Starting phenix.real_space_refine
on Wed Mar  4 08:53:17 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7whw_32513/03_2026/7whw_32513.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7whw_32513/03_2026/7whw_32513.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7whw_32513/03_2026/7whw_32513.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7whw_32513/03_2026/7whw_32513.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7whw_32513/03_2026/7whw_32513.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7whw_32513/03_2026/7whw_32513.cif"
  }
  resolution = 3.1
  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=   0.003
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    7706      2.51       5
     N    1987      2.21       5
     O    2224      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 50 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: 11978
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 8973
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1126, 8973
          Classifications: {'peptide': 1126}
          Link IDs: {'PTRANS': 35, 'TRANS': 1090}
          Chain breaks: 2
    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: 2.60, per 1000 atoms: 0.22
  Number of scatterers: 11978
  At special positions: 0
  Unit cell: (136.96, 109.14, 129.47, 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    2224      8.00
     N    1987      7.00
     C    7706      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=2.02
    Simple disulfide: pdb=" SG  CYS B 216 " - pdb=" SG  CYS B 231 " distance=2.02

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG C   2 " - " BMA C   3 "
    NAG-ASN
      " NAG C   1 " - " ASN B 240 "
  Time building additional restraints: 0.99
  Conformation dependent library (CDL) restraints added in 572.0 milliseconds
  

  2960 Ramachandran restraints generated.
    1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2782

  Finding SS restraints...
    Secondary structure from input PDB file:
      55 helices and 13 sheets defined
      41.3% alpha, 7.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.44
  Creating SS restraints...
    Processing helix  chain 'A' and resid 205 through 215
      removed outlier: 4.140A  pdb=" N   LYS A 209 " --> pdb=" O   THR A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 232
      removed outlier: 3.938A  pdb=" N   PHE A 223 " --> pdb=" O   ALA A 219 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   LEU A 224 " --> pdb=" O   ASN A 220 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   PHE A 232 " --> pdb=" O   ILE A 228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 236
    Processing helix  chain 'A' and resid 241 through 243
      No H-bonds generated for 'chain 'A' and resid 241 through 243'
    Processing helix  chain 'A' and resid 244 through 275
      removed outlier: 4.291A  pdb=" N   ILE A 250 " --> pdb=" O   PRO A 246 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   ARG A 265 " --> pdb=" O   GLU A 261 " (cutoff:3.500A)
      removed outlier: 4.633A  pdb=" N   LEU A 268 " --> pdb=" O   ARG A 264 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   ASP A 269 " --> pdb=" O   ARG A 265 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   VAL A 272 " --> pdb=" O   LEU A 268 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ASN A 274 " --> pdb=" O   LEU A 270 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   THR A 275 " --> pdb=" O   GLU A 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 461 through 465
      removed outlier: 3.505A  pdb=" N   ARG A 464 " --> pdb=" O   ASP A 461 " (cutoff:3.500A)
      removed outlier: 3.622A  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 544 through 576
      removed outlier: 4.836A  pdb=" N   ASN A 550 " --> pdb=" O   SER A 546 " (cutoff:3.500A)
      removed outlier: 4.634A  pdb=" N   PHE A 551 " --> pdb=" O   ARG A 547 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   SER A 552 " --> pdb=" O   GLU A 548 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   VAL A 554 " --> pdb=" O   ASN A 550 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   TYR A 574 " --> pdb=" O   ALA A 570 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ASP A 576 " --> pdb=" O   GLY A 572 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 595 through 609
      removed outlier: 3.702A  pdb=" N   TRP A 603 " --> pdb=" O   PHE A 599 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 617 through 634
    Processing helix  chain 'A' and resid 654 through 660
    Processing helix  chain 'A' and resid 695 through 703
      removed outlier: 4.050A  pdb=" N   GLY A 699 " --> pdb=" O   ALA A 696 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   LEU A 700 " --> pdb=" O   LEU A 697 " (cutoff:3.500A)
      removed outlier: 5.144A  pdb=" N   ARG A 701 " --> pdb=" O   ALA A 698 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   LYS A 702 " --> pdb=" O   GLY A 699 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   ARG A 703 " --> pdb=" O   LEU A 700 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 708 through 719
      removed outlier: 3.631A  pdb=" N   GLU A 715 " --> pdb=" O   GLU A 711 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 761 through 777
      removed outlier: 4.214A  pdb=" N   ARG A 765 " --> pdb=" O   GLU A 761 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   GLU A 768 " --> pdb=" O   GLN A 764 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 798 through 812
      removed outlier: 3.569A  pdb=" N   ALA A 803 " --> pdb=" O   PRO A 799 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   LEU A 804 " --> pdb=" O   ASP A 800 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   VAL A 805 " --> pdb=" O   GLU A 801 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   ASP A 810 " --> pdb=" O   ALA A 806 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 876 through 880
    Processing helix  chain 'A' and resid 892 through 903
      removed outlier: 3.969A  pdb=" N   LEU A 898 " --> pdb=" O   GLU A 894 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 919 through 933
      removed outlier: 5.439A  pdb=" N   LYS A 925 " --> pdb=" O   SER A 921 " (cutoff:3.500A)
      removed outlier: 4.163A  pdb=" N   TRP A 926 " --> pdb=" O   GLU A 922 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 934 through 935
      No H-bonds generated for 'chain 'A' and resid 934 through 935'
    Processing helix  chain 'A' and resid 936 through 941
      removed outlier: 3.950A  pdb=" N   ASN A 939 " --> pdb=" O   SER A 936 " (cutoff:3.500A)
      removed outlier: 4.563A  pdb=" N   ARG A 940 " --> pdb=" O   LEU A 937 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 942 through 948
      removed outlier: 4.187A  pdb=" N   VAL A 946 " --> pdb=" O   ASP A 942 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   VAL A 947 " --> pdb=" O   GLU A 943 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 970 through 975
      removed outlier: 3.838A  pdb=" N   CYS A 974 " --> pdb=" O   GLY A 970 " (cutoff:3.500A)
      removed outlier: 4.492A  pdb=" N   ILE A 975 " --> pdb=" O   VAL A 971 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 970 through 975'
    Processing helix  chain 'A' and resid 992 through 1001
    Processing helix  chain 'A' and resid 1034 through 1044
      removed outlier: 3.683A  pdb=" N   SER A1038 " --> pdb=" O   ASP A1034 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   LYS A1039 " --> pdb=" O   ALA A1035 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   TYR A1040 " --> pdb=" O   LEU A1036 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   LEU A1041 " --> pdb=" O   LEU A1037 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   LYS A1042 " --> pdb=" O   SER A1038 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1056 through 1060
    Processing helix  chain 'A' and resid 1073 through 1081
    Processing helix  chain 'A' and resid 1086 through 1094
      removed outlier: 3.674A  pdb=" N   LEU A1093 " --> pdb=" O   LYS A1089 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1107 through 1121
    Processing helix  chain 'A' and resid 1131 through 1135
      removed outlier: 3.831A  pdb=" N   VAL A1135 " --> pdb=" O   SER A1132 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1136 through 1141
    Processing helix  chain 'A' and resid 1153 through 1158
      removed outlier: 3.614A  pdb=" N   MET A1157 " --> pdb=" O   ARG A1153 " (cutoff:3.500A)
    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 1175 through 1200
      Proline residue:  A1189  - end of helix
      removed outlier: 3.514A  pdb=" N   ASN A1195 " --> pdb=" O   PHE A1191 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   PHE A1198 " --> pdb=" O   LYS A1194 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1203 through 1208
      removed outlier: 3.614A  pdb=" N   ILE A1207 " --> pdb=" O   TRP A1204 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1230 through 1240
      removed outlier: 4.433A  pdb=" N   VAL A1234 " --> pdb=" O   THR A1230 " (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: 3.570A  pdb=" N   ILE A1260 " --> pdb=" O   TYR A1256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1266 through 1293
      Proline residue:  A1288  - end of helix
    Processing helix  chain 'A' and resid 1307 through 1329
    Processing helix  chain 'A' and resid 1335 through 1347
    Processing helix  chain 'A' and resid 1347 through 1357
      removed outlier: 4.016A  pdb=" N   THR A1353 " --> pdb=" O   VAL A1349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1367 through 1373
      removed outlier: 3.552A  pdb=" N   ARG A1371 " --> pdb=" O   LYS A1367 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1375 through 1383
      removed outlier: 3.844A  pdb=" N   TRP A1379 " --> pdb=" O   ALA A1375 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1386 through 1404
      Proline residue:  A1392  - end of helix
    Processing helix  chain 'A' and resid 1406 through 1417
      removed outlier: 3.625A  pdb=" N   HIS A1417 " --> pdb=" O   GLU A1413 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 71 through 98
      removed outlier: 3.535A  pdb=" N   LEU B  76 " --> pdb=" O   PRO B  72 " (cutoff:3.500A)
      Proline residue:  B  77  - end of helix
      removed outlier: 3.561A  pdb=" N   ILE B  88 " --> pdb=" O   VAL B  84 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   LEU B  94 " --> pdb=" O   GLY B  90 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 109 through 114
      removed outlier: 3.599A  pdb=" N   ALA B 114 " --> pdb=" O   CYS B 110 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 186 through 191
      removed outlier: 3.763A  pdb=" N   LEU B 191 " --> pdb=" O   ARG B 187 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 194 through 199
    Processing helix  chain 'B' and resid 205 through 210
    Processing helix  chain 'B' and resid 232 through 237
    Processing helix  chain 'B' and resid 266 through 272
      removed outlier: 3.529A  pdb=" N   ARG B 272 " --> pdb=" O   ASP B 269 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 308 through 315
    Processing helix  chain 'B' and resid 372 through 395
    Processing sheet with id=AA1, first strand: chain 'A' and resid 406 through 409
      removed outlier: 3.562A  pdb=" N   GLY A 520 " --> pdb=" O   VAL A 407 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 445 through 448
    Processing sheet with id=AA3, first strand: chain 'A' and resid 485 through 488
      removed outlier: 4.417A  pdb=" N   MET A 485 " --> pdb=" O   GLU A 498 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   GLU A 498 " --> pdb=" O   MET A 485 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   TRP A 487 " --> pdb=" O   ARG A 496 " (cutoff:3.500A)
      removed outlier: 4.171A  pdb=" N   ARG A 496 " --> pdb=" O   TRP A 487 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 663 through 664
      removed outlier: 6.189A  pdb=" N   ILE A 664 " --> pdb=" O   TRP A 986 " (cutoff:3.500A)
      removed outlier: 7.263A  pdb=" N   LEU A 985 " --> pdb=" O   VAL A1100 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 682 through 684
    Processing sheet with id=AA6, first strand: chain 'A' and resid 781 through 783
      removed outlier: 3.504A  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 817
      removed outlier: 6.920A  pdb=" N   ILE A 824 " --> pdb=" O   VAL A 816 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 848 through 851
      removed outlier: 5.865A  pdb=" N   GLN A 915 " --> pdb=" O   LEU A 957 " (cutoff:3.500A)
      removed outlier: 4.918A  pdb=" N   LEU A 957 " --> pdb=" O   GLN A 915 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 1012 through 1013
    Processing sheet with id=AB1, first strand: chain 'A' and resid 1145 through 1147
      removed outlier: 6.306A  pdb=" N   GLY A1146 " --> pdb=" O   ILE A1163 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'B' and resid 126 through 129
      removed outlier: 6.032A  pdb=" N   TYR B 177 " --> pdb=" O   LEU B 326 " (cutoff:3.500A)
      removed outlier: 5.935A  pdb=" N   LEU B 326 " --> pdb=" O   TYR B 177 " (cutoff:3.500A)
      removed outlier: 7.416A  pdb=" N   LEU B 179 " --> pdb=" O   THR B 324 " (cutoff:3.500A)
      removed outlier: 5.552A  pdb=" N   THR B 324 " --> pdb=" O   LEU B 179 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 119 through 120
      removed outlier: 5.628A  pdb=" N   ASP B 343 " --> pdb=" O   GLN B 246 " (cutoff:3.500A)
      removed outlier: 7.997A  pdb=" N   GLN B 246 " --> pdb=" O   ASP B 343 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 227 through 228
      removed outlier: 6.341A  pdb=" N   ILE B 227 " --> pdb=" O   ALA B 284 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4

    409 hydrogen bonds defined for protein.
    1125 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.31

  Time building geometry restraints manager: 1.34 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2962
        1.33 -     1.45: 2814
        1.45 -     1.58: 6390
        1.58 -     1.70: 6
        1.70 -     1.82: 86
  Bond restraints: 12258
  Sorted by residual:
  bond pdb=" O2B ACP A1601 "
       pdb=" PB  ACP A1601 "
    ideal  model  delta    sigma   weight residual
    1.507  1.605 -0.098 2.00e-02 2.50e+03 2.42e+01
  bond pdb=" O3A ACP A1601 "
       pdb=" PB  ACP A1601 "
    ideal  model  delta    sigma   weight residual
    1.698  1.603  0.095 2.00e-02 2.50e+03 2.28e+01
  bond pdb=" C4  ACP A1601 "
       pdb=" C5  ACP A1601 "
    ideal  model  delta    sigma   weight residual
    1.386  1.465 -0.079 2.00e-02 2.50e+03 1.58e+01
  bond pdb=" O3G ACP A1601 "
       pdb=" PG  ACP A1601 "
    ideal  model  delta    sigma   weight residual
    1.532  1.608 -0.076 2.00e-02 2.50e+03 1.45e+01
  bond pdb=" C5  ACP A1601 "
       pdb=" C6  ACP A1601 "
    ideal  model  delta    sigma   weight residual
    1.407  1.479 -0.072 2.00e-02 2.50e+03 1.30e+01
  ... (remaining 12253 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.00: 16156
        3.00 -     6.00: 403
        6.00 -     9.00: 61
        9.00 -    12.00: 11
       12.00 -    15.00: 3
  Bond angle restraints: 16634
  Sorted by residual:
  angle pdb=" N   ILE A1086 "
        pdb=" CA  ILE A1086 "
        pdb=" C   ILE A1086 "
      ideal   model   delta    sigma   weight residual
     113.53  107.28    6.25 9.80e-01 1.04e+00 4.07e+01
  angle pdb=" CA  ARG A1333 "
        pdb=" CB  ARG A1333 "
        pdb=" CG  ARG A1333 "
      ideal   model   delta    sigma   weight residual
     114.10  124.64  -10.54 2.00e+00 2.50e-01 2.78e+01
  angle pdb=" C   LEU A1101 "
        pdb=" N   CYS A1102 "
        pdb=" CA  CYS A1102 "
      ideal   model   delta    sigma   weight residual
     122.21  114.02    8.19 1.62e+00 3.81e-01 2.56e+01
  angle pdb=" N   LEU A1101 "
        pdb=" CA  LEU A1101 "
        pdb=" C   LEU A1101 "
      ideal   model   delta    sigma   weight residual
     112.13  119.02   -6.89 1.37e+00 5.33e-01 2.53e+01
  angle pdb=" C   ASN B 240 "
        pdb=" CA  ASN B 240 "
        pdb=" CB  ASN B 240 "
      ideal   model   delta    sigma   weight residual
     110.90  103.68    7.22 1.58e+00 4.01e-01 2.09e+01
  ... (remaining 16629 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.61: 7121
       28.61 -    57.21: 174
       57.21 -    85.82: 14
       85.82 -   114.43: 5
      114.43 -   143.03: 1
  Dihedral angle restraints: 7315
    sinusoidal: 2977
      harmonic: 4338
  Sorted by residual:
  dihedral pdb=" CA  TYR A1219 "
           pdb=" C   TYR A1219 "
           pdb=" N   THR A1220 "
           pdb=" CA  THR A1220 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  134.93   45.07     0      5.00e+00 4.00e-02 8.12e+01
  dihedral pdb=" CA  VAL A1100 "
           pdb=" C   VAL A1100 "
           pdb=" N   LEU A1101 "
           pdb=" CA  LEU A1101 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -141.67  -38.33     0      5.00e+00 4.00e-02 5.88e+01
  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 -143.79  -36.21     0      5.00e+00 4.00e-02 5.24e+01
  ... (remaining 7312 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.070: 1393
       0.070 -    0.139: 389
       0.139 -    0.209: 50
       0.209 -    0.278: 17
       0.278 -    0.348: 3
  Chirality restraints: 1852
  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    2.30    0.35 2.00e-01 2.50e+01 3.02e+00
  chirality pdb=" CA  ARG A1333 "
            pdb=" N   ARG A1333 "
            pdb=" C   ARG A1333 "
            pdb=" CB  ARG A1333 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.32e+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 2.28e+00
  ... (remaining 1849 not shown)

  Planarity restraints: 2107
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE B 398 "    0.031 2.00e-02 2.50e+03   6.09e-02 3.70e+01
        pdb=" C   PHE B 398 "   -0.105 2.00e-02 2.50e+03
        pdb=" O   PHE B 398 "    0.039 2.00e-02 2.50e+03
        pdb=" N   GLY B 399 "    0.035 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A1408 "    0.028 2.00e-02 2.50e+03   5.36e-02 2.87e+01
        pdb=" C   VAL A1408 "   -0.093 2.00e-02 2.50e+03
        pdb=" O   VAL A1408 "    0.034 2.00e-02 2.50e+03
        pdb=" N   GLU A1409 "    0.031 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 142 "    0.029 2.00e-02 2.50e+03   3.24e-02 2.62e+01
        pdb=" CG  TRP B 142 "   -0.083 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 142 "    0.048 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 142 "   -0.010 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 142 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 142 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 142 "    0.011 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 142 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 142 "    0.012 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 142 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 2104 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 221
        2.67 -     3.22: 11166
        3.22 -     3.78: 19714
        3.78 -     4.34: 26724
        4.34 -     4.90: 42883
  Nonbonded interactions: 100708
  Sorted by model distance:
  nonbonded pdb=" O3G ACP A1601 "
            pdb="MG    MG A1602 "
     model   vdw
     2.107 2.170
  nonbonded pdb=" O   THR A 669 "
            pdb=" OG1 THR A 673 "
     model   vdw
     2.220 3.040
  nonbonded pdb=" OH  TYR A1193 "
            pdb=" OE1 GLN A1280 "
     model   vdw
     2.220 3.040
  nonbonded pdb=" O   THR A1353 "
            pdb=" OG  SER A1357 "
     model   vdw
     2.251 3.040
  nonbonded pdb=" OG  SER A1106 "
            pdb=" OE1 GLN A1109 "
     model   vdw
     2.273 3.040
  ... (remaining 100703 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.820
  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:          0.170
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     12.470
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.440
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7385
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      :  0.009   0.098  12263  Z= 0.400
  Angle     :  1.177  15.106  16647  Z= 0.624
  Chirality :  0.067   0.348   1852
  Planarity :  0.007   0.061   2106
  Dihedral  : 12.722 143.034   4527
  Min Nonbonded Distance : 2.107

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  8.38 %
    Favored  : 91.55 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  :  3.79 %
    Favored  : 95.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.35 %

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: -5.16 (0.16), residues: 1480
  helix: -4.19 (0.10), residues: 558
  sheet: -2.77 (0.35), residues: 165
  loop : -2.93 (0.19), residues: 757

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.021   0.001   ARG A1104 
 TYR   0.053   0.004   TYR A1217 
 PHE   0.051   0.004   PHE B 243 
 TRP   0.083   0.005   TRP B 142 
 HIS   0.013   0.002   HIS B 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00931 (12258)
  covalent geometry    : angle       1.16567 (16634)
  SS BOND              : bond        0.01163 (    2)
  SS BOND              : angle       1.91428 (    4)
  hydrogen bonds       : bond        0.26942 (  409)
  hydrogen bonds       : angle      11.01811 ( 1125)
  link_BETA1-4         : bond        0.01346 (    2)
  link_BETA1-4         : angle       7.02035 (    6)
  link_NAG-ASN         : bond        0.03246 (    1)
  link_NAG-ASN         : angle       7.14874 (    3)

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

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

  2960 Ramachandran restraints generated.
    1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2960 Ramachandran restraints generated.
    1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 227
  time to evaluate  : 0.439 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  263 SER cc_start: 0.6782 (t) cc_final: 0.6492 (p)
REVERT: A  265 ARG cc_start: 0.6690 (tpt-90) cc_final: 0.6443 (tpt-90)
REVERT: A  485 MET cc_start: -0.0067 (ppp) cc_final: -0.0306 (ttp)
REVERT: A  532 MET cc_start: 0.1316 (mtt) cc_final: 0.0144 (tpp)
REVERT: A  561 PHE cc_start: 0.7455 (m-80) cc_final: 0.6765 (t80)
REVERT: A  562 ILE cc_start: 0.8525 (mm) cc_final: 0.8299 (mt)
REVERT: A  903 TYR cc_start: 0.6586 (m-10) cc_final: 0.6327 (m-10)
REVERT: A  906 GLU cc_start: 0.6525 (pt0) cc_final: 0.6232 (pt0)
REVERT: A 1006 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7913 (pp)
REVERT: A 1044 TYR cc_start: 0.7883 (m-80) cc_final: 0.7667 (m-80)
REVERT: A 1068 TYR cc_start: 0.8119 (m-80) cc_final: 0.7806 (m-10)
REVERT: A 1088 ARG cc_start: 0.7890 (mtm-85) cc_final: 0.7665 (mtp180)
REVERT: A 1196 MET cc_start: 0.8197 (tpp) cc_final: 0.7988 (mmm)
REVERT: B  188 ARG cc_start: 0.7343 (ttt180) cc_final: 0.6852 (ttp-170)
REVERT: B  315 MET cc_start: 0.8751 (mmm) cc_final: 0.8490 (mmm)
  outliers start: 7
  outliers final: 3
  residues processed: 233
  average time/residue: 0.1184
  time to fit residues: 38.7891
Evaluate side-chains
  142 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 138
  time to evaluate  : 0.450 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue 1006 LEU
Chi-restraints excluded: chain B residue  248 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 98 optimal weight:    0.6980
   chunk 107 optimal weight:    0.5980
   chunk 10 optimal weight:    4.9990
   chunk 66 optimal weight:    0.6980
   chunk 130 optimal weight:    0.5980
   chunk 124 optimal weight:    0.5980
   chunk 103 optimal weight:    0.5980
   chunk 77 optimal weight:    0.8980
   chunk 122 optimal weight:    0.9980
   chunk 91 optimal weight:    0.6980
   chunk 55 optimal weight:    3.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 216 HIS
A 597 ASN
** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 675 ASN
A 736 ASN
A 738 GLN
** A 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1004 ASN
A1139 GLN
A1176 HIS
A1307 HIS
A1331 GLN
A1419 HIS
B  67 ASN
B 155 GLN
** B 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.193314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.140931 restraints weight = 14399.133|
|-----------------------------------------------------------------------------|
r_work (start): 0.3651 rms_B_bonded: 2.90
r_work: 0.3309 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
moved from start:          0.1959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  12263  Z= 0.179
  Angle     :  0.742  12.680  16647  Z= 0.379
  Chirality :  0.047   0.172   1852
  Planarity :  0.005   0.051   2106
  Dihedral  : 10.242 138.070   1724
  Min Nonbonded Distance : 1.977

Molprobity Statistics.
  All-atom Clashscore : 11.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.42 %
    Favored  : 93.58 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  :  8.51 %
    Favored  : 89.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

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: -3.75 (0.19), residues: 1480
  helix: -2.37 (0.17), residues: 563
  sheet: -2.77 (0.35), residues: 161
  loop : -2.49 (0.21), residues: 756

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 809 
 TYR   0.026   0.002   TYR A1219 
 PHE   0.022   0.002   PHE A 679 
 TRP   0.035   0.002   TRP B 142 
 HIS   0.004   0.001   HIS B 125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 (12258)
  covalent geometry    : angle       0.73346 (16634)
  SS BOND              : bond        0.00342 (    2)
  SS BOND              : angle       0.48026 (    4)
  hydrogen bonds       : bond        0.04784 (  409)
  hydrogen bonds       : angle       6.28011 ( 1125)
  link_BETA1-4         : bond        0.00797 (    2)
  link_BETA1-4         : angle       4.25184 (    6)
  link_NAG-ASN         : bond        0.01476 (    1)
  link_NAG-ASN         : angle       6.09365 (    3)

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

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

  2960 Ramachandran restraints generated.
    1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2960 Ramachandran restraints generated.
    1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 151
  time to evaluate  : 0.372 
Fit side-chains
REVERT: A  263 SER cc_start: 0.6467 (t) cc_final: 0.6136 (p)
REVERT: A  485 MET cc_start: -0.0395 (ppp) cc_final: -0.0701 (ttp)
REVERT: A  519 MET cc_start: 0.4440 (mtt) cc_final: 0.2769 (mmt)
REVERT: A  532 MET cc_start: 0.1450 (mtt) cc_final: 0.0349 (mmp)
REVERT: A  561 PHE cc_start: 0.7669 (m-80) cc_final: 0.6825 (t80)
REVERT: A  585 TYR cc_start: 0.8748 (m-80) cc_final: 0.7610 (m-80)
REVERT: A  691 ARG cc_start: 0.6888 (ttp-170) cc_final: 0.6221 (tpp-160)
REVERT: A  740 TYR cc_start: 0.6018 (p90) cc_final: 0.4630 (p90)
REVERT: A  847 LYS cc_start: 0.6594 (mttt) cc_final: 0.5812 (mttt)
REVERT: A  901 GLU cc_start: 0.7056 (tp30) cc_final: 0.6784 (tp30)
REVERT: A  903 TYR cc_start: 0.6454 (m-10) cc_final: 0.6230 (m-10)
REVERT: A  994 GLU cc_start: 0.6871 (tp30) cc_final: 0.6625 (mm-30)
REVERT: A 1004 ASN cc_start: 0.7443 (OUTLIER) cc_final: 0.7126 (t0)
REVERT: A 1006 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7798 (pp)
REVERT: A 1059 LYS cc_start: 0.6833 (ptpp) cc_final: 0.6595 (ptmt)
REVERT: A 1088 ARG cc_start: 0.7527 (mtm-85) cc_final: 0.7309 (mtm-85)
REVERT: A 1196 MET cc_start: 0.8603 (tpp) cc_final: 0.8351 (mmm)
  outliers start: 26
  outliers final: 13
  residues processed: 169
  average time/residue: 0.1075
  time to fit residues: 26.2901
Evaluate side-chains
  135 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 120
  time to evaluate  : 0.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  501 THR
Chi-restraints excluded: chain A residue  643 LEU
Chi-restraints excluded: chain A residue  966 ARG
Chi-restraints excluded: chain A residue 1004 ASN
Chi-restraints excluded: chain A residue 1006 LEU
Chi-restraints excluded: chain A residue 1037 LEU
Chi-restraints excluded: chain A residue 1184 LEU
Chi-restraints excluded: chain A residue 1212 ASP
Chi-restraints excluded: chain A residue 1278 LEU
Chi-restraints excluded: chain B residue   66 ILE
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain B residue  248 THR
Chi-restraints excluded: chain B residue  280 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 53 optimal weight:    0.8980
   chunk 74 optimal weight:    1.9990
   chunk 70 optimal weight:    2.9990
   chunk 18 optimal weight:    0.1980
   chunk 147 optimal weight:    4.9990
   chunk 115 optimal weight:    0.6980
   chunk 41 optimal weight:    0.6980
   chunk 21 optimal weight:    0.8980
   chunk 82 optimal weight:    0.8980
   chunk 14 optimal weight:    9.9990
   chunk 42 optimal weight:    3.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1004 ASN
A1331 GLN
B 265 ASN
** B 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4234 r_free = 0.4234 target = 0.192474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.141374 restraints weight = 14488.231|
|-----------------------------------------------------------------------------|
r_work (start): 0.3652 rms_B_bonded: 3.39
r_work: 0.3294 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work: 0.3159 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3159
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7864
moved from start:          0.2388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  12263  Z= 0.172
  Angle     :  0.685  11.487  16647  Z= 0.348
  Chirality :  0.047   0.163   1852
  Planarity :  0.004   0.039   2106
  Dihedral  :  9.322 136.985   1724
  Min Nonbonded Distance : 1.992

Molprobity Statistics.
  All-atom Clashscore : 11.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.89 %
    Favored  : 93.11 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  :  9.13 %
    Favored  : 88.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

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: -3.02 (0.20), residues: 1480
  helix: -1.45 (0.20), residues: 569
  sheet: -2.57 (0.36), residues: 163
  loop : -2.31 (0.22), residues: 748

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 316 
 TYR   0.026   0.002   TYR A1219 
 PHE   0.014   0.002   PHE B 353 
 TRP   0.021   0.002   TRP B 142 
 HIS   0.004   0.001   HIS B 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00394 (12258)
  covalent geometry    : angle       0.67619 (16634)
  SS BOND              : bond        0.00310 (    2)
  SS BOND              : angle       0.77495 (    4)
  hydrogen bonds       : bond        0.04158 (  409)
  hydrogen bonds       : angle       5.66526 ( 1125)
  link_BETA1-4         : bond        0.00471 (    2)
  link_BETA1-4         : angle       3.97468 (    6)
  link_NAG-ASN         : bond        0.01650 (    1)
  link_NAG-ASN         : angle       5.91120 (    3)

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

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

  2960 Ramachandran restraints generated.
    1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2960 Ramachandran restraints generated.
    1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 125
  time to evaluate  : 0.474 
Fit side-chains
REVERT: A  266 THR cc_start: 0.5204 (t) cc_final: 0.4974 (p)
REVERT: A  519 MET cc_start: 0.4191 (mtt) cc_final: 0.2624 (mmt)
REVERT: A  532 MET cc_start: 0.1586 (mtt) cc_final: 0.0363 (mmp)
REVERT: A  561 PHE cc_start: 0.8053 (m-80) cc_final: 0.6820 (t80)
REVERT: A  691 ARG cc_start: 0.6884 (ttp-170) cc_final: 0.6136 (tpp-160)
REVERT: A  730 LEU cc_start: 0.2401 (OUTLIER) cc_final: 0.1517 (mt)
REVERT: A  964 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.6892 (tt0)
REVERT: A 1006 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7763 (pp)
REVERT: A 1043 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7580 (tm-30)
REVERT: A 1059 LYS cc_start: 0.6768 (ptpp) cc_final: 0.6493 (ptmt)
REVERT: A 1089 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.8223 (mttm)
REVERT: A 1196 MET cc_start: 0.8786 (tpp) cc_final: 0.8468 (mmm)
REVERT: A 1212 ASP cc_start: 0.8793 (OUTLIER) cc_final: 0.8399 (t70)
REVERT: B  269 ASP cc_start: 0.8467 (t0) cc_final: 0.8240 (t70)
REVERT: B  359 ILE cc_start: 0.9035 (OUTLIER) cc_final: 0.8726 (pt)
  outliers start: 37
  outliers final: 19
  residues processed: 154
  average time/residue: 0.1023
  time to fit residues: 23.2750
Evaluate side-chains
  137 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 112
  time to evaluate  : 0.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  501 THR
Chi-restraints excluded: chain A residue  543 SER
Chi-restraints excluded: chain A residue  643 LEU
Chi-restraints excluded: chain A residue  661 VAL
Chi-restraints excluded: chain A residue  730 LEU
Chi-restraints excluded: chain A residue  964 GLU
Chi-restraints excluded: chain A residue  975 ILE
Chi-restraints excluded: chain A residue 1005 LEU
Chi-restraints excluded: chain A residue 1006 LEU
Chi-restraints excluded: chain A residue 1036 LEU
Chi-restraints excluded: chain A residue 1037 LEU
Chi-restraints excluded: chain A residue 1089 LYS
Chi-restraints excluded: chain A residue 1184 LEU
Chi-restraints excluded: chain A residue 1212 ASP
Chi-restraints excluded: chain A residue 1278 LEU
Chi-restraints excluded: chain A residue 1299 THR
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue  248 THR
Chi-restraints excluded: chain B residue  280 TYR
Chi-restraints excluded: chain B residue  300 THR
Chi-restraints excluded: chain B residue  359 ILE
Chi-restraints excluded: chain B residue  377 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 55 optimal weight:    8.9990
   chunk 117 optimal weight:    0.9990
   chunk 120 optimal weight:    1.9990
   chunk 124 optimal weight:    0.5980
   chunk 49 optimal weight:    1.9990
   chunk 81 optimal weight:    0.6980
   chunk 24 optimal weight:    0.6980
   chunk 16 optimal weight:    0.0770
   chunk 142 optimal weight:    0.7980
   chunk 28 optimal weight:    1.9990
   chunk 97 optimal weight:    0.9980
   overall best weight:    0.5738

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

Flipped N/Q/H residues before XYZ refinement:
** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 831 GLN
** B 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.193046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.140798 restraints weight = 14456.212|
|-----------------------------------------------------------------------------|
r_work (start): 0.3643 rms_B_bonded: 3.63
r_work: 0.3274 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7777
moved from start:          0.2658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  12263  Z= 0.157
  Angle     :  0.663  11.036  16647  Z= 0.336
  Chirality :  0.046   0.162   1852
  Planarity :  0.004   0.056   2106
  Dihedral  :  8.751 135.509   1724
  Min Nonbonded Distance : 2.009

Molprobity Statistics.
  All-atom Clashscore : 11.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.55 %
    Favored  : 93.45 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 10.53 %
    Favored  : 86.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

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: -2.68 (0.21), residues: 1480
  helix: -1.10 (0.20), residues: 576
  sheet: -2.35 (0.37), residues: 171
  loop : -2.18 (0.22), residues: 733

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 809 
 TYR   0.025   0.002   TYR A1219 
 PHE   0.013   0.002   PHE A1341 
 TRP   0.016   0.001   TRP A 986 
 HIS   0.003   0.001   HIS B 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 (12258)
  covalent geometry    : angle       0.65448 (16634)
  SS BOND              : bond        0.00286 (    2)
  SS BOND              : angle       0.69155 (    4)
  hydrogen bonds       : bond        0.03819 (  409)
  hydrogen bonds       : angle       5.46204 ( 1125)
  link_BETA1-4         : bond        0.00385 (    2)
  link_BETA1-4         : angle       3.72121 (    6)
  link_NAG-ASN         : bond        0.01413 (    1)
  link_NAG-ASN         : angle       5.69692 (    3)

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

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

  2960 Ramachandran restraints generated.
    1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2960 Ramachandran restraints generated.
    1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 115
  time to evaluate  : 0.435 
Fit side-chains
REVERT: A  224 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8257 (tm)
REVERT: A  266 THR cc_start: 0.5497 (t) cc_final: 0.5232 (p)
REVERT: A  519 MET cc_start: 0.3832 (mtt) cc_final: 0.2716 (mmt)
REVERT: A  532 MET cc_start: 0.1556 (mtt) cc_final: 0.0117 (mmm)
REVERT: A  561 PHE cc_start: 0.7901 (m-80) cc_final: 0.6798 (t80)
REVERT: A  585 TYR cc_start: 0.8740 (m-80) cc_final: 0.7693 (m-80)
REVERT: A  691 ARG cc_start: 0.6654 (ttp-170) cc_final: 0.6046 (tpp-160)
REVERT: A  730 LEU cc_start: 0.2352 (OUTLIER) cc_final: 0.1467 (mt)
REVERT: A  814 SER cc_start: 0.6329 (t) cc_final: 0.5632 (p)
REVERT: A  847 LYS cc_start: 0.6396 (mttt) cc_final: 0.5521 (mttt)
REVERT: A 1006 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7514 (pp)
REVERT: A 1059 LYS cc_start: 0.6837 (ptpp) cc_final: 0.6564 (ptmt)
REVERT: A 1100 VAL cc_start: 0.7938 (t) cc_final: 0.7709 (t)
REVERT: A 1196 MET cc_start: 0.8667 (tpp) cc_final: 0.8298 (mmm)
REVERT: A 1212 ASP cc_start: 0.8736 (OUTLIER) cc_final: 0.8356 (t70)
REVERT: B  359 ILE cc_start: 0.8974 (OUTLIER) cc_final: 0.8723 (pt)
  outliers start: 34
  outliers final: 18
  residues processed: 143
  average time/residue: 0.1034
  time to fit residues: 21.8892
Evaluate side-chains
  128 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 105
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  501 THR
Chi-restraints excluded: chain A residue  543 SER
Chi-restraints excluded: chain A residue  643 LEU
Chi-restraints excluded: chain A residue  661 VAL
Chi-restraints excluded: chain A residue  730 LEU
Chi-restraints excluded: chain A residue  801 GLU
Chi-restraints excluded: chain A residue  852 ILE
Chi-restraints excluded: chain A residue  966 ARG
Chi-restraints excluded: chain A residue  975 ILE
Chi-restraints excluded: chain A residue 1005 LEU
Chi-restraints excluded: chain A residue 1006 LEU
Chi-restraints excluded: chain A residue 1037 LEU
Chi-restraints excluded: chain A residue 1212 ASP
Chi-restraints excluded: chain A residue 1278 LEU
Chi-restraints excluded: chain A residue 1299 THR
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain B residue  248 THR
Chi-restraints excluded: chain B residue  280 TYR
Chi-restraints excluded: chain B residue  359 ILE
Chi-restraints excluded: chain B residue  377 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 58 optimal weight:    0.7980
   chunk 41 optimal weight:    2.9990
   chunk 129 optimal weight:    0.5980
   chunk 87 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 34 optimal weight:    0.0980
   chunk 52 optimal weight:    2.9990
   chunk 14 optimal weight:    0.5980
   chunk 69 optimal weight:    0.6980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A 484 ASN
** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 610 GLN
** A 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1004 ASN
** B 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4239 r_free = 0.4239 target = 0.193084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.141675 restraints weight = 14445.841|
|-----------------------------------------------------------------------------|
r_work (start): 0.3662 rms_B_bonded: 3.10
r_work: 0.3285 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3285
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7733
moved from start:          0.2881

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12263  Z= 0.151
  Angle     :  0.646  12.692  16647  Z= 0.325
  Chirality :  0.045   0.160   1852
  Planarity :  0.004   0.045   2106
  Dihedral  :  8.394 134.620   1724
  Min Nonbonded Distance : 2.000

Molprobity Statistics.
  All-atom Clashscore : 11.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.89 %
    Favored  : 93.11 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 11.15 %
    Favored  : 86.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

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: -2.44 (0.21), residues: 1480
  helix: -0.89 (0.21), residues: 585
  sheet: -2.16 (0.38), residues: 162
  loop : -2.08 (0.22), residues: 733

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 809 
 TYR   0.026   0.002   TYR A1219 
 PHE   0.014   0.002   PHE B 353 
 TRP   0.019   0.001   TRP A 986 
 HIS   0.003   0.001   HIS B 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 (12258)
  covalent geometry    : angle       0.63772 (16634)
  SS BOND              : bond        0.00268 (    2)
  SS BOND              : angle       0.65727 (    4)
  hydrogen bonds       : bond        0.03686 (  409)
  hydrogen bonds       : angle       5.31725 ( 1125)
  link_BETA1-4         : bond        0.00413 (    2)
  link_BETA1-4         : angle       3.55677 (    6)
  link_NAG-ASN         : bond        0.01389 (    1)
  link_NAG-ASN         : angle       5.61656 (    3)

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

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

  2960 Ramachandran restraints generated.
    1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2960 Ramachandran restraints generated.
    1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 109
  time to evaluate  : 0.458 
Fit side-chains
REVERT: A  223 PHE cc_start: 0.8392 (OUTLIER) cc_final: 0.8037 (t80)
REVERT: A  224 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8378 (tm)
REVERT: A  266 THR cc_start: 0.5489 (t) cc_final: 0.5273 (p)
REVERT: A  519 MET cc_start: 0.3804 (mtt) cc_final: 0.2798 (mmt)
REVERT: A  532 MET cc_start: 0.1632 (mtt) cc_final: 0.0122 (mmm)
REVERT: A  561 PHE cc_start: 0.7869 (m-80) cc_final: 0.6751 (t80)
REVERT: A  691 ARG cc_start: 0.6579 (ttp-170) cc_final: 0.5905 (tpp-160)
REVERT: A  730 LEU cc_start: 0.2442 (OUTLIER) cc_final: 0.1535 (mt)
REVERT: A  847 LYS cc_start: 0.6211 (mttt) cc_final: 0.5432 (mttt)
REVERT: A  964 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.6815 (tt0)
REVERT: A 1006 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7484 (pp)
REVERT: A 1059 LYS cc_start: 0.6849 (ptpp) cc_final: 0.6565 (ptmt)
REVERT: A 1196 MET cc_start: 0.8673 (tpp) cc_final: 0.8310 (mmm)
REVERT: A 1212 ASP cc_start: 0.8737 (OUTLIER) cc_final: 0.8353 (t70)
REVERT: B  359 ILE cc_start: 0.8956 (OUTLIER) cc_final: 0.8696 (pt)
REVERT: B  395 PHE cc_start: 0.7346 (m-80) cc_final: 0.6948 (m-10)
  outliers start: 36
  outliers final: 23
  residues processed: 141
  average time/residue: 0.0964
  time to fit residues: 20.7704
Evaluate side-chains
  132 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 102
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  223 PHE
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  446 VAL
Chi-restraints excluded: chain A residue  501 THR
Chi-restraints excluded: chain A residue  543 SER
Chi-restraints excluded: chain A residue  643 LEU
Chi-restraints excluded: chain A residue  661 VAL
Chi-restraints excluded: chain A residue  730 LEU
Chi-restraints excluded: chain A residue  801 GLU
Chi-restraints excluded: chain A residue  852 ILE
Chi-restraints excluded: chain A residue  964 GLU
Chi-restraints excluded: chain A residue  966 ARG
Chi-restraints excluded: chain A residue 1004 ASN
Chi-restraints excluded: chain A residue 1005 LEU
Chi-restraints excluded: chain A residue 1006 LEU
Chi-restraints excluded: chain A residue 1036 LEU
Chi-restraints excluded: chain A residue 1037 LEU
Chi-restraints excluded: chain A residue 1095 LYS
Chi-restraints excluded: chain A residue 1212 ASP
Chi-restraints excluded: chain A residue 1278 LEU
Chi-restraints excluded: chain A residue 1299 THR
Chi-restraints excluded: chain A residue 1353 THR
Chi-restraints excluded: chain B residue  248 THR
Chi-restraints excluded: chain B residue  280 TYR
Chi-restraints excluded: chain B residue  300 THR
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 58 optimal weight:    0.9980
   chunk 39 optimal weight:    0.7980
   chunk 41 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 90 optimal weight:    1.9990
   chunk 114 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 85 optimal weight:    0.5980
   chunk 89 optimal weight:    0.9990
   chunk 136 optimal weight:    0.6980
   chunk 31 optimal weight:    0.7980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1004 ASN
** B 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.191453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.139627 restraints weight = 14565.408|
|-----------------------------------------------------------------------------|
r_work (start): 0.3632 rms_B_bonded: 3.39
r_work: 0.3261 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7795
moved from start:          0.2983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  12263  Z= 0.180
  Angle     :  0.653  11.998  16647  Z= 0.331
  Chirality :  0.046   0.168   1852
  Planarity :  0.004   0.047   2106
  Dihedral  :  8.332 137.913   1724
  Min Nonbonded Distance : 2.025

Molprobity Statistics.
  All-atom Clashscore : 10.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.43 %
    Favored  : 92.57 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 11.69 %
    Favored  : 85.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

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: -2.33 (0.21), residues: 1480
  helix: -0.81 (0.21), residues: 590
  sheet: -2.07 (0.39), residues: 162
  loop : -2.02 (0.23), residues: 728

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1333 
 TYR   0.023   0.002   TYR A1219 
 PHE   0.016   0.002   PHE A1341 
 TRP   0.022   0.002   TRP A 986 
 HIS   0.004   0.001   HIS B 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00417 (12258)
  covalent geometry    : angle       0.64516 (16634)
  SS BOND              : bond        0.00297 (    2)
  SS BOND              : angle       0.74708 (    4)
  hydrogen bonds       : bond        0.03762 (  409)
  hydrogen bonds       : angle       5.25187 ( 1125)
  link_BETA1-4         : bond        0.00362 (    2)
  link_BETA1-4         : angle       3.59359 (    6)
  link_NAG-ASN         : bond        0.01532 (    1)
  link_NAG-ASN         : angle       5.67524 (    3)

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

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

  2960 Ramachandran restraints generated.
    1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2960 Ramachandran restraints generated.
    1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 110
  time to evaluate  : 0.464 
Fit side-chains
REVERT: A  223 PHE cc_start: 0.8490 (OUTLIER) cc_final: 0.8147 (t80)
REVERT: A  224 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8406 (tm)
REVERT: A  266 THR cc_start: 0.5487 (t) cc_final: 0.5277 (p)
REVERT: A  506 LEU cc_start: 0.1622 (OUTLIER) cc_final: 0.1382 (mt)
REVERT: A  519 MET cc_start: 0.3545 (mtt) cc_final: 0.2380 (mmt)
REVERT: A  532 MET cc_start: 0.1628 (mtt) cc_final: 0.0174 (mmt)
REVERT: A  561 PHE cc_start: 0.7884 (m-80) cc_final: 0.6794 (t80)
REVERT: A  691 ARG cc_start: 0.6551 (ttp-170) cc_final: 0.6031 (tpp-160)
REVERT: A  730 LEU cc_start: 0.2343 (OUTLIER) cc_final: 0.1457 (mt)
REVERT: A  814 SER cc_start: 0.6249 (t) cc_final: 0.5505 (p)
REVERT: A  847 LYS cc_start: 0.6128 (mttt) cc_final: 0.5348 (mttt)
REVERT: A  964 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.6955 (tt0)
REVERT: A 1006 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7567 (pp)
REVERT: A 1059 LYS cc_start: 0.6898 (ptpp) cc_final: 0.6582 (ptmt)
REVERT: A 1196 MET cc_start: 0.8635 (tpp) cc_final: 0.8404 (mmm)
REVERT: A 1212 ASP cc_start: 0.8749 (OUTLIER) cc_final: 0.8366 (t70)
REVERT: A 1219 TYR cc_start: 0.8414 (t80) cc_final: 0.7784 (t80)
REVERT: B  359 ILE cc_start: 0.8954 (OUTLIER) cc_final: 0.8718 (pt)
REVERT: B  395 PHE cc_start: 0.7537 (m-80) cc_final: 0.7070 (m-10)
  outliers start: 40
  outliers final: 27
  residues processed: 146
  average time/residue: 0.1013
  time to fit residues: 21.8613
Evaluate side-chains
  136 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 101
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  223 PHE
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  435 THR
Chi-restraints excluded: chain A residue  446 VAL
Chi-restraints excluded: chain A residue  501 THR
Chi-restraints excluded: chain A residue  506 LEU
Chi-restraints excluded: chain A residue  543 SER
Chi-restraints excluded: chain A residue  596 THR
Chi-restraints excluded: chain A residue  643 LEU
Chi-restraints excluded: chain A residue  661 VAL
Chi-restraints excluded: chain A residue  730 LEU
Chi-restraints excluded: chain A residue  801 GLU
Chi-restraints excluded: chain A residue  811 VAL
Chi-restraints excluded: chain A residue  852 ILE
Chi-restraints excluded: chain A residue  964 GLU
Chi-restraints excluded: chain A residue  966 ARG
Chi-restraints excluded: chain A residue  975 ILE
Chi-restraints excluded: chain A residue 1005 LEU
Chi-restraints excluded: chain A residue 1006 LEU
Chi-restraints excluded: chain A residue 1036 LEU
Chi-restraints excluded: chain A residue 1037 LEU
Chi-restraints excluded: chain A residue 1095 LYS
Chi-restraints excluded: chain A residue 1101 LEU
Chi-restraints excluded: chain A residue 1212 ASP
Chi-restraints excluded: chain A residue 1278 LEU
Chi-restraints excluded: chain A residue 1299 THR
Chi-restraints excluded: chain A residue 1353 THR
Chi-restraints excluded: chain B residue  248 THR
Chi-restraints excluded: chain B residue  280 TYR
Chi-restraints excluded: chain B residue  300 THR
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 118 optimal weight:    2.9990
   chunk 116 optimal weight:    1.9990
   chunk 133 optimal weight:    0.2980
   chunk 36 optimal weight:    0.6980
   chunk 143 optimal weight:    0.7980
   chunk 13 optimal weight:    0.6980
   chunk 84 optimal weight:    0.0170
   chunk 77 optimal weight:    0.7980
   chunk 2 optimal weight:    3.9990
   chunk 74 optimal weight:    0.9990
   chunk 122 optimal weight:    1.9990
   overall best weight:    0.5018

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

Flipped N/Q/H residues before XYZ refinement:
** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 927 ASN
** B 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.192944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.141427 restraints weight = 14430.539|
|-----------------------------------------------------------------------------|
r_work (start): 0.3660 rms_B_bonded: 3.16
r_work: 0.3281 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7736
moved from start:          0.3143

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12263  Z= 0.143
  Angle     :  0.630  12.867  16647  Z= 0.319
  Chirality :  0.045   0.161   1852
  Planarity :  0.003   0.036   2106
  Dihedral  :  8.144 140.039   1724
  Min Nonbonded Distance : 2.024

Molprobity Statistics.
  All-atom Clashscore : 10.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.16 %
    Favored  : 92.84 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 12.54 %
    Favored  : 84.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

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: -2.20 (0.21), residues: 1480
  helix: -0.69 (0.21), residues: 592
  sheet: -2.04 (0.38), residues: 172
  loop : -1.95 (0.23), residues: 716

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 264 
 TYR   0.022   0.002   TYR B 280 
 PHE   0.012   0.001   PHE A1341 
 TRP   0.018   0.001   TRP A 986 
 HIS   0.003   0.001   HIS B 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 (12258)
  covalent geometry    : angle       0.62248 (16634)
  SS BOND              : bond        0.00287 (    2)
  SS BOND              : angle       0.68329 (    4)
  hydrogen bonds       : bond        0.03579 (  409)
  hydrogen bonds       : angle       5.17014 ( 1125)
  link_BETA1-4         : bond        0.00395 (    2)
  link_BETA1-4         : angle       3.41691 (    6)
  link_NAG-ASN         : bond        0.01174 (    1)
  link_NAG-ASN         : angle       5.52574 (    3)

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

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

  2960 Ramachandran restraints generated.
    1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2960 Ramachandran restraints generated.
    1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 109
  time to evaluate  : 0.401 
Fit side-chains
REVERT: A  223 PHE cc_start: 0.8404 (OUTLIER) cc_final: 0.8097 (t80)
REVERT: A  224 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8347 (tm)
REVERT: A  506 LEU cc_start: 0.1481 (OUTLIER) cc_final: 0.1136 (mt)
REVERT: A  519 MET cc_start: 0.3523 (mtt) cc_final: 0.2366 (mmt)
REVERT: A  532 MET cc_start: 0.1720 (mtt) cc_final: 0.0212 (mmt)
REVERT: A  561 PHE cc_start: 0.7688 (m-80) cc_final: 0.6704 (t80)
REVERT: A  691 ARG cc_start: 0.6401 (ttp-170) cc_final: 0.5870 (tpp-160)
REVERT: A  730 LEU cc_start: 0.2464 (OUTLIER) cc_final: 0.1552 (mt)
REVERT: A  847 LYS cc_start: 0.6111 (mttt) cc_final: 0.5383 (mttt)
REVERT: A  964 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7083 (tt0)
REVERT: A 1006 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7587 (pp)
REVERT: A 1084 GLU cc_start: 0.7104 (tp30) cc_final: 0.6860 (tp30)
REVERT: A 1091 LEU cc_start: 0.7931 (tp) cc_final: 0.7562 (mp)
REVERT: A 1196 MET cc_start: 0.8667 (tpp) cc_final: 0.8387 (mmm)
REVERT: A 1212 ASP cc_start: 0.8735 (OUTLIER) cc_final: 0.8321 (t70)
REVERT: A 1219 TYR cc_start: 0.8367 (t80) cc_final: 0.7724 (t80)
REVERT: B   80 LEU cc_start: 0.7498 (tt) cc_final: 0.7115 (tp)
REVERT: B  359 ILE cc_start: 0.8947 (OUTLIER) cc_final: 0.8712 (pt)
REVERT: B  395 PHE cc_start: 0.7583 (m-80) cc_final: 0.7120 (m-10)
  outliers start: 38
  outliers final: 25
  residues processed: 142
  average time/residue: 0.0970
  time to fit residues: 20.8838
Evaluate side-chains
  136 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 103
  time to evaluate  : 0.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  223 PHE
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  446 VAL
Chi-restraints excluded: chain A residue  501 THR
Chi-restraints excluded: chain A residue  506 LEU
Chi-restraints excluded: chain A residue  543 SER
Chi-restraints excluded: chain A residue  596 THR
Chi-restraints excluded: chain A residue  643 LEU
Chi-restraints excluded: chain A residue  661 VAL
Chi-restraints excluded: chain A residue  730 LEU
Chi-restraints excluded: chain A residue  801 GLU
Chi-restraints excluded: chain A residue  811 VAL
Chi-restraints excluded: chain A residue  852 ILE
Chi-restraints excluded: chain A residue  964 GLU
Chi-restraints excluded: chain A residue  966 ARG
Chi-restraints excluded: chain A residue 1005 LEU
Chi-restraints excluded: chain A residue 1006 LEU
Chi-restraints excluded: chain A residue 1036 LEU
Chi-restraints excluded: chain A residue 1037 LEU
Chi-restraints excluded: chain A residue 1095 LYS
Chi-restraints excluded: chain A residue 1101 LEU
Chi-restraints excluded: chain A residue 1212 ASP
Chi-restraints excluded: chain A residue 1278 LEU
Chi-restraints excluded: chain A residue 1299 THR
Chi-restraints excluded: chain A residue 1353 THR
Chi-restraints excluded: chain B residue  248 THR
Chi-restraints excluded: chain B residue  280 TYR
Chi-restraints excluded: chain B residue  300 THR
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 124 optimal weight:    0.7980
   chunk 31 optimal weight:    0.4980
   chunk 50 optimal weight:    6.9990
   chunk 102 optimal weight:    0.7980
   chunk 95 optimal weight:    0.8980
   chunk 6 optimal weight:    0.0970
   chunk 106 optimal weight:    0.1980
   chunk 93 optimal weight:    0.7980
   chunk 27 optimal weight:    0.5980
   chunk 88 optimal weight:    0.6980
   chunk 138 optimal weight:    0.1980
   overall best weight:    0.3178

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

Flipped N/Q/H residues before XYZ refinement:
** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 675 ASN
** A 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.195183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.144758 restraints weight = 14291.301|
|-----------------------------------------------------------------------------|
r_work (start): 0.3698 rms_B_bonded: 3.30
r_work: 0.3337 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3337
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7696
moved from start:          0.3264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  12263  Z= 0.122
  Angle     :  0.615  13.304  16647  Z= 0.310
  Chirality :  0.044   0.159   1852
  Planarity :  0.003   0.037   2106
  Dihedral  :  7.982 139.654   1724
  Min Nonbonded Distance : 2.038

Molprobity Statistics.
  All-atom Clashscore : 10.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.76 %
    Favored  : 93.24 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 12.54 %
    Favored  : 84.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

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: -2.04 (0.22), residues: 1480
  helix: -0.55 (0.21), residues: 593
  sheet: -1.80 (0.40), residues: 171
  loop : -1.90 (0.23), residues: 716

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 272 
 TYR   0.021   0.002   TYR B 280 
 PHE   0.013   0.001   PHE A1402 
 TRP   0.016   0.001   TRP A 986 
 HIS   0.003   0.001   HIS A1330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 (12258)
  covalent geometry    : angle       0.60775 (16634)
  SS BOND              : bond        0.00201 (    2)
  SS BOND              : angle       0.56609 (    4)
  hydrogen bonds       : bond        0.03442 (  409)
  hydrogen bonds       : angle       5.09875 ( 1125)
  link_BETA1-4         : bond        0.00379 (    2)
  link_BETA1-4         : angle       3.29842 (    6)
  link_NAG-ASN         : bond        0.00944 (    1)
  link_NAG-ASN         : angle       5.39529 (    3)

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

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

  2960 Ramachandran restraints generated.
    1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2960 Ramachandran restraints generated.
    1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 115
  time to evaluate  : 0.400 
Fit side-chains
REVERT: A  223 PHE cc_start: 0.8341 (OUTLIER) cc_final: 0.8059 (t80)
REVERT: A  224 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8287 (tm)
REVERT: A  506 LEU cc_start: 0.1620 (OUTLIER) cc_final: 0.1110 (mt)
REVERT: A  519 MET cc_start: 0.3580 (mtt) cc_final: 0.2400 (mmt)
REVERT: A  532 MET cc_start: 0.1738 (mtt) cc_final: 0.0289 (mmt)
REVERT: A  561 PHE cc_start: 0.7659 (m-80) cc_final: 0.6675 (t80)
REVERT: A  585 TYR cc_start: 0.8713 (m-80) cc_final: 0.7851 (m-80)
REVERT: A  603 TRP cc_start: 0.8286 (m100) cc_final: 0.8016 (m100)
REVERT: A  691 ARG cc_start: 0.6289 (ttp-170) cc_final: 0.5640 (tpp-160)
REVERT: A  730 LEU cc_start: 0.2473 (OUTLIER) cc_final: 0.1545 (mt)
REVERT: A  847 LYS cc_start: 0.6109 (mttt) cc_final: 0.5410 (mttt)
REVERT: A  964 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7180 (tt0)
REVERT: A 1006 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7390 (pp)
REVERT: A 1091 LEU cc_start: 0.7905 (tp) cc_final: 0.7531 (mp)
REVERT: A 1092 LEU cc_start: 0.8442 (mp) cc_final: 0.8153 (pp)
REVERT: A 1115 LYS cc_start: 0.7293 (OUTLIER) cc_final: 0.6933 (ttmm)
REVERT: A 1118 LYS cc_start: 0.7868 (ttpp) cc_final: 0.7604 (ttpp)
REVERT: A 1212 ASP cc_start: 0.8669 (OUTLIER) cc_final: 0.8263 (t70)
REVERT: A 1219 TYR cc_start: 0.8352 (t80) cc_final: 0.7650 (t80)
REVERT: B   80 LEU cc_start: 0.7522 (tt) cc_final: 0.7168 (tp)
REVERT: B  269 ASP cc_start: 0.8286 (OUTLIER) cc_final: 0.7894 (t70)
REVERT: B  359 ILE cc_start: 0.8943 (OUTLIER) cc_final: 0.8717 (pt)
REVERT: B  395 PHE cc_start: 0.7557 (m-80) cc_final: 0.7168 (m-10)
  outliers start: 38
  outliers final: 23
  residues processed: 147
  average time/residue: 0.0973
  time to fit residues: 21.2870
Evaluate side-chains
  139 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 106
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  223 PHE
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  435 THR
Chi-restraints excluded: chain A residue  446 VAL
Chi-restraints excluded: chain A residue  501 THR
Chi-restraints excluded: chain A residue  506 LEU
Chi-restraints excluded: chain A residue  543 SER
Chi-restraints excluded: chain A residue  596 THR
Chi-restraints excluded: chain A residue  643 LEU
Chi-restraints excluded: chain A residue  661 VAL
Chi-restraints excluded: chain A residue  730 LEU
Chi-restraints excluded: chain A residue  852 ILE
Chi-restraints excluded: chain A residue  964 GLU
Chi-restraints excluded: chain A residue  966 ARG
Chi-restraints excluded: chain A residue  975 ILE
Chi-restraints excluded: chain A residue 1005 LEU
Chi-restraints excluded: chain A residue 1006 LEU
Chi-restraints excluded: chain A residue 1037 LEU
Chi-restraints excluded: chain A residue 1095 LYS
Chi-restraints excluded: chain A residue 1115 LYS
Chi-restraints excluded: chain A residue 1212 ASP
Chi-restraints excluded: chain A residue 1278 LEU
Chi-restraints excluded: chain A residue 1299 THR
Chi-restraints excluded: chain A residue 1353 THR
Chi-restraints excluded: chain B residue  238 MET
Chi-restraints excluded: chain B residue  248 THR
Chi-restraints excluded: chain B residue  269 ASP
Chi-restraints excluded: chain B residue  280 TYR
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: 148
   random chunks:
   chunk 9 optimal weight:    4.9990
   chunk 140 optimal weight:    1.9990
   chunk 71 optimal weight:    0.0000
   chunk 88 optimal weight:    0.9980
   chunk 146 optimal weight:    3.9990
   chunk 114 optimal weight:    0.8980
   chunk 42 optimal weight:   10.0000
   chunk 111 optimal weight:    0.9990
   chunk 61 optimal weight:    9.9990
   chunk 23 optimal weight:    7.9990
   chunk 133 optimal weight:    0.6980
   overall best weight:    0.7186

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

Flipped N/Q/H residues before XYZ refinement:
** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 366 HIS ** 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 = 0.4233 r_free = 0.4233 target = 0.192488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.140482 restraints weight = 14252.227|
|-----------------------------------------------------------------------------|
r_work (start): 0.3630 rms_B_bonded: 3.17
r_work: 0.3261 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7783
moved from start:          0.3323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  12263  Z= 0.173
  Angle     :  0.650  12.329  16647  Z= 0.328
  Chirality :  0.045   0.168   1852
  Planarity :  0.004   0.045   2106
  Dihedral  :  8.062 139.361   1724
  Min Nonbonded Distance : 1.970

Molprobity Statistics.
  All-atom Clashscore : 11.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.43 %
    Favored  : 92.57 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 12.54 %
    Favored  : 84.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

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: -2.04 (0.22), residues: 1480
  helix: -0.62 (0.21), residues: 600
  sheet: -1.57 (0.42), residues: 159
  loop : -1.91 (0.23), residues: 721

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 316 
 TYR   0.022   0.002   TYR B 280 
 PHE   0.020   0.002   PHE A1402 
 TRP   0.025   0.001   TRP A 986 
 HIS   0.004   0.001   HIS B 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 (12258)
  covalent geometry    : angle       0.64222 (16634)
  SS BOND              : bond        0.00262 (    2)
  SS BOND              : angle       0.78783 (    4)
  hydrogen bonds       : bond        0.03672 (  409)
  hydrogen bonds       : angle       5.09630 ( 1125)
  link_BETA1-4         : bond        0.00429 (    2)
  link_BETA1-4         : angle       3.60350 (    6)
  link_NAG-ASN         : bond        0.01403 (    1)
  link_NAG-ASN         : angle       5.55517 (    3)

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

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

  2960 Ramachandran restraints generated.
    1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2960 Ramachandran restraints generated.
    1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 109
  time to evaluate  : 0.281 
Fit side-chains
REVERT: A  223 PHE cc_start: 0.8426 (OUTLIER) cc_final: 0.8105 (t80)
REVERT: A  224 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8407 (tm)
REVERT: A  506 LEU cc_start: 0.1646 (OUTLIER) cc_final: 0.1115 (mt)
REVERT: A  519 MET cc_start: 0.3571 (mtt) cc_final: 0.2723 (mmt)
REVERT: A  532 MET cc_start: 0.2067 (mtt) cc_final: 0.0459 (mmt)
REVERT: A  561 PHE cc_start: 0.7717 (m-80) cc_final: 0.6736 (t80)
REVERT: A  603 TRP cc_start: 0.8297 (m100) cc_final: 0.8000 (m100)
REVERT: A  691 ARG cc_start: 0.6504 (ttp-170) cc_final: 0.5930 (tpp-160)
REVERT: A  847 LYS cc_start: 0.6232 (mttt) cc_final: 0.5650 (mttm)
REVERT: A  964 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7232 (tt0)
REVERT: A 1006 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7579 (pp)
REVERT: A 1091 LEU cc_start: 0.8018 (tp) cc_final: 0.7665 (mp)
REVERT: A 1115 LYS cc_start: 0.7447 (OUTLIER) cc_final: 0.7083 (ttmm)
REVERT: A 1212 ASP cc_start: 0.8704 (OUTLIER) cc_final: 0.8276 (t70)
REVERT: A 1219 TYR cc_start: 0.8353 (t80) cc_final: 0.7651 (t80)
REVERT: B   80 LEU cc_start: 0.7550 (tt) cc_final: 0.7186 (tp)
REVERT: B  269 ASP cc_start: 0.8362 (OUTLIER) cc_final: 0.7972 (t70)
REVERT: B  359 ILE cc_start: 0.8968 (OUTLIER) cc_final: 0.8747 (pt)
REVERT: B  395 PHE cc_start: 0.7768 (m-80) cc_final: 0.7349 (m-10)
  outliers start: 36
  outliers final: 24
  residues processed: 140
  average time/residue: 0.0945
  time to fit residues: 20.0006
Evaluate side-chains
  139 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 106
  time to evaluate  : 0.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  223 PHE
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  435 THR
Chi-restraints excluded: chain A residue  501 THR
Chi-restraints excluded: chain A residue  506 LEU
Chi-restraints excluded: chain A residue  543 SER
Chi-restraints excluded: chain A residue  596 THR
Chi-restraints excluded: chain A residue  643 LEU
Chi-restraints excluded: chain A residue  661 VAL
Chi-restraints excluded: chain A residue  811 VAL
Chi-restraints excluded: chain A residue  852 ILE
Chi-restraints excluded: chain A residue  964 GLU
Chi-restraints excluded: chain A residue  966 ARG
Chi-restraints excluded: chain A residue  975 ILE
Chi-restraints excluded: chain A residue 1005 LEU
Chi-restraints excluded: chain A residue 1006 LEU
Chi-restraints excluded: chain A residue 1037 LEU
Chi-restraints excluded: chain A residue 1095 LYS
Chi-restraints excluded: chain A residue 1101 LEU
Chi-restraints excluded: chain A residue 1115 LYS
Chi-restraints excluded: chain A residue 1212 ASP
Chi-restraints excluded: chain A residue 1278 LEU
Chi-restraints excluded: chain A residue 1299 THR
Chi-restraints excluded: chain A residue 1353 THR
Chi-restraints excluded: chain B residue  238 MET
Chi-restraints excluded: chain B residue  248 THR
Chi-restraints excluded: chain B residue  269 ASP
Chi-restraints excluded: chain B residue  280 TYR
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: 148
   random chunks:
   chunk 25 optimal weight:    0.0980
   chunk 27 optimal weight:    0.7980
   chunk 114 optimal weight:    0.0670
   chunk 100 optimal weight:    0.5980
   chunk 48 optimal weight:    6.9990
   chunk 103 optimal weight:    0.6980
   chunk 115 optimal weight:    0.5980
   chunk 14 optimal weight:    7.9990
   chunk 131 optimal weight:    0.8980
   chunk 51 optimal weight:    0.7980
   chunk 84 optimal weight:    0.0970
   overall best weight:    0.2916

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

Flipped N/Q/H residues before XYZ refinement:
** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1067 ASN
** B 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4265 r_free = 0.4265 target = 0.195659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.144245 restraints weight = 14393.712|
|-----------------------------------------------------------------------------|
r_work (start): 0.3681 rms_B_bonded: 2.94
r_work: 0.3325 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7731
moved from start:          0.3463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  12263  Z= 0.118
  Angle     :  0.621  14.004  16647  Z= 0.309
  Chirality :  0.044   0.159   1852
  Planarity :  0.003   0.031   2106
  Dihedral  :  7.851 138.068   1724
  Min Nonbonded Distance : 2.040

Molprobity Statistics.
  All-atom Clashscore : 10.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.08 %
    Favored  : 93.92 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 13.08 %
    Favored  : 84.52 %
  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: -1.94 (0.22), residues: 1480
  helix: -0.49 (0.21), residues: 600
  sheet: -1.56 (0.42), residues: 160
  loop : -1.91 (0.23), residues: 720

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 272 
 TYR   0.021   0.002   TYR B 280 
 PHE   0.012   0.001   PHE A1191 
 TRP   0.014   0.001   TRP A 986 
 HIS   0.003   0.001   HIS B 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 (12258)
  covalent geometry    : angle       0.61396 (16634)
  SS BOND              : bond        0.00192 (    2)
  SS BOND              : angle       0.59151 (    4)
  hydrogen bonds       : bond        0.03388 (  409)
  hydrogen bonds       : angle       5.06483 ( 1125)
  link_BETA1-4         : bond        0.00332 (    2)
  link_BETA1-4         : angle       3.27995 (    6)
  link_NAG-ASN         : bond        0.00744 (    1)
  link_NAG-ASN         : angle       5.28397 (    3)

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

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

  2960 Ramachandran restraints generated.
    1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2960 Ramachandran restraints generated.
    1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 110
  time to evaluate  : 0.453 
Fit side-chains
REVERT: A  223 PHE cc_start: 0.8341 (OUTLIER) cc_final: 0.8070 (t80)
REVERT: A  224 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8400 (tm)
REVERT: A  242 LEU cc_start: 0.8431 (mp) cc_final: 0.7698 (tp)
REVERT: A  506 LEU cc_start: 0.1640 (OUTLIER) cc_final: 0.1120 (mt)
REVERT: A  519 MET cc_start: 0.3404 (mtt) cc_final: 0.2558 (mmt)
REVERT: A  532 MET cc_start: 0.2161 (mtt) cc_final: 0.0511 (mmt)
REVERT: A  561 PHE cc_start: 0.7450 (m-80) cc_final: 0.6695 (t80)
REVERT: A  585 TYR cc_start: 0.8717 (m-80) cc_final: 0.7848 (m-80)
REVERT: A  603 TRP cc_start: 0.8300 (m100) cc_final: 0.8056 (m100)
REVERT: A  691 ARG cc_start: 0.6316 (ttp-170) cc_final: 0.5726 (tpp-160)
REVERT: A  795 LYS cc_start: 0.7157 (mmtm) cc_final: 0.6883 (mmtm)
REVERT: A  847 LYS cc_start: 0.6171 (mttt) cc_final: 0.5450 (mttt)
REVERT: A  964 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7253 (tt0)
REVERT: A 1006 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7632 (pp)
REVERT: A 1088 ARG cc_start: 0.7181 (mtm110) cc_final: 0.6940 (mtm180)
REVERT: A 1091 LEU cc_start: 0.7943 (tp) cc_final: 0.7597 (mp)
REVERT: A 1092 LEU cc_start: 0.8452 (mp) cc_final: 0.8195 (pp)
REVERT: A 1118 LYS cc_start: 0.7976 (ttpp) cc_final: 0.7717 (ttpp)
REVERT: A 1196 MET cc_start: 0.8613 (tpp) cc_final: 0.8288 (mmm)
REVERT: A 1212 ASP cc_start: 0.8638 (OUTLIER) cc_final: 0.8259 (t70)
REVERT: A 1219 TYR cc_start: 0.8329 (t80) cc_final: 0.7661 (t80)
REVERT: B   80 LEU cc_start: 0.7526 (tt) cc_final: 0.7143 (tp)
REVERT: B  269 ASP cc_start: 0.8220 (OUTLIER) cc_final: 0.7818 (t70)
REVERT: B  359 ILE cc_start: 0.8929 (OUTLIER) cc_final: 0.8666 (pt)
REVERT: B  395 PHE cc_start: 0.7643 (m-80) cc_final: 0.7298 (m-10)
  outliers start: 31
  outliers final: 20
  residues processed: 135
  average time/residue: 0.1006
  time to fit residues: 20.5748
Evaluate side-chains
  134 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 106
  time to evaluate  : 0.442 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  223 PHE
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  435 THR
Chi-restraints excluded: chain A residue  501 THR
Chi-restraints excluded: chain A residue  506 LEU
Chi-restraints excluded: chain A residue  596 THR
Chi-restraints excluded: chain A residue  643 LEU
Chi-restraints excluded: chain A residue  661 VAL
Chi-restraints excluded: chain A residue  852 ILE
Chi-restraints excluded: chain A residue  964 GLU
Chi-restraints excluded: chain A residue  966 ARG
Chi-restraints excluded: chain A residue  975 ILE
Chi-restraints excluded: chain A residue 1005 LEU
Chi-restraints excluded: chain A residue 1006 LEU
Chi-restraints excluded: chain A residue 1095 LYS
Chi-restraints excluded: chain A residue 1212 ASP
Chi-restraints excluded: chain A residue 1278 LEU
Chi-restraints excluded: chain A residue 1299 THR
Chi-restraints excluded: chain A residue 1353 THR
Chi-restraints excluded: chain B residue  238 MET
Chi-restraints excluded: chain B residue  248 THR
Chi-restraints excluded: chain B residue  269 ASP
Chi-restraints excluded: chain B residue  280 TYR
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: 148
   random chunks:
   chunk 146 optimal weight:    3.9990
   chunk 59 optimal weight:    4.9990
   chunk 134 optimal weight:    0.9990
   chunk 28 optimal weight:    0.8980
   chunk 41 optimal weight:    1.9990
   chunk 61 optimal weight:    4.9990
   chunk 3 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9980
   chunk 40 optimal weight:    3.9990
   chunk 145 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A 504 ASN
** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1139 GLN
** B 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.191466 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.139030 restraints weight = 14325.648|
|-----------------------------------------------------------------------------|
r_work (start): 0.3631 rms_B_bonded: 3.24
r_work: 0.3273 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work: 0.3136 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3136
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
moved from start:          0.3475

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.098  12263  Z= 0.204
  Angle     :  0.682  12.834  16647  Z= 0.340
  Chirality :  0.046   0.177   1852
  Planarity :  0.004   0.047   2106
  Dihedral  :  8.060 138.276   1724
  Min Nonbonded Distance : 1.949

Molprobity Statistics.
  All-atom Clashscore : 11.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.77 %
    Favored  : 92.23 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 13.54 %
    Favored  : 84.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

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: -2.01 (0.22), residues: 1480
  helix: -0.58 (0.21), residues: 602
  sheet: -1.60 (0.42), residues: 160
  loop : -1.91 (0.23), residues: 718

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 316 
 TYR   0.023   0.002   TYR A 903 
 PHE   0.024   0.002   PHE A1402 
 TRP   0.026   0.002   TRP A 986 
 HIS   0.004   0.001   HIS A1176 

Details of bonding type rmsd
  covalent geometry    : bond        0.00479 (12258)
  covalent geometry    : angle       0.67419 (16634)
  SS BOND              : bond        0.00294 (    2)
  SS BOND              : angle       0.84448 (    4)
  hydrogen bonds       : bond        0.03749 (  409)
  hydrogen bonds       : angle       5.14833 ( 1125)
  link_BETA1-4         : bond        0.00574 (    2)
  link_BETA1-4         : angle       3.74903 (    6)
  link_NAG-ASN         : bond        0.01485 (    1)
  link_NAG-ASN         : angle       5.63802 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3346.95 seconds
wall clock time: 58 minutes 3.26 seconds (3483.26 seconds total)