVERT: A  771 MET cc_start: 0.7962 (mmt) cc_final: 0.7569 (mmt)
REVERT: A  827 MET cc_start: 0.8347 (ppp) cc_final: 0.8036 (ppp)
REVERT: A  852 ILE cc_start: 0.7291 (OUTLIER) cc_final: 0.6809 (mt)
REVERT: A 1263 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.7832 (tmtt)
REVERT: A 1306 ASP cc_start: 0.6636 (OUTLIER) cc_final: 0.6264 (p0)
  outliers start: 39
  outliers final: 24
  residues processed: 128
  average time/residue: 0.0878
  time to fit residues: 17.8079
Evaluate side-chains
  118 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 89
  time to evaluate  : 0.515 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  234 ILE
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  267 VAL
Chi-restraints excluded: chain A residue  279 ILE
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  501 THR
Chi-restraints excluded: chain A residue  604 VAL
Chi-restraints excluded: chain A residue  613 VAL
Chi-restraints excluded: chain A residue  676 VAL
Chi-restraints excluded: chain A residue  730 LEU
Chi-restraints excluded: chain A residue  776 LEU
Chi-restraints excluded: chain A residue  807 THR
Chi-restraints excluded: chain A residue  811 VAL
Chi-restraints excluded: chain A residue  836 ILE
Chi-restraints excluded: chain A residue  852 ILE
Chi-restraints excluded: chain A residue  963 ILE
Chi-restraints excluded: chain A residue 1005 LEU
Chi-restraints excluded: chain A residue 1013 LEU
Chi-restraints excluded: chain A residue 1263 LYS
Chi-restraints excluded: chain A residue 1306 ASP
Chi-restraints excluded: chain A residue 1355 ILE
Chi-restraints excluded: chain A residue 1433 ASN
Chi-restraints excluded: chain B residue  110 CYS
Chi-restraints excluded: chain B residue  141 GLN
Chi-restraints excluded: chain B residue  169 MET
Chi-restraints excluded: chain B residue  212 THR
Chi-restraints excluded: chain B residue  280 TYR
Chi-restraints excluded: chain B residue  351 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 9 optimal weight:    5.9990
   chunk 114 optimal weight:    5.9990
   chunk 116 optimal weight:    0.9990
   chunk 115 optimal weight:    0.9980
   chunk 0 optimal weight:    8.9990
   chunk 91 optimal weight:    2.9990
   chunk 108 optimal weight:    0.9980
   chunk 102 optimal weight:    1.9990
   chunk 89 optimal weight:    0.6980
   chunk 56 optimal weight:    3.9990
   chunk 4 optimal weight:    3.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1165 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.130513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.096350 restraints weight = 20592.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.097861 restraints weight = 17475.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.098564 restraints weight = 14339.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.098545 restraints weight = 10476.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.098646 restraints weight = 10077.851|
|-----------------------------------------------------------------------------|
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7498
moved from start:          0.2617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059  12360  Z= 0.174
  Angle     :  0.657   8.397  16774  Z= 0.336
  Chirality :  0.046   0.197   1865
  Planarity :  0.004   0.041   2123
  Dihedral  :  8.604 175.219   1733
  Min Nonbonded Distance : 2.153

Molprobity Statistics.
  All-atom Clashscore : 10.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.77 %
    Favored  : 91.23 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 10.75 %
    Favored  : 85.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -3.44 (0.20), residues: 1494
  helix: -1.45 (0.22), residues: 528
  sheet: -2.81 (0.43), residues: 134
  loop : -2.85 (0.19), residues: 832

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1178 
 TYR   0.022   0.002   TYR A1040 
 PHE   0.019   0.002   PHE A1399 
 TRP   0.017   0.002   TRP A 986 
 HIS   0.006   0.001   HIS A 899 

Details of bonding type rmsd
  covalent geometry    : bond        0.00404 (12353)
  covalent geometry    : angle       0.64917 (16761)
  SS BOND              : bond        0.00272 (    2)
  SS BOND              : angle       1.44213 (    4)
  hydrogen bonds       : bond        0.03068 (  327)
  hydrogen bonds       : angle       5.25988 (  912)
  Misc. bond           : bond        0.00226 (    2)
  link_BETA1-4         : bond        0.00593 (    2)
  link_BETA1-4         : angle       3.95211 (    6)
  link_NAG-ASN         : bond        0.01079 (    1)
  link_NAG-ASN         : angle       5.26679 (    3)

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

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

  2988 Ramachandran restraints generated.
    1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2988 Ramachandran restraints generated.
    1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 96
  time to evaluate  : 0.438 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  200 LYS cc_start: 0.4893 (pttm) cc_final: 0.4507 (mtpt)
REVERT: A  267 VAL cc_start: 0.7436 (OUTLIER) cc_final: 0.7132 (t)
REVERT: A  477 ASN cc_start: 0.7609 (t0) cc_final: 0.6971 (t0)
REVERT: A  482 GLN cc_start: 0.6447 (pm20) cc_final: 0.6115 (mp10)
REVERT: A  827 MET cc_start: 0.8301 (ppp) cc_final: 0.7945 (ppp)
REVERT: A  852 ILE cc_start: 0.7369 (OUTLIER) cc_final: 0.7011 (mt)
REVERT: A 1263 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.8018 (tmtt)
REVERT: A 1306 ASP cc_start: 0.6727 (OUTLIER) cc_final: 0.6381 (p0)
  outliers start: 46
  outliers final: 33
  residues processed: 133
  average time/residue: 0.0959
  time to fit residues: 19.6588
Evaluate side-chains
  124 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 87
  time to evaluate  : 0.476 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  234 ILE
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  267 VAL
Chi-restraints excluded: chain A residue  279 ILE
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  501 THR
Chi-restraints excluded: chain A residue  554 VAL
Chi-restraints excluded: chain A residue  604 VAL
Chi-restraints excluded: chain A residue  613 VAL
Chi-restraints excluded: chain A residue  676 VAL
Chi-restraints excluded: chain A residue  730 LEU
Chi-restraints excluded: chain A residue  776 LEU
Chi-restraints excluded: chain A residue  804 LEU
Chi-restraints excluded: chain A residue  807 THR
Chi-restraints excluded: chain A residue  811 VAL
Chi-restraints excluded: chain A residue  836 ILE
Chi-restraints excluded: chain A residue  852 ILE
Chi-restraints excluded: chain A residue  963 ILE
Chi-restraints excluded: chain A residue 1005 LEU
Chi-restraints excluded: chain A residue 1013 LEU
Chi-restraints excluded: chain A residue 1126 LEU
Chi-restraints excluded: chain A residue 1128 ILE
Chi-restraints excluded: chain A residue 1263 LYS
Chi-restraints excluded: chain A residue 1306 ASP
Chi-restraints excluded: chain A residue 1344 LEU
Chi-restraints excluded: chain A residue 1355 ILE
Chi-restraints excluded: chain A residue 1384 VAL
Chi-restraints excluded: chain A residue 1433 ASN
Chi-restraints excluded: chain B residue   67 ASN
Chi-restraints excluded: chain B residue  110 CYS
Chi-restraints excluded: chain B residue  141 GLN
Chi-restraints excluded: chain B residue  169 MET
Chi-restraints excluded: chain B residue  212 THR
Chi-restraints excluded: chain B residue  280 TYR
Chi-restraints excluded: chain B residue  351 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 82 optimal weight:    0.4980
   chunk 122 optimal weight:    3.9990
   chunk 74 optimal weight:    3.9990
   chunk 47 optimal weight:    3.9990
   chunk 85 optimal weight:    3.9990
   chunk 146 optimal weight:    3.9990
   chunk 126 optimal weight:    1.9990
   chunk 121 optimal weight:    0.8980
   chunk 42 optimal weight:    0.7980
   chunk 22 optimal weight:    0.8980
   chunk 99 optimal weight:    1.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.130519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.096710 restraints weight = 20603.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.096135 restraints weight = 17596.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.097322 restraints weight = 17525.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.097390 restraints weight = 11891.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.097574 restraints weight = 11912.146|
|-----------------------------------------------------------------------------|
r_work (final): 0.3454
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7514
moved from start:          0.2769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  12360  Z= 0.160
  Angle     :  0.648   8.994  16774  Z= 0.330
  Chirality :  0.046   0.188   1865
  Planarity :  0.003   0.041   2123
  Dihedral  :  8.501 176.642   1733
  Min Nonbonded Distance : 2.129

Molprobity Statistics.
  All-atom Clashscore : 10.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.63 %
    Favored  : 91.37 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 11.52 %
    Favored  : 84.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -3.27 (0.20), residues: 1494
  helix: -1.25 (0.22), residues: 527
  sheet: -2.78 (0.42), residues: 146
  loop : -2.77 (0.20), residues: 821

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 765 
 TYR   0.023   0.002   TYR A1040 
 PHE   0.021   0.002   PHE A1399 
 TRP   0.014   0.001   TRP A 986 
 HIS   0.005   0.001   HIS A 899 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 (12353)
  covalent geometry    : angle       0.64000 (16761)
  SS BOND              : bond        0.00340 (    2)
  SS BOND              : angle       1.42751 (    4)
  hydrogen bonds       : bond        0.02924 (  327)
  hydrogen bonds       : angle       5.13316 (  912)
  Misc. bond           : bond        0.00179 (    2)
  link_BETA1-4         : bond        0.00508 (    2)
  link_BETA1-4         : angle       3.83569 (    6)
  link_NAG-ASN         : bond        0.00967 (    1)
  link_NAG-ASN         : angle       5.29058 (    3)

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

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

  2988 Ramachandran restraints generated.
    1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2988 Ramachandran restraints generated.
    1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 100
  time to evaluate  : 0.371 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  200 LYS cc_start: 0.5191 (pttm) cc_final: 0.4696 (mtpt)
REVERT: A  267 VAL cc_start: 0.7507 (OUTLIER) cc_final: 0.7193 (t)
REVERT: A  477 ASN cc_start: 0.7573 (t0) cc_final: 0.6940 (t0)
REVERT: A  482 GLN cc_start: 0.6444 (pm20) cc_final: 0.6143 (mp10)
REVERT: A  679 PHE cc_start: 0.6563 (t80) cc_final: 0.6286 (t80)
REVERT: A  827 MET cc_start: 0.8286 (ppp) cc_final: 0.7955 (ppp)
REVERT: A  852 ILE cc_start: 0.7322 (OUTLIER) cc_final: 0.6841 (mt)
REVERT: A 1263 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.8051 (tmtt)
REVERT: A 1306 ASP cc_start: 0.6684 (OUTLIER) cc_final: 0.6371 (p0)
REVERT: B  127 GLN cc_start: 0.7487 (OUTLIER) cc_final: 0.7027 (mp10)
  outliers start: 47
  outliers final: 38
  residues processed: 138
  average time/residue: 0.0927
  time to fit residues: 19.7262
Evaluate side-chains
  135 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 92
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  234 ILE
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  267 VAL
Chi-restraints excluded: chain A residue  279 ILE
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  501 THR
Chi-restraints excluded: chain A residue  554 VAL
Chi-restraints excluded: chain A residue  604 VAL
Chi-restraints excluded: chain A residue  613 VAL
Chi-restraints excluded: chain A residue  730 LEU
Chi-restraints excluded: chain A residue  776 LEU
Chi-restraints excluded: chain A residue  804 LEU
Chi-restraints excluded: chain A residue  807 THR
Chi-restraints excluded: chain A residue  811 VAL
Chi-restraints excluded: chain A residue  836 ILE
Chi-restraints excluded: chain A residue  852 ILE
Chi-restraints excluded: chain A residue  963 ILE
Chi-restraints excluded: chain A residue  989 THR
Chi-restraints excluded: chain A residue 1005 LEU
Chi-restraints excluded: chain A residue 1013 LEU
Chi-restraints excluded: chain A residue 1105 VAL
Chi-restraints excluded: chain A residue 1109 GLN
Chi-restraints excluded: chain A residue 1126 LEU
Chi-restraints excluded: chain A residue 1128 ILE
Chi-restraints excluded: chain A residue 1163 ILE
Chi-restraints excluded: chain A residue 1263 LYS
Chi-restraints excluded: chain A residue 1306 ASP
Chi-restraints excluded: chain A residue 1355 ILE
Chi-restraints excluded: chain A residue 1384 VAL
Chi-restraints excluded: chain A residue 1433 ASN
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue  110 CYS
Chi-restraints excluded: chain B residue  127 GLN
Chi-restraints excluded: chain B residue  141 GLN
Chi-restraints excluded: chain B residue  169 MET
Chi-restraints excluded: chain B residue  212 THR
Chi-restraints excluded: chain B residue  280 TYR
Chi-restraints excluded: chain B residue  348 TRP
Chi-restraints excluded: chain B residue  351 LEU
Chi-restraints excluded: chain B residue  377 VAL
Chi-restraints excluded: chain B residue  409 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 59 optimal weight:    4.9990
   chunk 88 optimal weight:    0.0770
   chunk 125 optimal weight:    0.9990
   chunk 62 optimal weight:    5.9990
   chunk 137 optimal weight:    0.3980
   chunk 91 optimal weight:    1.9990
   chunk 50 optimal weight:    4.9990
   chunk 61 optimal weight:   10.0000
   chunk 95 optimal weight:    0.9990
   chunk 133 optimal weight:    4.9990
   chunk 148 optimal weight:    0.7980
   overall best weight:    0.6542

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

Flipped N/Q/H residues before XYZ refinement:
** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.131653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.098123 restraints weight = 20330.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.097186 restraints weight = 16775.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.098272 restraints weight = 17121.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.098629 restraints weight = 11391.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.098718 restraints weight = 11344.632|
|-----------------------------------------------------------------------------|
r_work (final): 0.3472
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7485
moved from start:          0.2897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  12360  Z= 0.127
  Angle     :  0.623   9.221  16774  Z= 0.316
  Chirality :  0.045   0.181   1865
  Planarity :  0.003   0.041   2123
  Dihedral  :  8.332 177.360   1733
  Min Nonbonded Distance : 2.133

Molprobity Statistics.
  All-atom Clashscore : 10.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.43 %
    Favored  : 91.57 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 11.52 %
    Favored  : 84.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -3.10 (0.21), residues: 1494
  helix: -1.07 (0.23), residues: 526
  sheet: -2.69 (0.42), residues: 146
  loop : -2.69 (0.20), residues: 822

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 909 
 TYR   0.022   0.001   TYR A1040 
 PHE   0.019   0.001   PHE A1399 
 TRP   0.012   0.001   TRP A 517 
 HIS   0.005   0.001   HIS A 899 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 (12353)
  covalent geometry    : angle       0.61461 (16761)
  SS BOND              : bond        0.00344 (    2)
  SS BOND              : angle       1.43344 (    4)
  hydrogen bonds       : bond        0.02752 (  327)
  hydrogen bonds       : angle       5.00321 (  912)
  Misc. bond           : bond        0.00135 (    2)
  link_BETA1-4         : bond        0.00435 (    2)
  link_BETA1-4         : angle       3.65167 (    6)
  link_NAG-ASN         : bond        0.00720 (    1)
  link_NAG-ASN         : angle       5.22258 (    3)

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

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

  2988 Ramachandran restraints generated.
    1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2988 Ramachandran restraints generated.
    1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 100
  time to evaluate  : 0.452 
Fit side-chains
   revert: symmetry clash
REVERT: A  200 LYS cc_start: 0.5246 (pttm) cc_final: 0.4707 (mtpt)
REVERT: A  246 PRO cc_start: 0.8146 (Cg_exo) cc_final: 0.7882 (Cg_endo)
REVERT: A  267 VAL cc_start: 0.7484 (OUTLIER) cc_final: 0.7170 (t)
REVERT: A  477 ASN cc_start: 0.7548 (t0) cc_final: 0.6893 (t0)
REVERT: A  482 GLN cc_start: 0.6269 (pm20) cc_final: 0.5958 (mp10)
REVERT: A  827 MET cc_start: 0.8301 (ppp) cc_final: 0.7945 (ppp)
REVERT: A  849 MET cc_start: 0.5402 (tpt) cc_final: 0.5180 (tpt)
REVERT: A  852 ILE cc_start: 0.7291 (OUTLIER) cc_final: 0.6902 (mt)
REVERT: A 1196 MET cc_start: 0.7485 (OUTLIER) cc_final: 0.6833 (ppp)
REVERT: A 1263 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.8052 (tmtt)
REVERT: A 1306 ASP cc_start: 0.6576 (OUTLIER) cc_final: 0.6307 (p0)
REVERT: B  127 GLN cc_start: 0.7508 (OUTLIER) cc_final: 0.7128 (mp10)
  outliers start: 52
  outliers final: 38
  residues processed: 140
  average time/residue: 0.0942
  time to fit residues: 20.4938
Evaluate side-chains
  135 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 91
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  234 ILE
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  267 VAL
Chi-restraints excluded: chain A residue  279 ILE
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  501 THR
Chi-restraints excluded: chain A residue  554 VAL
Chi-restraints excluded: chain A residue  604 VAL
Chi-restraints excluded: chain A residue  613 VAL
Chi-restraints excluded: chain A residue  676 VAL
Chi-restraints excluded: chain A residue  730 LEU
Chi-restraints excluded: chain A residue  776 LEU
Chi-restraints excluded: chain A residue  804 LEU
Chi-restraints excluded: chain A residue  807 THR
Chi-restraints excluded: chain A residue  811 VAL
Chi-restraints excluded: chain A residue  836 ILE
Chi-restraints excluded: chain A residue  852 ILE
Chi-restraints excluded: chain A residue  963 ILE
Chi-restraints excluded: chain A residue 1005 LEU
Chi-restraints excluded: chain A residue 1013 LEU
Chi-restraints excluded: chain A residue 1105 VAL
Chi-restraints excluded: chain A residue 1109 GLN
Chi-restraints excluded: chain A residue 1126 LEU
Chi-restraints excluded: chain A residue 1163 ILE
Chi-restraints excluded: chain A residue 1196 MET
Chi-restraints excluded: chain A residue 1263 LYS
Chi-restraints excluded: chain A residue 1306 ASP
Chi-restraints excluded: chain A residue 1344 LEU
Chi-restraints excluded: chain A residue 1381 VAL
Chi-restraints excluded: chain A residue 1384 VAL
Chi-restraints excluded: chain A residue 1433 ASN
Chi-restraints excluded: chain B residue   67 ASN
Chi-restraints excluded: chain B residue  110 CYS
Chi-restraints excluded: chain B residue  127 GLN
Chi-restraints excluded: chain B residue  141 GLN
Chi-restraints excluded: chain B residue  169 MET
Chi-restraints excluded: chain B residue  212 THR
Chi-restraints excluded: chain B residue  280 TYR
Chi-restraints excluded: chain B residue  348 TRP
Chi-restraints excluded: chain B residue  351 LEU
Chi-restraints excluded: chain B residue  377 VAL
Chi-restraints excluded: chain B residue  409 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 18 optimal weight:    5.9990
   chunk 98 optimal weight:    0.5980
   chunk 55 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   chunk 41 optimal weight:    5.9990
   chunk 43 optimal weight:    0.6980
   chunk 126 optimal weight:    0.2980
   chunk 113 optimal weight:    3.9990
   chunk 117 optimal weight:    0.9980
   chunk 133 optimal weight:    3.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.130577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.096855 restraints weight = 20405.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.097010 restraints weight = 16784.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.097834 restraints weight = 16095.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.098127 restraints weight = 11014.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.098259 restraints weight = 10448.009|
|-----------------------------------------------------------------------------|
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7496
moved from start:          0.3031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  12360  Z= 0.150
  Angle     :  0.641   8.956  16774  Z= 0.325
  Chirality :  0.045   0.185   1865
  Planarity :  0.003   0.040   2123
  Dihedral  :  8.330 178.064   1733
  Min Nonbonded Distance : 2.136

Molprobity Statistics.
  All-atom Clashscore : 10.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.43 %
    Favored  : 91.57 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 11.75 %
    Favored  : 84.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -3.06 (0.21), residues: 1494
  helix: -1.07 (0.22), residues: 537
  sheet: -2.75 (0.42), residues: 146
  loop : -2.65 (0.20), residues: 811

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 703 
 TYR   0.020   0.002   TYR A1040 
 PHE   0.021   0.002   PHE A 679 
 TRP   0.013   0.001   TRP A 986 
 HIS   0.004   0.001   HIS A 899 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 (12353)
  covalent geometry    : angle       0.63286 (16761)
  SS BOND              : bond        0.00349 (    2)
  SS BOND              : angle       1.33294 (    4)
  hydrogen bonds       : bond        0.02805 (  327)
  hydrogen bonds       : angle       4.90230 (  912)
  Misc. bond           : bond        0.00134 (    2)
  link_BETA1-4         : bond        0.00518 (    2)
  link_BETA1-4         : angle       3.76011 (    6)
  link_NAG-ASN         : bond        0.00880 (    1)
  link_NAG-ASN         : angle       5.06023 (    3)

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

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

  2988 Ramachandran restraints generated.
    1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2988 Ramachandran restraints generated.
    1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 91
  time to evaluate  : 0.499 
Fit side-chains
   revert: symmetry clash
REVERT: A  246 PRO cc_start: 0.7958 (Cg_exo) cc_final: 0.7717 (Cg_endo)
REVERT: A  267 VAL cc_start: 0.7521 (OUTLIER) cc_final: 0.7200 (t)
REVERT: A  477 ASN cc_start: 0.7564 (t0) cc_final: 0.6901 (t0)
REVERT: A  482 GLN cc_start: 0.6240 (pm20) cc_final: 0.5932 (mp10)
REVERT: A  827 MET cc_start: 0.8271 (ppp) cc_final: 0.8025 (ppp)
REVERT: A  849 MET cc_start: 0.5452 (tpt) cc_final: 0.5183 (tpt)
REVERT: A  852 ILE cc_start: 0.7316 (OUTLIER) cc_final: 0.6867 (mt)
REVERT: A 1263 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.8067 (tmtt)
REVERT: A 1306 ASP cc_start: 0.6566 (OUTLIER) cc_final: 0.6217 (p0)
  outliers start: 51
  outliers final: 39
  residues processed: 132
  average time/residue: 0.0990
  time to fit residues: 19.9722
Evaluate side-chains
  131 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 88
  time to evaluate  : 0.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  234 ILE
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  267 VAL
Chi-restraints excluded: chain A residue  279 ILE
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  501 THR
Chi-restraints excluded: chain A residue  554 VAL
Chi-restraints excluded: chain A residue  604 VAL
Chi-restraints excluded: chain A residue  613 VAL
Chi-restraints excluded: chain A residue  676 VAL
Chi-restraints excluded: chain A residue  730 LEU
Chi-restraints excluded: chain A residue  776 LEU
Chi-restraints excluded: chain A residue  807 THR
Chi-restraints excluded: chain A residue  811 VAL
Chi-restraints excluded: chain A residue  836 ILE
Chi-restraints excluded: chain A residue  852 ILE
Chi-restraints excluded: chain A residue  963 ILE
Chi-restraints excluded: chain A residue 1005 LEU
Chi-restraints excluded: chain A residue 1013 LEU
Chi-restraints excluded: chain A residue 1109 GLN
Chi-restraints excluded: chain A residue 1126 LEU
Chi-restraints excluded: chain A residue 1128 ILE
Chi-restraints excluded: chain A residue 1163 ILE
Chi-restraints excluded: chain A residue 1196 MET
Chi-restraints excluded: chain A residue 1263 LYS
Chi-restraints excluded: chain A residue 1306 ASP
Chi-restraints excluded: chain A residue 1344 LEU
Chi-restraints excluded: chain A residue 1381 VAL
Chi-restraints excluded: chain A residue 1384 VAL
Chi-restraints excluded: chain A residue 1433 ASN
Chi-restraints excluded: chain B residue   67 ASN
Chi-restraints excluded: chain B residue  110 CYS
Chi-restraints excluded: chain B residue  141 GLN
Chi-restraints excluded: chain B residue  169 MET
Chi-restraints excluded: chain B residue  212 THR
Chi-restraints excluded: chain B residue  280 TYR
Chi-restraints excluded: chain B residue  348 TRP
Chi-restraints excluded: chain B residue  351 LEU
Chi-restraints excluded: chain B residue  359 ILE
Chi-restraints excluded: chain B residue  377 VAL
Chi-restraints excluded: chain B residue  409 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 106 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 52 optimal weight:   10.0000
   chunk 51 optimal weight:    2.9990
   chunk 36 optimal weight:    3.9990
   chunk 80 optimal weight:    1.9990
   chunk 138 optimal weight:    1.9990
   chunk 14 optimal weight:    9.9990
   chunk 47 optimal weight:    0.9980
   chunk 110 optimal weight:    2.9990
   chunk 75 optimal weight:    3.9990
   overall best weight:    2.1988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.126272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.092695 restraints weight = 20711.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.092648 restraints weight = 18160.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.093364 restraints weight = 16921.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.093769 restraints weight = 12039.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.093804 restraints weight = 11293.726|
|-----------------------------------------------------------------------------|
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7604
moved from start:          0.3197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.086  12360  Z= 0.294
  Angle     :  0.783  11.758  16774  Z= 0.395
  Chirality :  0.050   0.228   1865
  Planarity :  0.004   0.040   2123
  Dihedral  :  8.735 178.966   1733
  Min Nonbonded Distance : 2.103

Molprobity Statistics.
  All-atom Clashscore : 12.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.64 %
    Favored  : 90.36 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 12.21 %
    Favored  : 84.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -3.35 (0.20), residues: 1494
  helix: -1.32 (0.21), residues: 542
  sheet: -2.79 (0.42), residues: 136
  loop : -2.84 (0.20), residues: 816

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 401 
 TYR   0.021   0.003   TYR A 693 
 PHE   0.022   0.003   PHE A1366 
 TRP   0.023   0.002   TRP A 986 
 HIS   0.005   0.002   HIS B 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00683 (12353)
  covalent geometry    : angle       0.77613 (16761)
  SS BOND              : bond        0.00208 (    2)
  SS BOND              : angle       1.16823 (    4)
  hydrogen bonds       : bond        0.03386 (  327)
  hydrogen bonds       : angle       5.16943 (  912)
  Misc. bond           : bond        0.00310 (    2)
  link_BETA1-4         : bond        0.01023 (    2)
  link_BETA1-4         : angle       4.30454 (    6)
  link_NAG-ASN         : bond        0.01642 (    1)
  link_NAG-ASN         : angle       5.01429 (    3)

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

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

  2988 Ramachandran restraints generated.
    1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2988 Ramachandran restraints generated.
    1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 87
  time to evaluate  : 0.364 
Fit side-chains
   revert: symmetry clash
REVERT: A  267 VAL cc_start: 0.7717 (OUTLIER) cc_final: 0.7433 (t)
REVERT: A  477 ASN cc_start: 0.7628 (t0) cc_final: 0.6941 (t0)
REVERT: A  827 MET cc_start: 0.8259 (ppp) cc_final: 0.8001 (ppp)
REVERT: A  849 MET cc_start: 0.5471 (tpt) cc_final: 0.5233 (tpt)
REVERT: A 1109 GLN cc_start: 0.7859 (OUTLIER) cc_final: 0.7365 (mp-120)
REVERT: A 1306 ASP cc_start: 0.6733 (OUTLIER) cc_final: 0.6451 (p0)
REVERT: B  127 GLN cc_start: 0.7491 (OUTLIER) cc_final: 0.7037 (mp10)
  outliers start: 49
  outliers final: 40
  residues processed: 126
  average time/residue: 0.0911
  time to fit residues: 17.6048
Evaluate side-chains
  125 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 81
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  234 ILE
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  267 VAL
Chi-restraints excluded: chain A residue  279 ILE
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  501 THR
Chi-restraints excluded: chain A residue  554 VAL
Chi-restraints excluded: chain A residue  604 VAL
Chi-restraints excluded: chain A residue  613 VAL
Chi-restraints excluded: chain A residue  676 VAL
Chi-restraints excluded: chain A residue  730 LEU
Chi-restraints excluded: chain A residue  776 LEU
Chi-restraints excluded: chain A residue  804 LEU
Chi-restraints excluded: chain A residue  807 THR
Chi-restraints excluded: chain A residue  811 VAL
Chi-restraints excluded: chain A residue  963 ILE
Chi-restraints excluded: chain A residue  964 GLU
Chi-restraints excluded: chain A residue  995 THR
Chi-restraints excluded: chain A residue 1005 LEU
Chi-restraints excluded: chain A residue 1013 LEU
Chi-restraints excluded: chain A residue 1109 GLN
Chi-restraints excluded: chain A residue 1113 VAL
Chi-restraints excluded: chain A residue 1126 LEU
Chi-restraints excluded: chain A residue 1128 ILE
Chi-restraints excluded: chain A residue 1163 ILE
Chi-restraints excluded: chain A residue 1196 MET
Chi-restraints excluded: chain A residue 1306 ASP
Chi-restraints excluded: chain A residue 1344 LEU
Chi-restraints excluded: chain A residue 1355 ILE
Chi-restraints excluded: chain A residue 1381 VAL
Chi-restraints excluded: chain A residue 1384 VAL
Chi-restraints excluded: chain A residue 1433 ASN
Chi-restraints excluded: chain B residue  110 CYS
Chi-restraints excluded: chain B residue  127 GLN
Chi-restraints excluded: chain B residue  141 GLN
Chi-restraints excluded: chain B residue  169 MET
Chi-restraints excluded: chain B residue  212 THR
Chi-restraints excluded: chain B residue  280 TYR
Chi-restraints excluded: chain B residue  351 LEU
Chi-restraints excluded: chain B residue  359 ILE
Chi-restraints excluded: chain B residue  377 VAL
Chi-restraints excluded: chain B residue  409 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 89 optimal weight:    0.5980
   chunk 38 optimal weight:    0.8980
   chunk 105 optimal weight:    0.6980
   chunk 56 optimal weight:   10.0000
   chunk 113 optimal weight:    0.5980
   chunk 122 optimal weight:    0.4980
   chunk 88 optimal weight:    0.2980
   chunk 93 optimal weight:    0.5980
   chunk 41 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 145 optimal weight:    0.5980
   overall best weight:    0.5180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.130776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.097394 restraints weight = 20489.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.096490 restraints weight = 16750.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.097498 restraints weight = 17498.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.097829 restraints weight = 11714.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.097959 restraints weight = 11462.483|
|-----------------------------------------------------------------------------|
r_work (final): 0.3458
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7505
moved from start:          0.3227

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  12360  Z= 0.126
  Angle     :  0.651  11.163  16774  Z= 0.326
  Chirality :  0.045   0.161   1865
  Planarity :  0.003   0.042   2123
  Dihedral  :  8.321 179.442   1733
  Min Nonbonded Distance : 2.147

Molprobity Statistics.
  All-atom Clashscore : 10.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.23 %
    Favored  : 91.77 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 13.59 %
    Favored  : 83.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -2.97 (0.21), residues: 1494
  helix: -0.97 (0.22), residues: 543
  sheet: -2.68 (0.46), residues: 125
  loop : -2.64 (0.20), residues: 826

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 703 
 TYR   0.026   0.002   TYR A 693 
 PHE   0.023   0.002   PHE A1399 
 TRP   0.013   0.001   TRP A 468 
 HIS   0.004   0.001   HIS A 899 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 (12353)
  covalent geometry    : angle       0.64356 (16761)
  SS BOND              : bond        0.00355 (    2)
  SS BOND              : angle       1.59735 (    4)
  hydrogen bonds       : bond        0.02780 (  327)
  hydrogen bonds       : angle       4.91834 (  912)
  Misc. bond           : bond        0.00200 (    2)
  link_BETA1-4         : bond        0.00202 (    2)
  link_BETA1-4         : angle       3.55284 (    6)
  link_NAG-ASN         : bond        0.00626 (    1)
  link_NAG-ASN         : angle       5.20582 (    3)

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

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

  2988 Ramachandran restraints generated.
    1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2988 Ramachandran restraints generated.
    1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 86
  time to evaluate  : 0.475 
Fit side-chains
   revert: symmetry clash
REVERT: A  246 PRO cc_start: 0.7890 (Cg_exo) cc_final: 0.7687 (Cg_endo)
REVERT: A  267 VAL cc_start: 0.7689 (OUTLIER) cc_final: 0.7378 (t)
REVERT: A  477 ASN cc_start: 0.7552 (t0) cc_final: 0.6879 (t0)
REVERT: A  827 MET cc_start: 0.8223 (ppp) cc_final: 0.7848 (ppp)
REVERT: A  849 MET cc_start: 0.5471 (tpt) cc_final: 0.5229 (tpt)
REVERT: A 1306 ASP cc_start: 0.6525 (OUTLIER) cc_final: 0.6186 (p0)
REVERT: B  127 GLN cc_start: 0.7456 (OUTLIER) cc_final: 0.6972 (mp10)
  outliers start: 38
  outliers final: 34
  residues processed: 117
  average time/residue: 0.0899
  time to fit residues: 16.1269
Evaluate side-chains
  119 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 82
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  267 VAL
Chi-restraints excluded: chain A residue  279 ILE
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  501 THR
Chi-restraints excluded: chain A residue  604 VAL
Chi-restraints excluded: chain A residue  613 VAL
Chi-restraints excluded: chain A residue  676 VAL
Chi-restraints excluded: chain A residue  730 LEU
Chi-restraints excluded: chain A residue  776 LEU
Chi-restraints excluded: chain A residue  804 LEU
Chi-restraints excluded: chain A residue  807 THR
Chi-restraints excluded: chain A residue  963 ILE
Chi-restraints excluded: chain A residue  995 THR
Chi-restraints excluded: chain A residue 1005 LEU
Chi-restraints excluded: chain A residue 1013 LEU
Chi-restraints excluded: chain A residue 1109 GLN
Chi-restraints excluded: chain A residue 1126 LEU
Chi-restraints excluded: chain A residue 1128 ILE
Chi-restraints excluded: chain A residue 1163 ILE
Chi-restraints excluded: chain A residue 1196 MET
Chi-restraints excluded: chain A residue 1306 ASP
Chi-restraints excluded: chain A residue 1344 LEU
Chi-restraints excluded: chain A residue 1381 VAL
Chi-restraints excluded: chain A residue 1384 VAL
Chi-restraints excluded: chain A residue 1433 ASN
Chi-restraints excluded: chain B residue  110 CYS
Chi-restraints excluded: chain B residue  127 GLN
Chi-restraints excluded: chain B residue  141 GLN
Chi-restraints excluded: chain B residue  169 MET
Chi-restraints excluded: chain B residue  212 THR
Chi-restraints excluded: chain B residue  280 TYR
Chi-restraints excluded: chain B residue  351 LEU
Chi-restraints excluded: chain B residue  377 VAL
Chi-restraints excluded: chain B residue  409 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 55 optimal weight:    1.9990
   chunk 70 optimal weight:    0.6980
   chunk 114 optimal weight:    0.0030
   chunk 84 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 28 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9980
   chunk 16 optimal weight:    4.9990
   chunk 123 optimal weight:    0.0770
   chunk 62 optimal weight:    6.9990
   chunk 72 optimal weight:   10.0000
   overall best weight:    0.7550

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

Flipped N/Q/H residues before XYZ refinement:
** A 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.130495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.097035 restraints weight = 20592.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.096699 restraints weight = 17216.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.097767 restraints weight = 16721.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.097817 restraints weight = 11393.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.097974 restraints weight = 11519.684|
|-----------------------------------------------------------------------------|
r_work (final): 0.3457
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7506
moved from start:          0.3276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  12360  Z= 0.140
  Angle     :  0.650   9.729  16774  Z= 0.327
  Chirality :  0.045   0.174   1865
  Planarity :  0.003   0.042   2123
  Dihedral  :  8.263 178.450   1733
  Min Nonbonded Distance : 2.168

Molprobity Statistics.
  All-atom Clashscore : 11.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.70 %
    Favored  : 91.30 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 13.90 %
    Favored  : 83.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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: -2.89 (0.21), residues: 1494
  helix: -0.84 (0.23), residues: 535
  sheet: -2.62 (0.46), residues: 125
  loop : -2.62 (0.20), residues: 834

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 703 
 TYR   0.024   0.002   TYR A 693 
 PHE   0.023   0.002   PHE A1399 
 TRP   0.012   0.001   TRP A 517 
 HIS   0.004   0.001   HIS A 899 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 (12353)
  covalent geometry    : angle       0.64287 (16761)
  SS BOND              : bond        0.00308 (    2)
  SS BOND              : angle       1.40852 (    4)
  hydrogen bonds       : bond        0.02808 (  327)
  hydrogen bonds       : angle       4.87070 (  912)
  Misc. bond           : bond        0.00189 (    2)
  link_BETA1-4         : bond        0.00396 (    2)
  link_BETA1-4         : angle       3.63732 (    6)
  link_NAG-ASN         : bond        0.00820 (    1)
  link_NAG-ASN         : angle       5.09371 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1762.01 seconds
wall clock time: 31 minutes 20.87 seconds (1880.87 seconds total)