Starting phenix.real_space_refine
on Thu May 15 22:08:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ip2_60755/05_2025/9ip2_60755.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ip2_60755/05_2025/9ip2_60755.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ip2_60755/05_2025/9ip2_60755.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ip2_60755/05_2025/9ip2_60755.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ip2_60755/05_2025/9ip2_60755.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ip2_60755/05_2025/9ip2_60755.cif"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.052
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     S      69      5.16       5
     C    8738      2.51       5
     N    2311      2.21       5
     O    2487      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 82 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 13606
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 11040
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1363, 11040
          Classifications: {'peptide': 1363}
          Link IDs: {'PCIS': 1, 'PTRANS': 58, 'TRANS': 1303}
          Chain breaks: 6
    Chain: "B"
      Number of atoms: 1649
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 1649
          Classifications: {'peptide': 217}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 15, 'TRANS': 201}
    Chain: "C"
      Number of atoms: 471
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 63, 471
          Classifications: {'peptide': 63}
          Link IDs: {'PTRANS': 5, 'TRANS': 57}
    Chain: "D"
      Number of atoms: 244
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 32, 244
          Classifications: {'peptide': 32}
          Link IDs: {'PTRANS': 1, 'TRANS': 30}
    Chain: "E"
      Number of atoms: 201
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 26, 201
          Classifications: {'peptide': 26}
          Link IDs: {'TRANS': 25}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   8878  SG  CYS A1108      32.108  20.473  35.084  1.00 61.94           S
  ATOM  10710  SG  CYS A1376      28.360  21.941  34.231  1.00 83.79           S
  ATOM  10716  SG  CYS A1377      30.727  23.468  36.500  1.00 67.25           S

  Time building chain proxies: 7.55, per 1000 atoms: 0.55
  Number of scatterers: 13606
  At special positions: 0
  Unit cell: (97.865, 124.246, 125.097, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      1     29.99
     S      69     16.00
     O    2487      8.00
     N    2311      7.00
     C    8738      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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
  Time building additional restraints: 3.26
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A2801 "
        pdb="ZN    ZN A2801 " - pdb=" SG  CYS A1108 "
        pdb="ZN    ZN A2801 " - pdb=" SG  CYS A1377 "
        pdb="ZN    ZN A2801 " - pdb=" SG  CYS A1376 "


  3358 Ramachandran restraints generated.
    1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3240

  Finding SS restraints...
    Secondary structure from input PDB file:
      91 helices and 9 sheets defined
      60.4% alpha, 6.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.52
  Creating SS restraints...
    Processing helix  chain 'A' and resid 18 through 28
      removed outlier: 4.077A  pdb=" N   ASP A  22 " --> pdb=" O   LEU A  18 " (cutoff:3.500A)
      removed outlier: 4.029A  pdb=" N   LEU A  23 " --> pdb=" O   ASP A  19 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 38 through 43
      removed outlier: 4.373A  pdb=" N   ASN A  42 " --> pdb=" O   PRO A  38 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 46 through 51
    Processing helix  chain 'A' and resid 52 through 54
      No H-bonds generated for 'chain 'A' and resid 52 through 54'
    Processing helix  chain 'A' and resid 55 through 62
    Processing helix  chain 'A' and resid 72 through 87
      removed outlier: 3.659A  pdb=" N   ASP A  77 " --> pdb=" O   HIS A  73 " (cutoff:3.500A)
      removed outlier: 5.234A  pdb=" N   HIS A  78 " --> pdb=" O   SER A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 88 through 95
      removed outlier: 4.032A  pdb=" N   VAL A  91 " --> pdb=" O   ILE A  88 " (cutoff:3.500A)
      removed outlier: 5.568A  pdb=" N   ASP A  92 " --> pdb=" O   ASN A  89 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   LYS A  95 " --> pdb=" O   ASP A  92 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 98 through 122
    Processing helix  chain 'A' and resid 137 through 143
    Processing helix  chain 'A' and resid 145 through 165
    Processing helix  chain 'A' and resid 195 through 200
    Processing helix  chain 'A' and resid 204 through 209
    Processing helix  chain 'A' and resid 210 through 215
      removed outlier: 3.656A  pdb=" N   ILE A 214 " --> pdb=" O   GLY A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 221 through 225
    Processing helix  chain 'A' and resid 237 through 264
    Processing helix  chain 'A' and resid 272 through 291
    Processing helix  chain 'A' and resid 293 through 299
      removed outlier: 3.844A  pdb=" N   LEU A 297 " --> pdb=" O   ASP A 293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 300 through 310
    Processing helix  chain 'A' and resid 316 through 319
    Processing helix  chain 'A' and resid 320 through 341
    Processing helix  chain 'A' and resid 348 through 361
      removed outlier: 4.237A  pdb=" N   GLN A 352 " --> pdb=" O   ALA A 348 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ALA A 361 " --> pdb=" O   THR A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 372
    Processing helix  chain 'A' and resid 384 through 398
      removed outlier: 4.009A  pdb=" N   LYS A 391 " --> pdb=" O   VAL A 387 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   VAL A 392 " --> pdb=" O   ALA A 388 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   SER A 398 " --> pdb=" O   LYS A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 427
    Processing helix  chain 'A' and resid 435 through 438
      removed outlier: 3.591A  pdb=" N   LEU A 438 " --> pdb=" O   ASP A 435 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 435 through 438'
    Processing helix  chain 'A' and resid 439 through 448
      removed outlier: 3.591A  pdb=" N   GLN A 444 " --> pdb=" O   PRO A 440 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   HIS A 445 " --> pdb=" O   TYR A 441 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   SER A 448 " --> pdb=" O   GLN A 444 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 460 through 466
    Processing helix  chain 'A' and resid 493 through 501
      removed outlier: 3.917A  pdb=" N   TRP A 497 " --> pdb=" O   GLN A 494 " (cutoff:3.500A)
      removed outlier: 5.712A  pdb=" N   ASP A 498 " --> pdb=" O   GLU A 495 " (cutoff:3.500A)
      removed outlier: 4.276A  pdb=" N   SER A 499 " --> pdb=" O   CYS A 496 " (cutoff:3.500A)
      removed outlier: 4.172A  pdb=" N   VAL A 500 " --> pdb=" O   TRP A 497 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 502 through 507
    Processing helix  chain 'A' and resid 518 through 524
      removed outlier: 3.712A  pdb=" N   LEU A 524 " --> pdb=" O   PRO A 520 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 530 through 540
      removed outlier: 3.935A  pdb=" N   ILE A 534 " --> pdb=" O   SER A 530 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 541 through 549
      Proline residue:  A 546  - end of helix
      removed outlier: 3.770A  pdb=" N   ARG A 549 " --> pdb=" O   PRO A 546 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 570 through 587
    Processing helix  chain 'A' and resid 588 through 592
      removed outlier: 3.599A  pdb=" N   PHE A 592 " --> pdb=" O   ALA A 589 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 599 through 603
    Processing helix  chain 'A' and resid 604 through 612
    Processing helix  chain 'A' and resid 637 through 643
      removed outlier: 3.729A  pdb=" N   ASN A 640 " --> pdb=" O   GLU A 637 " (cutoff:3.500A)
      removed outlier: 4.484A  pdb=" N   LEU A 641 " --> pdb=" O   LYS A 638 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   PHE A 643 " --> pdb=" O   ASN A 640 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 644 through 660
      removed outlier: 5.832A  pdb=" N   HIS A 650 " --> pdb=" O   GLU A 646 " (cutoff:3.500A)
      removed outlier: 5.059A  pdb=" N   PHE A 651 " --> pdb=" O   PHE A 647 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 666 through 672
    Processing helix  chain 'A' and resid 691 through 695
      removed outlier: 3.582A  pdb=" N   ARG A 694 " --> pdb=" O   GLU A 691 " (cutoff:3.500A)
      removed outlier: 4.437A  pdb=" N   ASN A 695 " --> pdb=" O   ASP A 692 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 691 through 695'
    Processing helix  chain 'A' and resid 715 through 735
    Processing helix  chain 'A' and resid 760 through 785
      removed outlier: 3.520A  pdb=" N   GLU A 769 " --> pdb=" O   GLU A 765 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 791 through 795
      removed outlier: 3.501A  pdb=" N   THR A 795 " --> pdb=" O   PRO A 792 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 818 through 823
    Processing helix  chain 'A' and resid 835 through 853
    Processing helix  chain 'A' and resid 857 through 878
      removed outlier: 3.759A  pdb=" N   ILE A 863 " --> pdb=" O   PRO A 859 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 887 through 894
    Processing helix  chain 'A' and resid 898 through 908
    Processing helix  chain 'A' and resid 909 through 913
    Processing helix  chain 'A' and resid 919 through 924
    Processing helix  chain 'A' and resid 930 through 947
      removed outlier: 3.571A  pdb=" N   SER A 934 " --> pdb=" O   ASP A 930 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 948 through 950
      No H-bonds generated for 'chain 'A' and resid 948 through 950'
    Processing helix  chain 'A' and resid 951 through 957
      removed outlier: 3.620A  pdb=" N   SER A 957 " --> pdb=" O   TYR A 953 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 964 through 971
      removed outlier: 3.635A  pdb=" N   PHE A 968 " --> pdb=" O   ASP A 964 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 977 through 981
      removed outlier: 3.556A  pdb=" N   SER A 980 " --> pdb=" O   VAL A 977 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   LYS A 981 " --> pdb=" O   PRO A 978 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 977 through 981'
    Processing helix  chain 'A' and resid 983 through 999
      removed outlier: 3.816A  pdb=" N   LEU A 987 " --> pdb=" O   ILE A 983 " (cutoff:3.500A)
      removed outlier: 4.882A  pdb=" N   GLN A 989 " --> pdb=" O   THR A 985 " (cutoff:3.500A)
      removed outlier: 5.051A  pdb=" N   THR A 990 " --> pdb=" O   PHE A 986 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ILE A 997 " --> pdb=" O   GLU A 993 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   SER A 999 " --> pdb=" O   ILE A 995 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1001 through 1008
    Processing helix  chain 'A' and resid 1011 through 1024
      removed outlier: 3.539A  pdb=" N   GLU A1015 " --> pdb=" O   GLY A1011 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   LEU A1024 " --> pdb=" O   CYS A1020 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1031 through 1039
    Processing helix  chain 'A' and resid 1041 through 1055
      removed outlier: 4.531A  pdb=" N   GLY A1055 " --> pdb=" O   GLY A1051 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1072 through 1090
    Processing helix  chain 'A' and resid 1096 through 1104
    Processing helix  chain 'A' and resid 1108 through 1121
    Processing helix  chain 'A' and resid 1121 through 1126
    Processing helix  chain 'A' and resid 1137 through 1141
    Processing helix  chain 'A' and resid 1150 through 1157
      removed outlier: 3.691A  pdb=" N   GLU A1155 " --> pdb=" O   GLU A1151 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   GLN A1156 " --> pdb=" O   ASP A1152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1207 through 1209
      No H-bonds generated for 'chain 'A' and resid 1207 through 1209'
    Processing helix  chain 'A' and resid 1216 through 1221
      removed outlier: 4.160A  pdb=" N   GLY A1220 " --> pdb=" O   ALA A1216 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   SER A1221 " --> pdb=" O   PRO A1217 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1216 through 1221'
    Processing helix  chain 'A' and resid 1238 through 1255
    Processing helix  chain 'A' and resid 1260 through 1270
      removed outlier: 4.090A  pdb=" N   LEU A1264 " --> pdb=" O   ASP A1260 " (cutoff:3.500A)
      Proline residue:  A1267  - end of helix
    Processing helix  chain 'A' and resid 1276 through 1282
      removed outlier: 3.806A  pdb=" N   VAL A1280 " --> pdb=" O   ASP A1276 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   LEU A1281 " --> pdb=" O   TYR A1277 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   ASN A1282 " --> pdb=" O   GLN A1278 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1276 through 1282'
    Processing helix  chain 'A' and resid 1291 through 1301
      removed outlier: 4.060A  pdb=" N   ASN A1297 " --> pdb=" O   VAL A1293 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   ASP A1298 " --> pdb=" O   HIS A1294 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1313 through 1315
      No H-bonds generated for 'chain 'A' and resid 1313 through 1315'
    Processing helix  chain 'A' and resid 1324 through 1328
    Processing helix  chain 'A' and resid 1342 through 1356
      removed outlier: 3.903A  pdb=" N   ASN A1346 " --> pdb=" O   GLN A1342 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   LEU A1356 " --> pdb=" O   LEU A1352 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 114 through 138
      removed outlier: 4.090A  pdb=" N   ILE B 120 " --> pdb=" O   THR B 116 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 144 through 156
    Processing helix  chain 'B' and resid 167 through 173
    Processing helix  chain 'B' and resid 183 through 197
    Processing helix  chain 'B' and resid 209 through 220
    Processing helix  chain 'B' and resid 226 through 242
      removed outlier: 3.686A  pdb=" N   ILE B 230 " --> pdb=" O   THR B 226 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 244 through 258
    Processing helix  chain 'B' and resid 261 through 273
    Processing helix  chain 'B' and resid 274 through 277
    Processing helix  chain 'B' and resid 293 through 298
      removed outlier: 4.551A  pdb=" N   LYS B 298 " --> pdb=" O   PRO B 295 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 308 through 311
    Processing helix  chain 'C' and resid 111 through 132
      removed outlier: 3.595A  pdb=" N   LYS C 122 " --> pdb=" O   GLU C 118 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 141 through 156
    Processing helix  chain 'C' and resid 162 through 168
    Processing helix  chain 'D' and resid 108 through 135
      removed outlier: 4.275A  pdb=" N   GLU D 118 " --> pdb=" O   GLY D 114 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   ALA D 119 " --> pdb=" O   ARG D 115 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   ASP D 132 " --> pdb=" O   LEU D 128 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   HIS D 133 " --> pdb=" O   ALA D 129 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 111 through 135
      removed outlier: 3.840A  pdb=" N   LEU E 134 " --> pdb=" O   LYS E 130 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   VAL E 135 " --> pdb=" O   TYR E 131 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 69
      removed outlier: 5.802A  pdb=" N   VAL A 232 " --> pdb=" O   SER A  66 " (cutoff:3.500A)
      removed outlier: 7.113A  pdb=" N   LEU A  68 " --> pdb=" O   VAL A 232 " (cutoff:3.500A)
      removed outlier: 8.271A  pdb=" N   VAL A 234 " --> pdb=" O   LEU A  68 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 401 through 402
    Processing sheet with id=AA3, first strand: chain 'A' and resid 565 through 568
    Processing sheet with id=AA4, first strand: chain 'A' and resid 737 through 742
      removed outlier: 4.323A  pdb=" N   LYS A 737 " --> pdb=" O   LEU A 752 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 801 through 803
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1028 through 1030
      removed outlier: 6.263A  pdb=" N   VAL A1029 " --> pdb=" O   ILE A1131 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1142 through 1149
      removed outlier: 6.769A  pdb=" N   THR A1368 " --> pdb=" O   ILE A1147 " (cutoff:3.500A)
      removed outlier: 5.367A  pdb=" N   VAL A1367 " --> pdb=" O   LEU A1194 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1200 through 1201
      removed outlier: 3.846A  pdb=" N   GLN A1200 " --> pdb=" O   ILE A1212 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 283 through 285
      removed outlier: 3.979A  pdb=" N   CYS B 315 " --> pdb=" O   LEU B 327 " (cutoff:3.500A)

    680 hydrogen bonds defined for protein.
    1926 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: 4.66

  Time building geometry restraints manager: 3.83 seconds

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

  Histogram of bond lengths:
        1.19 -     1.33: 2799
        1.33 -     1.46: 4578
        1.46 -     1.60: 6445
        1.60 -     1.74: 7
        1.74 -     1.87: 100
  Bond restraints: 13929
  Sorted by residual:
  bond pdb=" CB  LYS A1398 "
       pdb=" CG  LYS A1398 "
    ideal  model  delta    sigma   weight residual
    1.520  1.386  0.134 3.00e-02 1.11e+03 1.98e+01
  bond pdb=" CG  LYS A1263 "
       pdb=" CD  LYS A1263 "
    ideal  model  delta    sigma   weight residual
    1.520  1.400  0.120 3.00e-02 1.11e+03 1.59e+01
  bond pdb=" CB  ASN A 702 "
       pdb=" CG  ASN A 702 "
    ideal  model  delta    sigma   weight residual
    1.516  1.423  0.093 2.50e-02 1.60e+03 1.37e+01
  bond pdb=" C   HIS A  73 "
       pdb=" O   HIS A  73 "
    ideal  model  delta    sigma   weight residual
    1.236  1.280 -0.044 1.22e-02 6.72e+03 1.30e+01
  bond pdb=" CB  ARG A 649 "
       pdb=" CG  ARG A 649 "
    ideal  model  delta    sigma   weight residual
    1.520  1.415  0.105 3.00e-02 1.11e+03 1.22e+01
  ... (remaining 13924 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.35: 18719
        5.35 -    10.70: 134
       10.70 -    16.06: 16
       16.06 -    21.41: 5
       21.41 -    26.76: 4
  Bond angle restraints: 18878
  Sorted by residual:
  angle pdb=" C   GLN C 161 "
        pdb=" N   PRO C 162 "
        pdb=" CA  PRO C 162 "
      ideal   model   delta    sigma   weight residual
     120.45  131.86  -11.41 1.11e+00 8.12e-01 1.06e+02
  angle pdb=" CB  MET C 113 "
        pdb=" CG  MET C 113 "
        pdb=" SD  MET C 113 "
      ideal   model   delta    sigma   weight residual
     112.70   85.94   26.76 3.00e+00 1.11e-01 7.96e+01
  angle pdb=" CG  LYS A1263 "
        pdb=" CD  LYS A1263 "
        pdb=" CE  LYS A1263 "
      ideal   model   delta    sigma   weight residual
     111.30   91.31   19.99 2.30e+00 1.89e-01 7.56e+01
  angle pdb=" CG  ARG A  26 "
        pdb=" CD  ARG A  26 "
        pdb=" NE  ARG A  26 "
      ideal   model   delta    sigma   weight residual
     112.00   92.95   19.05 2.20e+00 2.07e-01 7.50e+01
  angle pdb=" CB  LEU A1241 "
        pdb=" CG  LEU A1241 "
        pdb=" CD2 LEU A1241 "
      ideal   model   delta    sigma   weight residual
     110.70   86.39   24.31 3.00e+00 1.11e-01 6.57e+01
  ... (remaining 18873 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.92: 7657
       17.92 -    35.84: 593
       35.84 -    53.76: 88
       53.76 -    71.68: 12
       71.68 -    89.60: 12
  Dihedral angle restraints: 8362
    sinusoidal: 3365
      harmonic: 4997
  Sorted by residual:
  dihedral pdb=" C   ASN A 624 "
           pdb=" N   ASN A 624 "
           pdb=" CA  ASN A 624 "
           pdb=" CB  ASN A 624 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -136.11   13.51     0      2.50e+00 1.60e-01 2.92e+01
  dihedral pdb=" N   ASN A 624 "
           pdb=" C   ASN A 624 "
           pdb=" CA  ASN A 624 "
           pdb=" CB  ASN A 624 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  135.95  -13.15     0      2.50e+00 1.60e-01 2.77e+01
  dihedral pdb=" CA  ASN A1291 "
           pdb=" C   ASN A1291 "
           pdb=" N   ILE A1292 "
           pdb=" CA  ILE A1292 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.93  -24.07     0      5.00e+00 4.00e-02 2.32e+01
  ... (remaining 8359 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.160: 2009
       0.160 -    0.321: 91
       0.321 -    0.481: 5
       0.481 -    0.641: 1
       0.641 -    0.801: 1
  Chirality restraints: 2107
  Sorted by residual:
  chirality pdb=" CG  LEU A1275 "
            pdb=" CB  LEU A1275 "
            pdb=" CD1 LEU A1275 "
            pdb=" CD2 LEU A1275 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -1.79   -0.80 2.00e-01 2.50e+01 1.61e+01
  chirality pdb=" CA  ASN A 624 "
            pdb=" N   ASN A 624 "
            pdb=" C   ASN A 624 "
            pdb=" CB  ASN A 624 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.98    0.53 2.00e-01 2.50e+01 7.01e+00
  chirality pdb=" CG  LEU A 636 "
            pdb=" CB  LEU A 636 "
            pdb=" CD1 LEU A 636 "
            pdb=" CD2 LEU A 636 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.99    0.40 2.00e-01 2.50e+01 4.05e+00
  ... (remaining 2104 not shown)

  Planarity restraints: 2401
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN A 726 "   -0.034 2.00e-02 2.50e+03   6.62e-02 4.39e+01
        pdb=" CD  GLN A 726 "    0.115 2.00e-02 2.50e+03
        pdb=" OE1 GLN A 726 "   -0.042 2.00e-02 2.50e+03
        pdb=" NE2 GLN A 726 "   -0.039 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU A 949 "   -0.028 2.00e-02 2.50e+03   5.89e-02 3.47e+01
        pdb=" CD  GLU A 949 "    0.102 2.00e-02 2.50e+03
        pdb=" OE1 GLU A 949 "   -0.039 2.00e-02 2.50e+03
        pdb=" OE2 GLU A 949 "   -0.035 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 430 "   -0.031 2.00e-02 2.50e+03   3.58e-02 2.56e+01
        pdb=" CG  TYR A 430 "    0.086 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 430 "   -0.010 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 430 "   -0.035 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 430 "   -0.016 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 430 "    0.009 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 430 "   -0.012 2.00e-02 2.50e+03
        pdb=" OH  TYR A 430 "    0.008 2.00e-02 2.50e+03
  ... (remaining 2398 not shown)

  Histogram of nonbonded interaction distances:
        1.71 -     2.35: 20
        2.35 -     2.98: 6951
        2.98 -     3.62: 18276
        3.62 -     4.26: 29563
        4.26 -     4.90: 51538
  Nonbonded interactions: 106348
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU A 539 "
            pdb=" O   LYS A 662 "
     model   vdw
     1.708 3.040
  nonbonded pdb=" NH1 ARG A1040 "
            pdb=" OE1 GLU A1246 "
     model   vdw
     1.962 3.120
  nonbonded pdb=" N   GLU A 623 "
            pdb=" OE1 GLU A 623 "
     model   vdw
     2.078 3.120
  nonbonded pdb=" OE2 GLU A1140 "
            pdb="ZN    ZN A2801 "
     model   vdw
     2.082 2.230
  nonbonded pdb=" O   ASP A1260 "
            pdb=" NZ  LYS A1263 "
     model   vdw
     2.121 3.120
  ... (remaining 106343 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:             1.720
  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:          0.560
  Check model and map are aligned:         0.100
  Set scattering table:                    0.130
  Process input model:                     33.350
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.050
  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:10.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   46.820
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8491
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      :  0.012   0.134  13932  Z= 0.552
  Angle     :  1.442  26.762  18878  Z= 0.786
  Chirality :  0.078   0.801   2107
  Planarity :  0.008   0.084   2401
  Dihedral  : 13.141  89.596   5122
  Min Nonbonded Distance : 1.708

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  3.93 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  1.20 %
    Favored  : 98.67 %
  Cbeta Deviations :  0.19 %
  Peptide Plane:
    Cis-proline     : 1.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.04 (0.20), residues: 1679
  helix:  0.95 (0.18), residues: 861
  sheet:  0.78 (0.51), residues: 92
  loop : -1.35 (0.21), residues: 726

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.065   0.006   TRP A1253 
 HIS   0.027   0.005   HIS A 687 
 PHE   0.057   0.006   PHE A 529 
 TYR   0.086   0.005   TYR A 430 
 ARG   0.054   0.002   ARG A  26 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.19347 (  680)
  hydrogen bonds       : angle       6.32314 ( 1926)
  metal coordination   : bond        0.03387 (    3)
  covalent geometry    : bond        0.01229 (13929)
  covalent geometry    : angle       1.44190 (18878)

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

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

  3358 Ramachandran restraints generated.
    1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3358 Ramachandran restraints generated.
    1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 256
  time to evaluate  : 1.578 
Fit side-chains
REVERT: A   59 LYS cc_start: 0.8566 (mtmt) cc_final: 0.8347 (mttm)
REVERT: A  141 LYS cc_start: 0.8379 (ttpp) cc_final: 0.8040 (ttpt)
REVERT: A  217 ARG cc_start: 0.7316 (mpp-170) cc_final: 0.6566 (mmt-90)
REVERT: A  349 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7143 (pt0)
REVERT: A  436 LEU cc_start: 0.7663 (mm) cc_final: 0.7426 (mm)
REVERT: A  443 ARG cc_start: 0.8130 (ttt180) cc_final: 0.7809 (ttm-80)
REVERT: A  459 GLN cc_start: 0.8444 (tt0) cc_final: 0.7944 (tp40)
REVERT: A  536 GLU cc_start: 0.8082 (tp30) cc_final: 0.7620 (mm-30)
REVERT: A  572 ARG cc_start: 0.7607 (mtp85) cc_final: 0.7220 (mtp180)
REVERT: A  574 ARG cc_start: 0.7743 (tpp80) cc_final: 0.7271 (tpt170)
REVERT: A  688 CYS cc_start: 0.8267 (p) cc_final: 0.8054 (p)
REVERT: A  740 SER cc_start: 0.8711 (p) cc_final: 0.8504 (m)
REVERT: A  802 ILE cc_start: 0.8936 (mt) cc_final: 0.8525 (tp)
REVERT: A  848 GLU cc_start: 0.8207 (pt0) cc_final: 0.7967 (pt0)
REVERT: A  926 ARG cc_start: 0.8881 (mtt180) cc_final: 0.8561 (mtt180)
REVERT: A  947 GLU cc_start: 0.8274 (mm-30) cc_final: 0.8006 (mp0)
REVERT: A  949 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7750 (mt-10)
REVERT: A 1013 ASP cc_start: 0.7725 (m-30) cc_final: 0.7342 (m-30)
REVERT: A 1018 ARG cc_start: 0.7777 (mmt-90) cc_final: 0.7510 (mpt180)
REVERT: A 1243 GLU cc_start: 0.7177 (mt-10) cc_final: 0.6592 (mm-30)
REVERT: A 1253 TRP cc_start: 0.8210 (t60) cc_final: 0.7982 (t-100)
REVERT: A 1283 PHE cc_start: 0.7026 (m-80) cc_final: 0.6688 (m-10)
REVERT: A 1395 ASP cc_start: 0.8127 (t70) cc_final: 0.7412 (t70)
REVERT: B  126 GLU cc_start: 0.8636 (tt0) cc_final: 0.8377 (tt0)
REVERT: B  127 MET cc_start: 0.8312 (tmm) cc_final: 0.8047 (ttp)
REVERT: B  254 GLN cc_start: 0.8194 (tt0) cc_final: 0.7985 (tt0)
REVERT: B  298 LYS cc_start: 0.8137 (ttmt) cc_final: 0.7928 (mtpp)
REVERT: D  128 LEU cc_start: 0.8031 (mm) cc_final: 0.7638 (mt)
  outliers start: 2
  outliers final: 1
  residues processed: 256
  average time/residue: 1.4552
  time to fit residues: 402.9990
Evaluate side-chains
  199 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 198
  time to evaluate  : 1.462 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  309 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 141 optimal weight:    0.9990
   chunk 127 optimal weight:    0.3980
   chunk 70 optimal weight:    2.9990
   chunk 43 optimal weight:    0.6980
   chunk 85 optimal weight:    0.8980
   chunk 68 optimal weight:    0.8980
   chunk 131 optimal weight:    3.9990
   chunk 50 optimal weight:    1.9990
   chunk 80 optimal weight:    2.9990
   chunk 98 optimal weight:    1.9990
   chunk 152 optimal weight:    2.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A  64 ASN
** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 509 ASN
A 624 ASN
A 746 ASN
A 764 GLN
A1141 GLN
A1156 GLN
A1188 ASN
A1270 ASN
A1322 ASN
A1374 ASN
A1408 ASN
C 161 GLN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.147722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.109560 restraints weight = 13826.922|
|-----------------------------------------------------------------------------|
r_work (start): 0.3166 rms_B_bonded: 1.85
r_work: 0.2975 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.2851 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.2851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8531
moved from start:          0.1641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  13932  Z= 0.145
  Angle     :  0.599  10.684  18878  Z= 0.321
  Chirality :  0.043   0.151   2107
  Planarity :  0.005   0.042   2401
  Dihedral  :  4.912  26.041   1836
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 3.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  :  7.32 %
    Favored  : 90.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.42 (0.20), residues: 1679
  helix:  1.23 (0.18), residues: 871
  sheet:  0.87 (0.50), residues: 86
  loop : -0.97 (0.22), residues: 722

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  76 
 HIS   0.006   0.001   HIS A 154 
 PHE   0.017   0.002   PHE A 372 
 TYR   0.019   0.002   TYR A 803 
 ARG   0.006   0.001   ARG A  41 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06587 (  680)
  hydrogen bonds       : angle       4.58456 ( 1926)
  metal coordination   : bond        0.01467 (    3)
  covalent geometry    : bond        0.00300 (13929)
  covalent geometry    : angle       0.59948 (18878)

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

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

  3358 Ramachandran restraints generated.
    1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3358 Ramachandran restraints generated.
    1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 223
  time to evaluate  : 1.555 
Fit side-chains
REVERT: A  141 LYS cc_start: 0.8279 (ttpp) cc_final: 0.7850 (ttpt)
REVERT: A  217 ARG cc_start: 0.6981 (mpp-170) cc_final: 0.6225 (mmt-90)
REVERT: A  229 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7408 (tp30)
REVERT: A  391 LYS cc_start: 0.8596 (tttt) cc_final: 0.8170 (ttpp)
REVERT: A  431 LYS cc_start: 0.8293 (tptp) cc_final: 0.8013 (tptp)
REVERT: A  536 GLU cc_start: 0.7854 (tp30) cc_final: 0.7449 (mm-30)
REVERT: A  597 MET cc_start: 0.6077 (OUTLIER) cc_final: 0.5548 (ttm)
REVERT: A  662 LYS cc_start: 0.6874 (ttpp) cc_final: 0.6582 (ttpp)
REVERT: A  688 CYS cc_start: 0.8156 (p) cc_final: 0.7507 (m)
REVERT: A  740 SER cc_start: 0.8835 (p) cc_final: 0.8633 (m)
REVERT: A  762 ASP cc_start: 0.7561 (OUTLIER) cc_final: 0.7293 (m-30)
REVERT: A  778 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.7854 (tm-30)
REVERT: A  802 ILE cc_start: 0.8614 (mt) cc_final: 0.8355 (tp)
REVERT: A  820 LYS cc_start: 0.8993 (ttpt) cc_final: 0.8746 (ttmt)
REVERT: A  926 ARG cc_start: 0.8953 (mtt180) cc_final: 0.8615 (mtt180)
REVERT: A  947 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7971 (mp0)
REVERT: A  992 ARG cc_start: 0.6978 (ttm-80) cc_final: 0.5856 (mtp180)
REVERT: A 1000 GLN cc_start: 0.7930 (mt0) cc_final: 0.7695 (mt0)
REVERT: A 1013 ASP cc_start: 0.7593 (m-30) cc_final: 0.7331 (m-30)
REVERT: A 1018 ARG cc_start: 0.7766 (mmt-90) cc_final: 0.7450 (mpt180)
REVERT: A 1073 MET cc_start: 0.7605 (mmm) cc_final: 0.7116 (tmm)
REVERT: A 1104 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7070 (pt0)
REVERT: A 1243 GLU cc_start: 0.7166 (mt-10) cc_final: 0.6570 (mm-30)
REVERT: A 1265 LEU cc_start: 0.8410 (mt) cc_final: 0.7928 (mm)
REVERT: A 1283 PHE cc_start: 0.7047 (m-80) cc_final: 0.6713 (m-10)
REVERT: A 1336 ASP cc_start: 0.6671 (t70) cc_final: 0.6225 (t0)
REVERT: A 1360 LYS cc_start: 0.8463 (mttp) cc_final: 0.7940 (mptt)
REVERT: B  254 GLN cc_start: 0.8372 (tt0) cc_final: 0.8134 (tt0)
REVERT: B  268 ARG cc_start: 0.7659 (ttm170) cc_final: 0.7454 (ttm170)
REVERT: C  166 LYS cc_start: 0.7596 (mptt) cc_final: 0.7242 (mmtt)
REVERT: D  128 LEU cc_start: 0.8146 (mm) cc_final: 0.7720 (mt)
REVERT: E  113 MET cc_start: 0.6229 (mmp) cc_final: 0.5646 (tpp)
  outliers start: 28
  outliers final: 11
  residues processed: 235
  average time/residue: 1.4338
  time to fit residues: 365.8169
Evaluate side-chains
  215 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 200
  time to evaluate  : 1.535 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ASP
Chi-restraints excluded: chain A residue  137 ASP
Chi-restraints excluded: chain A residue  149 MET
Chi-restraints excluded: chain A residue  187 ASP
Chi-restraints excluded: chain A residue  229 GLU
Chi-restraints excluded: chain A residue  425 SER
Chi-restraints excluded: chain A residue  597 MET
Chi-restraints excluded: chain A residue  603 GLU
Chi-restraints excluded: chain A residue  609 LEU
Chi-restraints excluded: chain A residue  762 ASP
Chi-restraints excluded: chain A residue  778 GLU
Chi-restraints excluded: chain A residue  907 ILE
Chi-restraints excluded: chain A residue  997 ILE
Chi-restraints excluded: chain B residue  142 THR
Chi-restraints excluded: chain E residue  124 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 154 optimal weight:    6.9990
   chunk 34 optimal weight:    2.9990
   chunk 41 optimal weight:    5.9990
   chunk 127 optimal weight:    4.9990
   chunk 102 optimal weight:    1.9990
   chunk 72 optimal weight:    3.9990
   chunk 0 optimal weight:    7.9990
   chunk 133 optimal weight:   10.0000
   chunk 56 optimal weight:    0.9980
   chunk 89 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
A  64 ASN
** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 696 ASN
A 746 ASN
A1188 ASN
A1270 ASN
A1322 ASN
A1374 ASN
A1408 ASN
D 133 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.143854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.105070 restraints weight = 13985.298|
|-----------------------------------------------------------------------------|
r_work (start): 0.3099 rms_B_bonded: 1.88
r_work: 0.2899 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.2772 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.2772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8607
moved from start:          0.1933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051  13932  Z= 0.212
  Angle     :  0.665  12.273  18878  Z= 0.350
  Chirality :  0.046   0.176   2107
  Planarity :  0.005   0.045   2401
  Dihedral  :  4.961  26.771   1834
  Min Nonbonded Distance : 2.285

Molprobity Statistics.
  All-atom Clashscore : 3.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 10.71 %
    Favored  : 86.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.33 (0.20), residues: 1679
  helix:  1.13 (0.18), residues: 868
  sheet:  1.30 (0.51), residues: 86
  loop : -1.04 (0.21), residues: 725

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 261 
 HIS   0.006   0.001   HIS A 687 
 PHE   0.028   0.002   PHE A 372 
 TYR   0.020   0.002   TYR A 803 
 ARG   0.005   0.001   ARG B 271 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07885 (  680)
  hydrogen bonds       : angle       4.47539 ( 1926)
  metal coordination   : bond        0.01880 (    3)
  covalent geometry    : bond        0.00518 (13929)
  covalent geometry    : angle       0.66513 (18878)

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

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

  3358 Ramachandran restraints generated.
    1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3358 Ramachandran restraints generated.
    1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 204
  time to evaluate  : 1.768 
Fit side-chains
   revert: symmetry clash
REVERT: A  141 LYS cc_start: 0.8232 (ttpp) cc_final: 0.7795 (ttmm)
REVERT: A  217 ARG cc_start: 0.7169 (mpp-170) cc_final: 0.6319 (mmt-90)
REVERT: A  229 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7387 (tp30)
REVERT: A  391 LYS cc_start: 0.8634 (tttt) cc_final: 0.8188 (ttpp)
REVERT: A  431 LYS cc_start: 0.8382 (tptp) cc_final: 0.8171 (tptt)
REVERT: A  443 ARG cc_start: 0.8032 (ttm-80) cc_final: 0.7750 (ttt180)
REVERT: A  536 GLU cc_start: 0.7928 (tp30) cc_final: 0.7517 (mm-30)
REVERT: A  572 ARG cc_start: 0.7629 (mtp85) cc_final: 0.7348 (mtp180)
REVERT: A  597 MET cc_start: 0.6108 (OUTLIER) cc_final: 0.5580 (ttm)
REVERT: A  688 CYS cc_start: 0.8227 (p) cc_final: 0.7578 (m)
REVERT: A  740 SER cc_start: 0.8886 (p) cc_final: 0.8640 (m)
REVERT: A  762 ASP cc_start: 0.7524 (OUTLIER) cc_final: 0.7263 (m-30)
REVERT: A  778 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.7746 (tm-30)
REVERT: A  802 ILE cc_start: 0.8660 (mt) cc_final: 0.8359 (tp)
REVERT: A  926 ARG cc_start: 0.8976 (mtt180) cc_final: 0.8708 (mtt180)
REVERT: A 1002 ARG cc_start: 0.7729 (ttp80) cc_final: 0.7469 (ttp-110)
REVERT: A 1018 ARG cc_start: 0.7808 (mmt-90) cc_final: 0.7515 (mmt-90)
REVERT: A 1073 MET cc_start: 0.7606 (mmm) cc_final: 0.7192 (tmm)
REVERT: A 1104 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7113 (pt0)
REVERT: A 1253 TRP cc_start: 0.8349 (t60) cc_final: 0.8100 (t-100)
REVERT: A 1283 PHE cc_start: 0.7176 (m-80) cc_final: 0.6838 (m-10)
REVERT: A 1299 GLN cc_start: 0.6755 (tp-100) cc_final: 0.6338 (tp-100)
REVERT: A 1336 ASP cc_start: 0.6643 (t70) cc_final: 0.6053 (t0)
REVERT: A 1360 LYS cc_start: 0.8503 (mttp) cc_final: 0.8249 (mttp)
REVERT: B  254 GLN cc_start: 0.8473 (tt0) cc_final: 0.8229 (tt0)
REVERT: C  166 LYS cc_start: 0.7560 (mptt) cc_final: 0.7185 (mmtm)
REVERT: D  128 LEU cc_start: 0.8212 (mm) cc_final: 0.7832 (mt)
  outliers start: 36
  outliers final: 18
  residues processed: 223
  average time/residue: 1.4402
  time to fit residues: 348.3744
Evaluate side-chains
  223 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 201
  time to evaluate  : 1.498 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ASP
Chi-restraints excluded: chain A residue  187 ASP
Chi-restraints excluded: chain A residue  229 GLU
Chi-restraints excluded: chain A residue  248 ILE
Chi-restraints excluded: chain A residue  425 SER
Chi-restraints excluded: chain A residue  584 LEU
Chi-restraints excluded: chain A residue  597 MET
Chi-restraints excluded: chain A residue  603 GLU
Chi-restraints excluded: chain A residue  609 LEU
Chi-restraints excluded: chain A residue  762 ASP
Chi-restraints excluded: chain A residue  778 GLU
Chi-restraints excluded: chain A residue  785 TYR
Chi-restraints excluded: chain A residue  851 THR
Chi-restraints excluded: chain A residue  907 ILE
Chi-restraints excluded: chain A residue 1251 LEU
Chi-restraints excluded: chain A residue 1367 VAL
Chi-restraints excluded: chain B residue  140 ARG
Chi-restraints excluded: chain B residue  142 THR
Chi-restraints excluded: chain B residue  309 ILE
Chi-restraints excluded: chain C residue  152 LEU
Chi-restraints excluded: chain C residue  170 VAL
Chi-restraints excluded: chain E residue  124 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 92 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9980
   chunk 157 optimal weight:    2.9990
   chunk 149 optimal weight:    0.8980
   chunk 37 optimal weight:    0.7980
   chunk 23 optimal weight:    5.9990
   chunk 108 optimal weight:    1.9990
   chunk 161 optimal weight:    4.9990
   chunk 147 optimal weight:    5.9990
   chunk 62 optimal weight:    8.9990
   chunk 11 optimal weight:    2.9990
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:
A  64 ASN
** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 696 ASN
A 746 ASN
A1270 ASN
A1322 ASN
A1374 ASN
A1408 ASN
D 133 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.146012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.107229 restraints weight = 13910.678|
|-----------------------------------------------------------------------------|
r_work (start): 0.3135 rms_B_bonded: 1.87
r_work: 0.2942 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.2816 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.2816
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8563
moved from start:          0.2205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  13932  Z= 0.152
  Angle     :  0.584  11.042  18878  Z= 0.308
  Chirality :  0.043   0.162   2107
  Planarity :  0.005   0.046   2401
  Dihedral  :  4.750  25.527   1834
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 3.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 12.24 %
    Favored  : 85.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.58 (0.20), residues: 1679
  helix:  1.34 (0.18), residues: 863
  sheet:  1.41 (0.51), residues: 86
  loop : -0.92 (0.21), residues: 730

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 261 
 HIS   0.005   0.001   HIS A 154 
 PHE   0.025   0.002   PHE A 372 
 TYR   0.019   0.002   TYR A 803 
 ARG   0.004   0.000   ARG B 271 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06442 (  680)
  hydrogen bonds       : angle       4.30949 ( 1926)
  metal coordination   : bond        0.00726 (    3)
  covalent geometry    : bond        0.00354 (13929)
  covalent geometry    : angle       0.58367 (18878)

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

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

  3358 Ramachandran restraints generated.
    1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3358 Ramachandran restraints generated.
    1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 210
  time to evaluate  : 1.569 
Fit side-chains
   revert: symmetry clash
REVERT: A    9 ASP cc_start: 0.7670 (OUTLIER) cc_final: 0.7434 (t0)
REVERT: A  141 LYS cc_start: 0.8143 (ttpp) cc_final: 0.7717 (ttmm)
REVERT: A  217 ARG cc_start: 0.7046 (mpp-170) cc_final: 0.6176 (mmt-90)
REVERT: A  219 GLN cc_start: 0.7705 (mt0) cc_final: 0.7158 (mt0)
REVERT: A  229 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7257 (tp30)
REVERT: A  391 LYS cc_start: 0.8529 (tttt) cc_final: 0.8116 (ttpp)
REVERT: A  431 LYS cc_start: 0.8337 (tptp) cc_final: 0.8124 (tptt)
REVERT: A  443 ARG cc_start: 0.7996 (ttm-80) cc_final: 0.7744 (ttt180)
REVERT: A  536 GLU cc_start: 0.7869 (tp30) cc_final: 0.7470 (mm-30)
REVERT: A  572 ARG cc_start: 0.7563 (mtp85) cc_final: 0.7280 (mtp180)
REVERT: A  688 CYS cc_start: 0.8302 (p) cc_final: 0.7782 (m)
REVERT: A  740 SER cc_start: 0.8862 (p) cc_final: 0.8624 (m)
REVERT: A  778 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.7661 (tm-30)
REVERT: A  802 ILE cc_start: 0.8648 (mt) cc_final: 0.8323 (tp)
REVERT: A  926 ARG cc_start: 0.8941 (mtt180) cc_final: 0.8682 (mtt180)
REVERT: A  992 ARG cc_start: 0.6901 (ttm-80) cc_final: 0.5719 (mtp180)
REVERT: A  996 THR cc_start: 0.8144 (t) cc_final: 0.7735 (p)
REVERT: A 1002 ARG cc_start: 0.7652 (ttp80) cc_final: 0.7341 (ttp-110)
REVERT: A 1018 ARG cc_start: 0.7788 (mmt-90) cc_final: 0.7500 (mmt-90)
REVERT: A 1073 MET cc_start: 0.7399 (mmm) cc_final: 0.7021 (tmm)
REVERT: A 1104 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7086 (pt0)
REVERT: A 1253 TRP cc_start: 0.8307 (t60) cc_final: 0.8075 (t-100)
REVERT: A 1283 PHE cc_start: 0.7273 (m-80) cc_final: 0.6904 (m-10)
REVERT: A 1299 GLN cc_start: 0.6795 (tp-100) cc_final: 0.6378 (tp-100)
REVERT: A 1336 ASP cc_start: 0.6701 (t70) cc_final: 0.5983 (t0)
REVERT: A 1360 LYS cc_start: 0.8465 (mttp) cc_final: 0.8224 (mttp)
REVERT: B  254 GLN cc_start: 0.8405 (tt0) cc_final: 0.8169 (tt0)
REVERT: C  166 LYS cc_start: 0.7557 (mptt) cc_final: 0.7204 (mmtm)
REVERT: C  167 ASP cc_start: 0.7435 (OUTLIER) cc_final: 0.6895 (m-30)
  outliers start: 37
  outliers final: 20
  residues processed: 228
  average time/residue: 1.3860
  time to fit residues: 343.2443
Evaluate side-chains
  226 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 202
  time to evaluate  : 1.593 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ASP
Chi-restraints excluded: chain A residue  187 ASP
Chi-restraints excluded: chain A residue  229 GLU
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  248 ILE
Chi-restraints excluded: chain A residue  425 SER
Chi-restraints excluded: chain A residue  459 GLN
Chi-restraints excluded: chain A residue  584 LEU
Chi-restraints excluded: chain A residue  603 GLU
Chi-restraints excluded: chain A residue  609 LEU
Chi-restraints excluded: chain A residue  778 GLU
Chi-restraints excluded: chain A residue  785 TYR
Chi-restraints excluded: chain A residue  821 THR
Chi-restraints excluded: chain A residue  851 THR
Chi-restraints excluded: chain A residue  907 ILE
Chi-restraints excluded: chain A residue 1251 LEU
Chi-restraints excluded: chain A residue 1254 VAL
Chi-restraints excluded: chain B residue  140 ARG
Chi-restraints excluded: chain B residue  142 THR
Chi-restraints excluded: chain B residue  308 THR
Chi-restraints excluded: chain B residue  309 ILE
Chi-restraints excluded: chain C residue  135 VAL
Chi-restraints excluded: chain C residue  167 ASP
Chi-restraints excluded: chain E residue  124 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 26 optimal weight:    0.1980
   chunk 118 optimal weight:    6.9990
   chunk 38 optimal weight:    2.9990
   chunk 146 optimal weight:    0.7980
   chunk 91 optimal weight:    2.9990
   chunk 135 optimal weight:    4.9990
   chunk 29 optimal weight:    0.5980
   chunk 81 optimal weight:    2.9990
   chunk 119 optimal weight:    2.9990
   chunk 51 optimal weight:    0.0050
   overall best weight:    0.7196

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

Flipped N/Q/H residues before XYZ refinement:
A  64 ASN
** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 696 ASN
A 746 ASN
A1270 ASN
A1322 ASN
A1408 ASN
D 133 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.149654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.111471 restraints weight = 13998.679|
|-----------------------------------------------------------------------------|
r_work (start): 0.3197 rms_B_bonded: 1.85
r_work: 0.3015 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.2891 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.2891
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8512
moved from start:          0.2461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  13932  Z= 0.112
  Angle     :  0.515  10.132  18878  Z= 0.270
  Chirality :  0.040   0.165   2107
  Planarity :  0.004   0.044   2401
  Dihedral  :  4.372  22.620   1834
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 2.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 13.24 %
    Favored  : 84.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.00 (0.20), residues: 1679
  helix:  1.67 (0.18), residues: 862
  sheet:  1.42 (0.50), residues: 86
  loop : -0.65 (0.22), residues: 731

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  76 
 HIS   0.004   0.001   HIS A 154 
 PHE   0.019   0.001   PHE A 372 
 TYR   0.016   0.001   TYR A 803 
 ARG   0.003   0.000   ARG A  53 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04931 (  680)
  hydrogen bonds       : angle       4.07731 ( 1926)
  metal coordination   : bond        0.01432 (    3)
  covalent geometry    : bond        0.00238 (13929)
  covalent geometry    : angle       0.51512 (18878)

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

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

  3358 Ramachandran restraints generated.
    1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3358 Ramachandran restraints generated.
    1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 207
  time to evaluate  : 1.633 
Fit side-chains
   revert: symmetry clash
REVERT: A    9 ASP cc_start: 0.7668 (OUTLIER) cc_final: 0.7355 (t0)
REVERT: A   77 ASP cc_start: 0.7603 (t0) cc_final: 0.7147 (p0)
REVERT: A  141 LYS cc_start: 0.8068 (ttpp) cc_final: 0.7657 (ttmm)
REVERT: A  217 ARG cc_start: 0.6984 (mpp-170) cc_final: 0.6190 (mmt-90)
REVERT: A  219 GLN cc_start: 0.7683 (mt0) cc_final: 0.7135 (mt0)
REVERT: A  391 LYS cc_start: 0.8428 (tttt) cc_final: 0.7741 (pttp)
REVERT: A  443 ARG cc_start: 0.8019 (ttm-80) cc_final: 0.7777 (ttt180)
REVERT: A  536 GLU cc_start: 0.7819 (tp30) cc_final: 0.7431 (mm-30)
REVERT: A  688 CYS cc_start: 0.8204 (p) cc_final: 0.7741 (m)
REVERT: A  740 SER cc_start: 0.8833 (p) cc_final: 0.8632 (m)
REVERT: A  778 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.7640 (tm-30)
REVERT: A  802 ILE cc_start: 0.8522 (mt) cc_final: 0.8296 (tp)
REVERT: A  992 ARG cc_start: 0.6909 (ttm-80) cc_final: 0.5789 (mtp180)
REVERT: A 1013 ASP cc_start: 0.7038 (OUTLIER) cc_final: 0.6747 (m-30)
REVERT: A 1018 ARG cc_start: 0.7758 (mmt-90) cc_final: 0.7470 (mmt-90)
REVERT: A 1104 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7108 (pt0)
REVERT: A 1253 TRP cc_start: 0.8283 (t60) cc_final: 0.8060 (t-100)
REVERT: A 1283 PHE cc_start: 0.7319 (m-80) cc_final: 0.6871 (m-10)
REVERT: A 1299 GLN cc_start: 0.6787 (tp-100) cc_final: 0.6379 (tp-100)
REVERT: A 1336 ASP cc_start: 0.6727 (t70) cc_final: 0.5983 (t0)
REVERT: A 1360 LYS cc_start: 0.8427 (mttp) cc_final: 0.8178 (mttm)
REVERT: A 1395 ASP cc_start: 0.8194 (t70) cc_final: 0.7568 (t70)
REVERT: B  254 GLN cc_start: 0.8370 (tt0) cc_final: 0.8143 (tt0)
REVERT: C  166 LYS cc_start: 0.7597 (mptt) cc_final: 0.7244 (mmtm)
REVERT: C  167 ASP cc_start: 0.7450 (OUTLIER) cc_final: 0.6914 (m-30)
  outliers start: 33
  outliers final: 13
  residues processed: 222
  average time/residue: 1.3848
  time to fit residues: 334.1825
Evaluate side-chains
  211 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 194
  time to evaluate  : 1.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ASP
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  609 LEU
Chi-restraints excluded: chain A residue  778 GLU
Chi-restraints excluded: chain A residue  785 TYR
Chi-restraints excluded: chain A residue  851 THR
Chi-restraints excluded: chain A residue  907 ILE
Chi-restraints excluded: chain A residue 1013 ASP
Chi-restraints excluded: chain A residue 1251 LEU
Chi-restraints excluded: chain A residue 1367 VAL
Chi-restraints excluded: chain B residue  142 THR
Chi-restraints excluded: chain B residue  308 THR
Chi-restraints excluded: chain B residue  309 ILE
Chi-restraints excluded: chain C residue  135 VAL
Chi-restraints excluded: chain C residue  167 ASP
Chi-restraints excluded: chain C residue  170 VAL
Chi-restraints excluded: chain E residue  124 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 123 optimal weight:    0.3980
   chunk 58 optimal weight:    0.0030
   chunk 12 optimal weight:    5.9990
   chunk 74 optimal weight:    4.9990
   chunk 75 optimal weight:    0.9990
   chunk 118 optimal weight:    7.9990
   chunk 148 optimal weight:    7.9990
   chunk 132 optimal weight:    3.9990
   chunk 147 optimal weight:    2.9990
   chunk 97 optimal weight:    4.9990
   chunk 44 optimal weight:    5.9990
   overall best weight:    1.6796

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

Flipped N/Q/H residues before XYZ refinement:
A  64 ASN
** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 696 ASN
** A 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 746 ASN
A1270 ASN
A1322 ASN
A1408 ASN
D 133 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.146225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.107611 restraints weight = 13993.164|
|-----------------------------------------------------------------------------|
r_work (start): 0.3126 rms_B_bonded: 1.86
r_work: 0.2936 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.2811 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.2811
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8555
moved from start:          0.2424

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  13932  Z= 0.163
  Angle     :  0.583  10.948  18878  Z= 0.305
  Chirality :  0.043   0.165   2107
  Planarity :  0.005   0.047   2401
  Dihedral  :  4.539  24.269   1834
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 3.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 12.97 %
    Favored  : 83.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.84 (0.20), residues: 1679
  helix:  1.54 (0.18), residues: 863
  sheet:  1.46 (0.51), residues: 86
  loop : -0.75 (0.22), residues: 730

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A 261 
 HIS   0.005   0.001   HIS A 154 
 PHE   0.023   0.002   PHE A 372 
 TYR   0.017   0.002   TYR A 803 
 ARG   0.004   0.000   ARG A  53 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06431 (  680)
  hydrogen bonds       : angle       4.18687 ( 1926)
  metal coordination   : bond        0.01005 (    3)
  covalent geometry    : bond        0.00390 (13929)
  covalent geometry    : angle       0.58332 (18878)

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

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

  3358 Ramachandran restraints generated.
    1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3358 Ramachandran restraints generated.
    1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 203
  time to evaluate  : 1.553 
Fit side-chains
   revert: symmetry clash
REVERT: A    9 ASP cc_start: 0.7658 (OUTLIER) cc_final: 0.7381 (t0)
REVERT: A  141 LYS cc_start: 0.8101 (ttpp) cc_final: 0.7683 (ttmm)
REVERT: A  217 ARG cc_start: 0.6956 (mpp-170) cc_final: 0.6158 (mmt-90)
REVERT: A  219 GLN cc_start: 0.7665 (mt0) cc_final: 0.7090 (mt0)
REVERT: A  229 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7231 (tp30)
REVERT: A  391 LYS cc_start: 0.8525 (tttt) cc_final: 0.8091 (ttpp)
REVERT: A  443 ARG cc_start: 0.8039 (ttm-80) cc_final: 0.7790 (ttt180)
REVERT: A  536 GLU cc_start: 0.7878 (tp30) cc_final: 0.7505 (mm-30)
REVERT: A  657 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7637 (mtm180)
REVERT: A  688 CYS cc_start: 0.8220 (p) cc_final: 0.7729 (m)
REVERT: A  740 SER cc_start: 0.8849 (p) cc_final: 0.8624 (m)
REVERT: A  743 MET cc_start: 0.5193 (mtt) cc_final: 0.3161 (mpt)
REVERT: A  778 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.7624 (tm-30)
REVERT: A  802 ILE cc_start: 0.8614 (mt) cc_final: 0.8323 (tp)
REVERT: A  884 LEU cc_start: 0.7118 (OUTLIER) cc_final: 0.6861 (tt)
REVERT: A  992 ARG cc_start: 0.7005 (ttm-80) cc_final: 0.5844 (mtp180)
REVERT: A 1002 ARG cc_start: 0.7681 (ttp80) cc_final: 0.7393 (ttp-110)
REVERT: A 1013 ASP cc_start: 0.7070 (OUTLIER) cc_final: 0.6792 (m-30)
REVERT: A 1018 ARG cc_start: 0.7825 (mmt-90) cc_final: 0.7533 (mmt180)
REVERT: A 1104 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7076 (pt0)
REVERT: A 1253 TRP cc_start: 0.8330 (t60) cc_final: 0.8080 (t-100)
REVERT: A 1283 PHE cc_start: 0.7340 (m-80) cc_final: 0.6885 (m-10)
REVERT: A 1299 GLN cc_start: 0.6783 (tp-100) cc_final: 0.6400 (tp-100)
REVERT: A 1336 ASP cc_start: 0.6742 (OUTLIER) cc_final: 0.5948 (t0)
REVERT: A 1360 LYS cc_start: 0.8464 (mttp) cc_final: 0.8199 (mttm)
REVERT: B  140 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.6968 (tmt170)
REVERT: B  254 GLN cc_start: 0.8390 (tt0) cc_final: 0.8165 (tt0)
REVERT: C  166 LYS cc_start: 0.7563 (mptt) cc_final: 0.7199 (mmtm)
REVERT: C  167 ASP cc_start: 0.7457 (OUTLIER) cc_final: 0.6910 (m-30)
  outliers start: 51
  outliers final: 26
  residues processed: 231
  average time/residue: 1.3433
  time to fit residues: 338.0533
Evaluate side-chains
  235 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 200
  time to evaluate  : 1.675 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ASP
Chi-restraints excluded: chain A residue  187 ASP
Chi-restraints excluded: chain A residue  229 GLU
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  248 ILE
Chi-restraints excluded: chain A residue  425 SER
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  512 VAL
Chi-restraints excluded: chain A residue  603 GLU
Chi-restraints excluded: chain A residue  609 LEU
Chi-restraints excluded: chain A residue  633 VAL
Chi-restraints excluded: chain A residue  657 ARG
Chi-restraints excluded: chain A residue  778 GLU
Chi-restraints excluded: chain A residue  785 TYR
Chi-restraints excluded: chain A residue  821 THR
Chi-restraints excluded: chain A residue  851 THR
Chi-restraints excluded: chain A residue  884 LEU
Chi-restraints excluded: chain A residue  907 ILE
Chi-restraints excluded: chain A residue 1013 ASP
Chi-restraints excluded: chain A residue 1060 LEU
Chi-restraints excluded: chain A residue 1079 GLU
Chi-restraints excluded: chain A residue 1251 LEU
Chi-restraints excluded: chain A residue 1254 VAL
Chi-restraints excluded: chain A residue 1336 ASP
Chi-restraints excluded: chain A residue 1367 VAL
Chi-restraints excluded: chain B residue  140 ARG
Chi-restraints excluded: chain B residue  142 THR
Chi-restraints excluded: chain B residue  308 THR
Chi-restraints excluded: chain B residue  309 ILE
Chi-restraints excluded: chain C residue  135 VAL
Chi-restraints excluded: chain C residue  152 LEU
Chi-restraints excluded: chain C residue  167 ASP
Chi-restraints excluded: chain C residue  170 VAL
Chi-restraints excluded: chain E residue  124 MET
Chi-restraints excluded: chain E residue  133 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 37 optimal weight:    4.9990
   chunk 55 optimal weight:    4.9990
   chunk 4 optimal weight:    3.9990
   chunk 137 optimal weight:    4.9990
   chunk 135 optimal weight:    1.9990
   chunk 51 optimal weight:    0.0060
   chunk 45 optimal weight:    0.8980
   chunk 14 optimal weight:    0.3980
   chunk 146 optimal weight:    3.9990
   chunk 20 optimal weight:    2.9990
   chunk 54 optimal weight:    3.9990
   overall best weight:    1.2600

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

Flipped N/Q/H residues before XYZ refinement:
A  64 ASN
** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 696 ASN
** A 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 746 ASN
A1270 ASN
A1322 ASN
A1408 ASN
D 133 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.146802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.108345 restraints weight = 13989.685|
|-----------------------------------------------------------------------------|
r_work (start): 0.3164 rms_B_bonded: 1.84
r_work: 0.2975 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.2851 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.2851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8597
moved from start:          0.2495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  13932  Z= 0.136
  Angle     :  0.551  10.251  18878  Z= 0.289
  Chirality :  0.042   0.162   2107
  Planarity :  0.005   0.046   2401
  Dihedral  :  4.470  23.841   1834
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 3.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 13.51 %
    Favored  : 83.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.99 (0.20), residues: 1679
  helix:  1.64 (0.18), residues: 856
  sheet:  1.53 (0.51), residues: 86
  loop : -0.62 (0.22), residues: 737

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 261 
 HIS   0.004   0.001   HIS A 154 
 PHE   0.022   0.002   PHE A 372 
 TYR   0.017   0.001   TYR A 803 
 ARG   0.006   0.000   ARG A 694 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05841 (  680)
  hydrogen bonds       : angle       4.14341 ( 1926)
  metal coordination   : bond        0.00858 (    3)
  covalent geometry    : bond        0.00309 (13929)
  covalent geometry    : angle       0.55140 (18878)

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

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

  3358 Ramachandran restraints generated.
    1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3358 Ramachandran restraints generated.
    1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 197
  time to evaluate  : 1.509 
Fit side-chains
REVERT: A    9 ASP cc_start: 0.7729 (OUTLIER) cc_final: 0.7443 (t0)
REVERT: A  141 LYS cc_start: 0.8109 (ttpp) cc_final: 0.7733 (ttmm)
REVERT: A  217 ARG cc_start: 0.6988 (mpp-170) cc_final: 0.6202 (mmt-90)
REVERT: A  219 GLN cc_start: 0.7754 (mt0) cc_final: 0.7198 (mt0)
REVERT: A  229 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7278 (tp30)
REVERT: A  391 LYS cc_start: 0.8542 (tttt) cc_final: 0.8150 (ttpp)
REVERT: A  443 ARG cc_start: 0.8124 (ttm-80) cc_final: 0.7813 (ttt180)
REVERT: A  444 GLN cc_start: 0.8185 (pp30) cc_final: 0.7942 (pt0)
REVERT: A  536 GLU cc_start: 0.7925 (tp30) cc_final: 0.7568 (mm-30)
REVERT: A  657 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7658 (mtm180)
REVERT: A  688 CYS cc_start: 0.8241 (p) cc_final: 0.7804 (m)
REVERT: A  702 ASN cc_start: 0.8524 (OUTLIER) cc_final: 0.8175 (m110)
REVERT: A  740 SER cc_start: 0.8865 (p) cc_final: 0.8655 (m)
REVERT: A  743 MET cc_start: 0.5231 (mtt) cc_final: 0.3237 (mpt)
REVERT: A  778 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.7724 (tm-30)
REVERT: A  802 ILE cc_start: 0.8633 (mt) cc_final: 0.8373 (tp)
REVERT: A  884 LEU cc_start: 0.7096 (OUTLIER) cc_final: 0.6838 (tt)
REVERT: A  992 ARG cc_start: 0.7124 (ttm-80) cc_final: 0.5964 (mtp180)
REVERT: A 1002 ARG cc_start: 0.7724 (ttp80) cc_final: 0.7459 (ttp-110)
REVERT: A 1013 ASP cc_start: 0.7100 (OUTLIER) cc_final: 0.6815 (m-30)
REVERT: A 1018 ARG cc_start: 0.7893 (mmt-90) cc_final: 0.7619 (mmt180)
REVERT: A 1104 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7176 (pt0)
REVERT: A 1143 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.8069 (pt0)
REVERT: A 1253 TRP cc_start: 0.8354 (t60) cc_final: 0.8127 (t-100)
REVERT: A 1283 PHE cc_start: 0.7475 (m-80) cc_final: 0.7021 (m-10)
REVERT: A 1299 GLN cc_start: 0.6892 (tp-100) cc_final: 0.6511 (tp-100)
REVERT: A 1336 ASP cc_start: 0.6806 (t70) cc_final: 0.6065 (t0)
REVERT: A 1360 LYS cc_start: 0.8487 (mttp) cc_final: 0.8242 (mttm)
REVERT: B  140 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.6841 (tmt170)
REVERT: B  254 GLN cc_start: 0.8476 (tt0) cc_final: 0.8257 (tt0)
REVERT: C  166 LYS cc_start: 0.7654 (mptt) cc_final: 0.7293 (mmtm)
REVERT: C  167 ASP cc_start: 0.7527 (OUTLIER) cc_final: 0.6992 (m-30)
  outliers start: 43
  outliers final: 25
  residues processed: 220
  average time/residue: 1.3250
  time to fit residues: 318.3289
Evaluate side-chains
  230 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 195
  time to evaluate  : 1.429 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ASP
Chi-restraints excluded: chain A residue  187 ASP
Chi-restraints excluded: chain A residue  229 GLU
Chi-restraints excluded: chain A residue  248 ILE
Chi-restraints excluded: chain A residue  425 SER
Chi-restraints excluded: chain A residue  475 THR
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  512 VAL
Chi-restraints excluded: chain A residue  584 LEU
Chi-restraints excluded: chain A residue  603 GLU
Chi-restraints excluded: chain A residue  609 LEU
Chi-restraints excluded: chain A residue  633 VAL
Chi-restraints excluded: chain A residue  657 ARG
Chi-restraints excluded: chain A residue  702 ASN
Chi-restraints excluded: chain A residue  778 GLU
Chi-restraints excluded: chain A residue  785 TYR
Chi-restraints excluded: chain A residue  821 THR
Chi-restraints excluded: chain A residue  851 THR
Chi-restraints excluded: chain A residue  884 LEU
Chi-restraints excluded: chain A residue  907 ILE
Chi-restraints excluded: chain A residue 1013 ASP
Chi-restraints excluded: chain A residue 1079 GLU
Chi-restraints excluded: chain A residue 1143 GLU
Chi-restraints excluded: chain A residue 1251 LEU
Chi-restraints excluded: chain A residue 1367 VAL
Chi-restraints excluded: chain B residue  140 ARG
Chi-restraints excluded: chain B residue  142 THR
Chi-restraints excluded: chain B residue  308 THR
Chi-restraints excluded: chain B residue  309 ILE
Chi-restraints excluded: chain C residue  135 VAL
Chi-restraints excluded: chain C residue  152 LEU
Chi-restraints excluded: chain C residue  167 ASP
Chi-restraints excluded: chain C residue  170 VAL
Chi-restraints excluded: chain E residue  124 MET
Chi-restraints excluded: chain E residue  133 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 20 optimal weight:    0.8980
   chunk 107 optimal weight:    0.9980
   chunk 103 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 148 optimal weight:    1.9990
   chunk 84 optimal weight:    1.9990
   chunk 138 optimal weight:    6.9990
   chunk 127 optimal weight:    0.9990
   chunk 13 optimal weight:    0.4980
   chunk 10 optimal weight:    3.9990
   chunk 164 optimal weight:    9.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A  64 ASN
** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 696 ASN
** A 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 746 ASN
A1270 ASN
A1322 ASN
A1408 ASN
D 133 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.149199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.110936 restraints weight = 14053.957|
|-----------------------------------------------------------------------------|
r_work (start): 0.3163 rms_B_bonded: 1.85
r_work: 0.2976 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.2851 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.2851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8511
moved from start:          0.2623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  13932  Z= 0.116
  Angle     :  0.523   9.961  18878  Z= 0.273
  Chirality :  0.041   0.168   2107
  Planarity :  0.004   0.045   2401
  Dihedral  :  4.297  22.604   1834
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 2.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 13.91 %
    Favored  : 83.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.12 (0.20), residues: 1679
  helix:  1.75 (0.18), residues: 862
  sheet:  1.56 (0.51), residues: 86
  loop : -0.58 (0.22), residues: 731

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 261 
 HIS   0.004   0.001   HIS A 154 
 PHE   0.020   0.001   PHE A 372 
 TYR   0.015   0.001   TYR A 803 
 ARG   0.006   0.000   ARG A 503 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05100 (  680)
  hydrogen bonds       : angle       4.05538 ( 1926)
  metal coordination   : bond        0.00851 (    3)
  covalent geometry    : bond        0.00253 (13929)
  covalent geometry    : angle       0.52320 (18878)

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

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

  3358 Ramachandran restraints generated.
    1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3358 Ramachandran restraints generated.
    1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 200
  time to evaluate  : 1.539 
Fit side-chains
REVERT: A    9 ASP cc_start: 0.7667 (OUTLIER) cc_final: 0.7353 (t0)
REVERT: A  141 LYS cc_start: 0.8081 (ttpp) cc_final: 0.7682 (ttmm)
REVERT: A  217 ARG cc_start: 0.6860 (mpp-170) cc_final: 0.6065 (mmt-90)
REVERT: A  219 GLN cc_start: 0.7681 (mt0) cc_final: 0.7105 (mt0)
REVERT: A  229 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7255 (tp30)
REVERT: A  391 LYS cc_start: 0.8429 (tttt) cc_final: 0.8029 (ttpp)
REVERT: A  536 GLU cc_start: 0.7805 (tp30) cc_final: 0.7433 (mm-30)
REVERT: A  657 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7342 (mtm-85)
REVERT: A  688 CYS cc_start: 0.8111 (p) cc_final: 0.7752 (m)
REVERT: A  743 MET cc_start: 0.5217 (mtt) cc_final: 0.3201 (mpt)
REVERT: A  778 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.7629 (tm-30)
REVERT: A  802 ILE cc_start: 0.8507 (mt) cc_final: 0.8254 (tp)
REVERT: A  884 LEU cc_start: 0.6975 (OUTLIER) cc_final: 0.6744 (tt)
REVERT: A  992 ARG cc_start: 0.6902 (ttm-80) cc_final: 0.5768 (mtp180)
REVERT: A 1013 ASP cc_start: 0.7021 (OUTLIER) cc_final: 0.6723 (m-30)
REVERT: A 1018 ARG cc_start: 0.7792 (mmt-90) cc_final: 0.7519 (mmt-90)
REVERT: A 1073 MET cc_start: 0.7294 (OUTLIER) cc_final: 0.6928 (ttt)
REVERT: A 1104 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7050 (pt0)
REVERT: A 1143 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.8014 (pt0)
REVERT: A 1253 TRP cc_start: 0.8280 (t60) cc_final: 0.8055 (t-100)
REVERT: A 1283 PHE cc_start: 0.7393 (m-80) cc_final: 0.6922 (m-10)
REVERT: A 1299 GLN cc_start: 0.6782 (tp-100) cc_final: 0.6382 (tp-100)
REVERT: A 1336 ASP cc_start: 0.6663 (OUTLIER) cc_final: 0.5882 (t0)
REVERT: A 1360 LYS cc_start: 0.8417 (mttp) cc_final: 0.8154 (mttm)
REVERT: A 1395 ASP cc_start: 0.8181 (t0) cc_final: 0.7595 (t70)
REVERT: B  254 GLN cc_start: 0.8348 (tt0) cc_final: 0.8124 (tt0)
REVERT: C  166 LYS cc_start: 0.7582 (mptt) cc_final: 0.7227 (mmtm)
REVERT: C  167 ASP cc_start: 0.7459 (OUTLIER) cc_final: 0.6920 (m-30)
  outliers start: 38
  outliers final: 22
  residues processed: 219
  average time/residue: 1.3141
  time to fit residues: 314.0146
Evaluate side-chains
  224 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 192
  time to evaluate  : 1.547 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ASP
Chi-restraints excluded: chain A residue  187 ASP
Chi-restraints excluded: chain A residue  229 GLU
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  425 SER
Chi-restraints excluded: chain A residue  475 THR
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  512 VAL
Chi-restraints excluded: chain A residue  603 GLU
Chi-restraints excluded: chain A residue  609 LEU
Chi-restraints excluded: chain A residue  657 ARG
Chi-restraints excluded: chain A residue  778 GLU
Chi-restraints excluded: chain A residue  785 TYR
Chi-restraints excluded: chain A residue  821 THR
Chi-restraints excluded: chain A residue  851 THR
Chi-restraints excluded: chain A residue  884 LEU
Chi-restraints excluded: chain A residue  907 ILE
Chi-restraints excluded: chain A residue 1013 ASP
Chi-restraints excluded: chain A residue 1060 LEU
Chi-restraints excluded: chain A residue 1073 MET
Chi-restraints excluded: chain A residue 1143 GLU
Chi-restraints excluded: chain A residue 1251 LEU
Chi-restraints excluded: chain A residue 1254 VAL
Chi-restraints excluded: chain A residue 1336 ASP
Chi-restraints excluded: chain A residue 1367 VAL
Chi-restraints excluded: chain B residue  308 THR
Chi-restraints excluded: chain B residue  309 ILE
Chi-restraints excluded: chain C residue  135 VAL
Chi-restraints excluded: chain C residue  152 LEU
Chi-restraints excluded: chain C residue  167 ASP
Chi-restraints excluded: chain C residue  170 VAL
Chi-restraints excluded: chain E residue  124 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    1.9990
   chunk 106 optimal weight:    0.5980
   chunk 114 optimal weight:    4.9990
   chunk 139 optimal weight:    7.9990
   chunk 95 optimal weight:    5.9990
   chunk 2 optimal weight:    3.9990
   chunk 92 optimal weight:    0.8980
   chunk 162 optimal weight:    0.9990
   chunk 41 optimal weight:    5.9990
   chunk 103 optimal weight:    3.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
A  64 ASN
** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 696 ASN
** A 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 746 ASN
A1270 ASN
A1322 ASN
A1408 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.148586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.110209 restraints weight = 13923.673|
|-----------------------------------------------------------------------------|
r_work (start): 0.3158 rms_B_bonded: 1.81
r_work: 0.2969 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.2845 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.2845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8534
moved from start:          0.2632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  13932  Z= 0.123
  Angle     :  0.535   9.869  18878  Z= 0.278
  Chirality :  0.041   0.166   2107
  Planarity :  0.004   0.045   2401
  Dihedral  :  4.311  22.866   1834
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 2.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 14.30 %
    Favored  : 83.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.12 (0.20), residues: 1679
  helix:  1.74 (0.18), residues: 862
  sheet:  1.56 (0.51), residues: 86
  loop : -0.57 (0.22), residues: 731

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 261 
 HIS   0.004   0.001   HIS A 154 
 PHE   0.020   0.002   PHE A 372 
 TYR   0.015   0.001   TYR A 803 
 ARG   0.006   0.000   ARG A1272 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05382 (  680)
  hydrogen bonds       : angle       4.06183 ( 1926)
  metal coordination   : bond        0.00747 (    3)
  covalent geometry    : bond        0.00275 (13929)
  covalent geometry    : angle       0.53483 (18878)

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

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

  3358 Ramachandran restraints generated.
    1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3358 Ramachandran restraints generated.
    1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 194
  time to evaluate  : 1.544 
Fit side-chains
REVERT: A    9 ASP cc_start: 0.7663 (OUTLIER) cc_final: 0.7375 (t0)
REVERT: A  141 LYS cc_start: 0.8075 (ttpp) cc_final: 0.7696 (ttmm)
REVERT: A  217 ARG cc_start: 0.6883 (mpp-170) cc_final: 0.6083 (mmt-90)
REVERT: A  219 GLN cc_start: 0.7658 (mt0) cc_final: 0.7135 (mt0)
REVERT: A  229 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7276 (tp30)
REVERT: A  391 LYS cc_start: 0.8465 (tttt) cc_final: 0.8062 (ttpp)
REVERT: A  536 GLU cc_start: 0.7915 (tp30) cc_final: 0.7560 (mm-30)
REVERT: A  657 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7245 (mtm-85)
REVERT: A  688 CYS cc_start: 0.8233 (p) cc_final: 0.7921 (m)
REVERT: A  743 MET cc_start: 0.5117 (mtt) cc_final: 0.3166 (mpt)
REVERT: A  778 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.7670 (tm-30)
REVERT: A  802 ILE cc_start: 0.8540 (mt) cc_final: 0.8284 (tp)
REVERT: A  884 LEU cc_start: 0.7020 (OUTLIER) cc_final: 0.6797 (tt)
REVERT: A  992 ARG cc_start: 0.7028 (ttm-80) cc_final: 0.5861 (mtp180)
REVERT: A 1013 ASP cc_start: 0.7050 (OUTLIER) cc_final: 0.6760 (m-30)
REVERT: A 1018 ARG cc_start: 0.7818 (mmt-90) cc_final: 0.7538 (mmt-90)
REVERT: A 1073 MET cc_start: 0.7394 (OUTLIER) cc_final: 0.7022 (ttt)
REVERT: A 1104 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7068 (pt0)
REVERT: A 1143 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.8002 (pt0)
REVERT: A 1253 TRP cc_start: 0.8314 (t60) cc_final: 0.8092 (t-100)
REVERT: A 1283 PHE cc_start: 0.7426 (m-80) cc_final: 0.6954 (m-10)
REVERT: A 1299 GLN cc_start: 0.6813 (tp-100) cc_final: 0.6418 (tp-100)
REVERT: A 1336 ASP cc_start: 0.6711 (OUTLIER) cc_final: 0.5926 (t0)
REVERT: A 1360 LYS cc_start: 0.8411 (mttp) cc_final: 0.8151 (mttm)
REVERT: A 1395 ASP cc_start: 0.8166 (t0) cc_final: 0.7568 (t70)
REVERT: B  254 GLN cc_start: 0.8379 (tt0) cc_final: 0.8157 (tt0)
REVERT: C  167 ASP cc_start: 0.7479 (OUTLIER) cc_final: 0.6940 (m-30)
  outliers start: 39
  outliers final: 22
  residues processed: 212
  average time/residue: 1.3936
  time to fit residues: 324.1560
Evaluate side-chains
  226 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 194
  time to evaluate  : 1.491 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ASP
Chi-restraints excluded: chain A residue  187 ASP
Chi-restraints excluded: chain A residue  229 GLU
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  248 ILE
Chi-restraints excluded: chain A residue  425 SER
Chi-restraints excluded: chain A residue  475 THR
Chi-restraints excluded: chain A residue  512 VAL
Chi-restraints excluded: chain A residue  603 GLU
Chi-restraints excluded: chain A residue  609 LEU
Chi-restraints excluded: chain A residue  657 ARG
Chi-restraints excluded: chain A residue  766 ASN
Chi-restraints excluded: chain A residue  778 GLU
Chi-restraints excluded: chain A residue  785 TYR
Chi-restraints excluded: chain A residue  821 THR
Chi-restraints excluded: chain A residue  851 THR
Chi-restraints excluded: chain A residue  884 LEU
Chi-restraints excluded: chain A residue  907 ILE
Chi-restraints excluded: chain A residue 1013 ASP
Chi-restraints excluded: chain A residue 1073 MET
Chi-restraints excluded: chain A residue 1143 GLU
Chi-restraints excluded: chain A residue 1251 LEU
Chi-restraints excluded: chain A residue 1254 VAL
Chi-restraints excluded: chain A residue 1336 ASP
Chi-restraints excluded: chain A residue 1367 VAL
Chi-restraints excluded: chain B residue  308 THR
Chi-restraints excluded: chain B residue  309 ILE
Chi-restraints excluded: chain C residue  135 VAL
Chi-restraints excluded: chain C residue  152 LEU
Chi-restraints excluded: chain C residue  167 ASP
Chi-restraints excluded: chain C residue  170 VAL
Chi-restraints excluded: chain E residue  124 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 68 optimal weight:    2.9990
   chunk 109 optimal weight:    0.7980
   chunk 44 optimal weight:    0.2980
   chunk 159 optimal weight:    6.9990
   chunk 59 optimal weight:    4.9990
   chunk 83 optimal weight:    0.6980
   chunk 154 optimal weight:    4.9990
   chunk 21 optimal weight:    0.5980
   chunk 27 optimal weight:    5.9990
   chunk 76 optimal weight:    2.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A  64 ASN
** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 696 ASN
A 702 ASN
A 746 ASN
A1270 ASN
A1322 ASN
A1408 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.149446 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.111227 restraints weight = 13960.980|
|-----------------------------------------------------------------------------|
r_work (start): 0.3177 rms_B_bonded: 1.78
r_work: 0.2989 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.2864 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.2864
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8506
moved from start:          0.2694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  13932  Z= 0.115
  Angle     :  0.522   9.435  18878  Z= 0.271
  Chirality :  0.040   0.164   2107
  Planarity :  0.004   0.044   2401
  Dihedral  :  4.235  22.354   1834
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 3.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 14.84 %
    Favored  : 82.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.17 (0.20), residues: 1679
  helix:  1.79 (0.18), residues: 862
  sheet:  1.56 (0.51), residues: 86
  loop : -0.54 (0.22), residues: 731

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  76 
 HIS   0.004   0.001   HIS A 154 
 PHE   0.020   0.001   PHE A 372 
 TYR   0.015   0.001   TYR A 803 
 ARG   0.005   0.000   ARG A  53 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05066 (  680)
  hydrogen bonds       : angle       4.03840 ( 1926)
  metal coordination   : bond        0.00714 (    3)
  covalent geometry    : bond        0.00251 (13929)
  covalent geometry    : angle       0.52150 (18878)

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

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

  3358 Ramachandran restraints generated.
    1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3358 Ramachandran restraints generated.
    1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 197
  time to evaluate  : 1.484 
Fit side-chains
REVERT: A    9 ASP cc_start: 0.7647 (OUTLIER) cc_final: 0.7333 (t0)
REVERT: A  141 LYS cc_start: 0.8063 (ttpp) cc_final: 0.7669 (ttmm)
REVERT: A  217 ARG cc_start: 0.6846 (mpp-170) cc_final: 0.6042 (mmt-90)
REVERT: A  219 GLN cc_start: 0.7612 (mt0) cc_final: 0.7088 (mt0)
REVERT: A  229 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7287 (tp30)
REVERT: A  391 LYS cc_start: 0.8421 (tttt) cc_final: 0.7675 (pttp)
REVERT: A  536 GLU cc_start: 0.7897 (tp30) cc_final: 0.7544 (mm-30)
REVERT: A  572 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.7134 (mtm180)
REVERT: A  657 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7334 (mtm-85)
REVERT: A  662 LYS cc_start: 0.6459 (ttpp) cc_final: 0.6254 (pttm)
REVERT: A  688 CYS cc_start: 0.8175 (p) cc_final: 0.7879 (m)
REVERT: A  743 MET cc_start: 0.5025 (mtt) cc_final: 0.3133 (mpt)
REVERT: A  778 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.7656 (tm-30)
REVERT: A  802 ILE cc_start: 0.8504 (mt) cc_final: 0.8258 (tp)
REVERT: A  992 ARG cc_start: 0.7027 (ttm-80) cc_final: 0.5845 (mtp180)
REVERT: A 1013 ASP cc_start: 0.7016 (OUTLIER) cc_final: 0.6725 (m-30)
REVERT: A 1018 ARG cc_start: 0.7801 (mmt-90) cc_final: 0.7521 (mmt-90)
REVERT: A 1073 MET cc_start: 0.7408 (ttm) cc_final: 0.7024 (ttt)
REVERT: A 1104 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7040 (pt0)
REVERT: A 1143 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.8042 (pt0)
REVERT: A 1253 TRP cc_start: 0.8300 (t60) cc_final: 0.8079 (t-100)
REVERT: A 1283 PHE cc_start: 0.7415 (m-80) cc_final: 0.6942 (m-10)
REVERT: A 1299 GLN cc_start: 0.6781 (tp-100) cc_final: 0.6387 (tp-100)
REVERT: A 1336 ASP cc_start: 0.6732 (OUTLIER) cc_final: 0.5939 (t0)
REVERT: A 1360 LYS cc_start: 0.8371 (mttp) cc_final: 0.8104 (mttm)
REVERT: A 1395 ASP cc_start: 0.8067 (t0) cc_final: 0.7472 (t70)
REVERT: B  254 GLN cc_start: 0.8350 (tt0) cc_final: 0.8127 (tt0)
REVERT: C  167 ASP cc_start: 0.7481 (OUTLIER) cc_final: 0.6940 (m-30)
  outliers start: 34
  outliers final: 23
  residues processed: 213
  average time/residue: 1.3461
  time to fit residues: 312.0413
Evaluate side-chains
  228 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 196
  time to evaluate  : 1.460 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ASP
Chi-restraints excluded: chain A residue  187 ASP
Chi-restraints excluded: chain A residue  229 GLU
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  248 ILE
Chi-restraints excluded: chain A residue  425 SER
Chi-restraints excluded: chain A residue  475 THR
Chi-restraints excluded: chain A residue  512 VAL
Chi-restraints excluded: chain A residue  572 ARG
Chi-restraints excluded: chain A residue  603 GLU
Chi-restraints excluded: chain A residue  609 LEU
Chi-restraints excluded: chain A residue  657 ARG
Chi-restraints excluded: chain A residue  766 ASN
Chi-restraints excluded: chain A residue  778 GLU
Chi-restraints excluded: chain A residue  785 TYR
Chi-restraints excluded: chain A residue  821 THR
Chi-restraints excluded: chain A residue  851 THR
Chi-restraints excluded: chain A residue  907 ILE
Chi-restraints excluded: chain A residue 1013 ASP
Chi-restraints excluded: chain A residue 1060 LEU
Chi-restraints excluded: chain A residue 1143 GLU
Chi-restraints excluded: chain A residue 1251 LEU
Chi-restraints excluded: chain A residue 1254 VAL
Chi-restraints excluded: chain A residue 1336 ASP
Chi-restraints excluded: chain A residue 1367 VAL
Chi-restraints excluded: chain B residue  308 THR
Chi-restraints excluded: chain B residue  309 ILE
Chi-restraints excluded: chain C residue  135 VAL
Chi-restraints excluded: chain C residue  152 LEU
Chi-restraints excluded: chain C residue  167 ASP
Chi-restraints excluded: chain C residue  170 VAL
Chi-restraints excluded: chain E residue  124 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 13 optimal weight:    0.7980
   chunk 26 optimal weight:    2.9990
   chunk 133 optimal weight:    6.9990
   chunk 138 optimal weight:    5.9990
   chunk 115 optimal weight:    4.9990
   chunk 122 optimal weight:    7.9990
   chunk 23 optimal weight:    0.8980
   chunk 165 optimal weight:    4.9990
   chunk 2 optimal weight:    3.9990
   chunk 77 optimal weight:    2.9990
   chunk 102 optimal weight:    3.9990
   overall best weight:    2.3386

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

Flipped N/Q/H residues before XYZ refinement:
A  64 ASN
** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 696 ASN
A 746 ASN
A1270 ASN
A1297 ASN
A1408 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.145193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.106373 restraints weight = 13863.291|
|-----------------------------------------------------------------------------|
r_work (start): 0.3130 rms_B_bonded: 1.84
r_work: 0.2936 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.2809 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.2809
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8639
moved from start:          0.2550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  13932  Z= 0.199
  Angle     :  0.626  11.593  18878  Z= 0.325
  Chirality :  0.045   0.178   2107
  Planarity :  0.005   0.048   2401
  Dihedral  :  4.611  25.525   1834
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 3.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 14.50 %
    Favored  : 83.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.79 (0.20), residues: 1679
  helix:  1.45 (0.18), residues: 863
  sheet:  1.61 (0.51), residues: 86
  loop : -0.74 (0.22), residues: 730

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 378 
 HIS   0.006   0.001   HIS A 707 
 PHE   0.025   0.002   PHE A 372 
 TYR   0.019   0.002   TYR A 803 
 ARG   0.005   0.001   ARG A  53 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07195 (  680)
  hydrogen bonds       : angle       4.23918 ( 1926)
  metal coordination   : bond        0.00562 (    3)
  covalent geometry    : bond        0.00486 (13929)
  covalent geometry    : angle       0.62553 (18878)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 10832.96 seconds
wall clock time: 186 minutes 42.90 seconds (11202.90 seconds total)