Starting phenix.real_space_refine
on Thu May 15 20:26:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ip4_60757/05_2025/9ip4_60757.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ip4_60757/05_2025/9ip4_60757.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.84
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ip4_60757/05_2025/9ip4_60757.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ip4_60757/05_2025/9ip4_60757.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ip4_60757/05_2025/9ip4_60757.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ip4_60757/05_2025/9ip4_60757.cif"
  }
  resolution = 2.84
  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=   0.044
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    8743      2.51       5
     N    2313      2.21       5
     O    2489      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 86 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: 13615
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 11049
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1364, 11049
          Classifications: {'peptide': 1364}
          Link IDs: {'PCIS': 1, 'PTRANS': 58, 'TRANS': 1304}
          Chain breaks: 5
    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   8887  SG  CYS A1108      65.500  72.380  21.911  1.00119.43           S
  ATOM  10719  SG  CYS A1376      68.913  70.519  22.769  1.00126.27           S
  ATOM  10725  SG  CYS A1377      66.627  71.766  25.182  1.00 86.82           S

  Time building chain proxies: 7.69, per 1000 atoms: 0.56
  Number of scatterers: 13615
  At special positions: 0
  Unit cell: (98.716, 128.501, 127.65, 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    2489      8.00
     N    2313      7.00
     C    8743      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: 3.09
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A2001 "
        pdb="ZN    ZN A2001 " - pdb=" SG  CYS A1377 "
        pdb="ZN    ZN A2001 " - pdb=" SG  CYS A1376 "
        pdb="ZN    ZN A2001 " - pdb=" SG  CYS A1108 "


  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3242

  Finding SS restraints...
    Secondary structure from input PDB file:
      92 helices and 9 sheets defined
      60.7% alpha, 6.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.72
  Creating SS restraints...
    Processing helix  chain 'A' and resid 18 through 28
      removed outlier: 4.173A  pdb=" N   ASP A  22 " --> pdb=" O   LEU A  18 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   LEU A  23 " --> pdb=" O   ASP A  19 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 38 through 43
      removed outlier: 4.369A  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: 4.133A  pdb=" N   ASP A  77 " --> pdb=" O   HIS A  73 " (cutoff:3.500A)
      removed outlier: 5.421A  pdb=" N   HIS A  78 " --> pdb=" O   SER A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 88 through 95
      removed outlier: 4.110A  pdb=" N   VAL A  91 " --> pdb=" O   ILE A  88 " (cutoff:3.500A)
      removed outlier: 5.513A  pdb=" N   ASP A  92 " --> pdb=" O   ASN A  89 " (cutoff:3.500A)
      removed outlier: 3.606A  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
      removed outlier: 3.514A  pdb=" N   GLN A 165 " --> pdb=" O   ARG A 161 " (cutoff:3.500A)
    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: 3.538A  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: 3.847A  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: 4.520A  pdb=" N   GLN A 352 " --> pdb=" O   ALA A 348 " (cutoff:3.500A)
      removed outlier: 3.629A  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: 4.037A  pdb=" N   LYS A 391 " --> pdb=" O   VAL A 387 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   VAL A 392 " --> pdb=" O   ALA A 388 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 427
    Processing helix  chain 'A' and resid 435 through 438
      removed outlier: 3.517A  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: 3.741A  pdb=" N   GLN A 444 " --> pdb=" O   PRO A 440 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   HIS A 445 " --> pdb=" O   TYR A 441 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   SER A 448 " --> pdb=" O   GLN A 444 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 460 through 466
      removed outlier: 3.608A  pdb=" N   PHE A 466 " --> pdb=" O   GLU A 463 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 493 through 501
      removed outlier: 3.883A  pdb=" N   TRP A 497 " --> pdb=" O   GLN A 494 " (cutoff:3.500A)
      removed outlier: 5.698A  pdb=" N   ASP A 498 " --> pdb=" O   GLU A 495 " (cutoff:3.500A)
      removed outlier: 4.430A  pdb=" N   SER A 499 " --> pdb=" O   CYS A 496 " (cutoff:3.500A)
      removed outlier: 4.161A  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: 3.688A  pdb=" N   LEU A 524 " --> pdb=" O   PRO A 520 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 530 through 540
      removed outlier: 3.837A  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: 3.913A  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
    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: 3.847A  pdb=" N   ASN A 640 " --> pdb=" O   GLU A 637 " (cutoff:3.500A)
      removed outlier: 4.460A  pdb=" N   LEU A 641 " --> pdb=" O   LYS A 638 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   PHE A 643 " --> pdb=" O   ASN A 640 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 644 through 660
      removed outlier: 5.780A  pdb=" N   HIS A 650 " --> pdb=" O   GLU A 646 " (cutoff:3.500A)
      removed outlier: 4.994A  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: 4.393A  pdb=" N   ASN A 695 " --> pdb=" O   ASP A 692 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 715 through 735
    Processing helix  chain 'A' and resid 760 through 785
      removed outlier: 3.633A  pdb=" N   GLU A 769 " --> pdb=" O   GLU A 765 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 791 through 795
    Processing helix  chain 'A' and resid 817 through 823
      removed outlier: 4.378A  pdb=" N   THR A 821 " --> pdb=" O   GLN A 817 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 835 through 853
    Processing helix  chain 'A' and resid 857 through 878
      removed outlier: 3.703A  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: 3.716A  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: 3.629A  pdb=" N   SER A 957 " --> pdb=" O   TYR A 953 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 964 through 971
      removed outlier: 3.710A  pdb=" N   PHE A 968 " --> pdb=" O   ASP A 964 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 977 through 981
      removed outlier: 3.594A  pdb=" N   SER A 980 " --> pdb=" O   VAL A 977 " (cutoff:3.500A)
      removed outlier: 3.565A  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: 3.808A  pdb=" N   LEU A 987 " --> pdb=" O   ILE A 983 " (cutoff:3.500A)
      removed outlier: 4.922A  pdb=" N   GLN A 989 " --> pdb=" O   THR A 985 " (cutoff:3.500A)
      removed outlier: 5.111A  pdb=" N   THR A 990 " --> pdb=" O   PHE A 986 " (cutoff:3.500A)
      removed outlier: 3.625A  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: 3.528A  pdb=" N   GLU A1015 " --> pdb=" O   GLY A1011 " (cutoff:3.500A)
      removed outlier: 3.750A  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: 4.543A  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
      removed outlier: 3.559A  pdb=" N   TRP A1121 " --> pdb=" O   ARG A1117 " (cutoff:3.500A)
    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: 3.767A  pdb=" N   GLU A1155 " --> pdb=" O   GLU A1151 " (cutoff:3.500A)
      removed outlier: 3.910A  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: 4.393A  pdb=" N   GLY A1220 " --> pdb=" O   ALA A1216 " (cutoff:3.500A)
      removed outlier: 4.207A  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: 4.119A  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 1281
      removed outlier: 3.878A  pdb=" N   VAL A1280 " --> pdb=" O   ASP A1276 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   LEU A1281 " --> pdb=" O   TYR A1277 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1276 through 1281'
    Processing helix  chain 'A' and resid 1282 through 1284
      No H-bonds generated for 'chain 'A' and resid 1282 through 1284'
    Processing helix  chain 'A' and resid 1291 through 1301
      removed outlier: 4.233A  pdb=" N   ASN A1297 " --> pdb=" O   VAL A1293 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   ASP A1298 " --> pdb=" O   HIS A1294 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1312 through 1315
    Processing helix  chain 'A' and resid 1324 through 1328
    Processing helix  chain 'A' and resid 1340 through 1356
      removed outlier: 3.759A  pdb=" N   THR A1344 " --> pdb=" O   ILE A1340 " (cutoff:3.500A)
      removed outlier: 4.202A  pdb=" N   ILE A1345 " --> pdb=" O   PHE A1341 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   ASN A1346 " --> pdb=" O   GLN A1342 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   LEU A1356 " --> pdb=" O   LEU A1352 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 114 through 138
      removed outlier: 4.088A  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: 3.815A  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: 4.494A  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: 3.568A  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: 4.590A  pdb=" N   GLU D 118 " --> pdb=" O   GLY D 114 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   ALA D 119 " --> pdb=" O   ARG D 115 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   ASP D 132 " --> pdb=" O   LEU D 128 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   HIS D 133 " --> pdb=" O   ALA D 129 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 111 through 135
      removed outlier: 3.608A  pdb=" N   LEU E 134 " --> pdb=" O   LYS E 130 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 69
      removed outlier: 5.820A  pdb=" N   VAL A 232 " --> pdb=" O   SER A  66 " (cutoff:3.500A)
      removed outlier: 7.004A  pdb=" N   LEU A  68 " --> pdb=" O   VAL A 232 " (cutoff:3.500A)
      removed outlier: 8.207A  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
      removed outlier: 4.588A  pdb=" N   PHE A 551 " --> pdb=" O   TYR A 676 " (cutoff:3.500A)
      removed outlier: 4.220A  pdb=" N   HIS A 678 " --> pdb=" O   PHE A 551 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 737 through 742
      removed outlier: 4.257A  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: 6.077A  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: 6.852A  pdb=" N   THR A1368 " --> pdb=" O   ILE A1147 " (cutoff:3.500A)
      removed outlier: 5.303A  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: 3.808A  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: 3.982A  pdb=" N   CYS B 315 " --> pdb=" O   LEU B 327 " (cutoff:3.500A)

    684 hydrogen bonds defined for protein.
    1932 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: 5.04

  Time building geometry restraints manager: 3.64 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 4248
        1.34 -     1.47: 3485
        1.47 -     1.60: 6099
        1.60 -     1.73: 4
        1.73 -     1.87: 103
  Bond restraints: 13939
  Sorted by residual:
  bond pdb=" CA  PRO C 158 "
       pdb=" C   PRO C 158 "
    ideal  model  delta    sigma   weight residual
    1.517  1.603 -0.086 6.70e-03 2.23e+04 1.63e+02
  bond pdb=" CA  PRO C 159 "
       pdb=" C   PRO C 159 "
    ideal  model  delta    sigma   weight residual
    1.514  1.547 -0.033 5.50e-03 3.31e+04 3.56e+01
  bond pdb=" CA  PRO B 281 "
       pdb=" C   PRO B 281 "
    ideal  model  delta    sigma   weight residual
    1.514  1.547 -0.033 5.50e-03 3.31e+04 3.54e+01
  bond pdb=" C   PRO C 158 "
       pdb=" O   PRO C 158 "
    ideal  model  delta    sigma   weight residual
    1.243  1.207  0.036 8.50e-03 1.38e+04 1.79e+01
  bond pdb=" SD  MET C 124 "
       pdb=" CE  MET C 124 "
    ideal  model  delta    sigma   weight residual
    1.791  1.690  0.101 2.50e-02 1.60e+03 1.64e+01
  ... (remaining 13934 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.82: 18767
        4.82 -     9.63: 104
        9.63 -    14.45: 13
       14.45 -    19.26: 8
       19.26 -    24.08: 1
  Bond angle restraints: 18893
  Sorted by residual:
  angle pdb=" O   PRO C 158 "
        pdb=" C   PRO C 158 "
        pdb=" N   PRO C 159 "
      ideal   model   delta    sigma   weight residual
     121.15  127.68   -6.53 4.70e-01 4.53e+00 1.93e+02
  angle pdb=" N   CYS A 892 "
        pdb=" CA  CYS A 892 "
        pdb=" C   CYS A 892 "
      ideal   model   delta    sigma   weight residual
     111.14  119.97   -8.83 1.08e+00 8.57e-01 6.68e+01
  angle pdb=" N   GLN A 515 "
        pdb=" CA  GLN A 515 "
        pdb=" C   GLN A 515 "
      ideal   model   delta    sigma   weight residual
     111.14  119.75   -8.61 1.08e+00 8.57e-01 6.36e+01
  angle pdb=" CG  MET A 743 "
        pdb=" SD  MET A 743 "
        pdb=" CE  MET A 743 "
      ideal   model   delta    sigma   weight residual
     100.90  117.97  -17.07 2.20e+00 2.07e-01 6.02e+01
  angle pdb=" CA  GLU A 794 "
        pdb=" CB  GLU A 794 "
        pdb=" CG  GLU A 794 "
      ideal   model   delta    sigma   weight residual
     114.10  129.17  -15.07 2.00e+00 2.50e-01 5.68e+01
  ... (remaining 18888 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.93: 7670
       17.93 -    35.85: 587
       35.85 -    53.78: 87
       53.78 -    71.70: 14
       71.70 -    89.63: 11
  Dihedral angle restraints: 8369
    sinusoidal: 3368
      harmonic: 5001
  Sorted by residual:
  dihedral pdb=" CA  ILE A 711 "
           pdb=" C   ILE A 711 "
           pdb=" N   GLU A 712 "
           pdb=" CA  GLU A 712 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.57  -25.43     0      5.00e+00 4.00e-02 2.59e+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 -156.31  -23.69     0      5.00e+00 4.00e-02 2.24e+01
  dihedral pdb=" CA  GLY A 805 "
           pdb=" C   GLY A 805 "
           pdb=" N   LYS A 806 "
           pdb=" CA  LYS A 806 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.38   22.62     0      5.00e+00 4.00e-02 2.05e+01
  ... (remaining 8366 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.113: 2006
       0.113 -    0.227: 87
       0.227 -    0.340: 11
       0.340 -    0.454: 2
       0.454 -    0.567: 2
  Chirality restraints: 2108
  Sorted by residual:
  chirality pdb=" CG  LEU A1099 "
            pdb=" CB  LEU A1099 "
            pdb=" CD1 LEU A1099 "
            pdb=" CD2 LEU A1099 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.02   -0.57 2.00e-01 2.50e+01 8.04e+00
  chirality pdb=" CG  LEU A 828 "
            pdb=" CB  LEU A 828 "
            pdb=" CD1 LEU A 828 "
            pdb=" CD2 LEU A 828 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -3.06    0.47 2.00e-01 2.50e+01 5.44e+00
  chirality pdb=" CA  LYS A 517 "
            pdb=" N   LYS A 517 "
            pdb=" C   LYS A 517 "
            pdb=" CB  LYS A 517 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.11    0.40 2.00e-01 2.50e+01 4.04e+00
  ... (remaining 2105 not shown)

  Planarity restraints: 2404
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A1106 "   -0.019 2.00e-02 2.50e+03   4.94e-02 4.27e+01
        pdb=" CG  PHE A1106 "    0.098 2.00e-02 2.50e+03
        pdb=" CD1 PHE A1106 "   -0.072 2.00e-02 2.50e+03
        pdb=" CD2 PHE A1106 "   -0.023 2.00e-02 2.50e+03
        pdb=" CE1 PHE A1106 "    0.029 2.00e-02 2.50e+03
        pdb=" CE2 PHE A1106 "   -0.020 2.00e-02 2.50e+03
        pdb=" CZ  PHE A1106 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU B 260 "   -0.031 2.00e-02 2.50e+03   6.43e-02 4.14e+01
        pdb=" CD  GLU B 260 "    0.111 2.00e-02 2.50e+03
        pdb=" OE1 GLU B 260 "   -0.040 2.00e-02 2.50e+03
        pdb=" OE2 GLU B 260 "   -0.040 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU A 794 "    0.030 2.00e-02 2.50e+03   6.10e-02 3.72e+01
        pdb=" CD  GLU A 794 "   -0.105 2.00e-02 2.50e+03
        pdb=" OE1 GLU A 794 "    0.040 2.00e-02 2.50e+03
        pdb=" OE2 GLU A 794 "    0.036 2.00e-02 2.50e+03
  ... (remaining 2401 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.63: 106
        2.63 -     3.20: 12033
        3.20 -     3.77: 19109
        3.77 -     4.33: 27405
        4.33 -     4.90: 46574
  Nonbonded interactions: 105227
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG A1040 "
            pdb=" OE1 GLU A1246 "
     model   vdw
     2.066 3.120
  nonbonded pdb=" OG1 THR A 490 "
            pdb=" O   LYS A 517 "
     model   vdw
     2.072 3.040
  nonbonded pdb=" OG  SER A1191 "
            pdb=" OG  SER A1320 "
     model   vdw
     2.164 3.040
  nonbonded pdb=" OD2 ASP A1260 "
            pdb=" NZ  LYS A1263 "
     model   vdw
     2.172 3.120
  nonbonded pdb=" OE2 GLU B 260 "
            pdb=" NH2 ARG B 268 "
     model   vdw
     2.189 3.120
  ... (remaining 105222 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:             0.970
  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:         0.090
  Set scattering table:                    0.130
  Process input model:                     35.450
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.060
  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:12.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   49.430
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7917
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      :  0.006   0.102  13942  Z= 0.318
  Angle     :  1.080  24.078  18893  Z= 0.590
  Chirality :  0.060   0.567   2108
  Planarity :  0.007   0.064   2404
  Dihedral  : 13.099  89.631   5127
  Min Nonbonded Distance : 2.066

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  3.98 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  1.13 %
    Favored  : 98.74 %
  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: -0.16 (0.20), residues: 1682
  helix:  0.83 (0.18), residues: 856
  sheet:  0.62 (0.53), residues: 90
  loop : -1.32 (0.21), residues: 736

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A1088 
 HIS   0.010   0.002   HIS A 669 
 PHE   0.098   0.004   PHE A1106 
 TYR   0.027   0.003   TYR A1091 
 ARG   0.027   0.001   ARG A 217 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17603 (  684)
  hydrogen bonds       : angle       5.92217 ( 1932)
  metal coordination   : bond        0.00693 (    3)
  covalent geometry    : bond        0.00586 (13939)
  covalent geometry    : angle       1.07959 (18893)

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

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

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  294 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 292
  time to evaluate  : 1.466 
Fit side-chains
REVERT: A    9 ASP cc_start: 0.7871 (t0) cc_final: 0.6894 (p0)
REVERT: A   41 ARG cc_start: 0.7974 (mmm160) cc_final: 0.7371 (mpt180)
REVERT: A   44 ARG cc_start: 0.7965 (ptt-90) cc_final: 0.7731 (ptt90)
REVERT: A   75 ILE cc_start: 0.7805 (mm) cc_final: 0.7278 (pt)
REVERT: A   92 ASP cc_start: 0.8396 (m-30) cc_final: 0.7415 (OUTLIER)
REVERT: A   95 LYS cc_start: 0.7812 (tppt) cc_final: 0.6975 (pmtt)
REVERT: A  104 LYS cc_start: 0.8146 (tttp) cc_final: 0.7598 (ttmm)
REVERT: A  141 LYS cc_start: 0.8078 (ttpp) cc_final: 0.7722 (mptt)
REVERT: A  178 THR cc_start: 0.7952 (m) cc_final: 0.7615 (p)
REVERT: A  196 LYS cc_start: 0.7064 (mptt) cc_final: 0.6820 (tmtm)
REVERT: A  217 ARG cc_start: 0.7123 (ptp-110) cc_final: 0.6666 (mpt180)
REVERT: A  229 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7127 (tt0)
REVERT: A  245 ASP cc_start: 0.8181 (m-30) cc_final: 0.7843 (m-30)
REVERT: A  278 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7500 (mm-30)
REVERT: A  390 ASP cc_start: 0.7028 (m-30) cc_final: 0.6322 (t70)
REVERT: A  503 ARG cc_start: 0.7148 (mtt-85) cc_final: 0.6170 (mtp-110)
REVERT: A  533 GLN cc_start: 0.7559 (pp30) cc_final: 0.7008 (pp30)
REVERT: A  540 LYS cc_start: 0.7738 (mmtt) cc_final: 0.7143 (mppt)
REVERT: A  564 ARG cc_start: 0.8024 (mtp180) cc_final: 0.6767 (mpt180)
REVERT: A  581 GLU cc_start: 0.7533 (tt0) cc_final: 0.6981 (pp20)
REVERT: A  597 MET cc_start: 0.6976 (tpt) cc_final: 0.6756 (tpt)
REVERT: A  677 MET cc_start: 0.9175 (mmm) cc_final: 0.8631 (mmt)
REVERT: A  742 VAL cc_start: 0.7556 (t) cc_final: 0.7101 (p)
REVERT: A  745 ASP cc_start: 0.5383 (t0) cc_final: 0.5079 (p0)
REVERT: A  763 TYR cc_start: 0.7497 (t80) cc_final: 0.7247 (t80)
REVERT: A  767 GLU cc_start: 0.7561 (mm-30) cc_final: 0.7157 (mm-30)
REVERT: A  778 GLU cc_start: 0.7730 (tp30) cc_final: 0.7294 (tp30)
REVERT: A  793 GLU cc_start: 0.7613 (mm-30) cc_final: 0.6989 (mt-10)
REVERT: A  794 GLU cc_start: 0.8349 (mp0) cc_final: 0.7730 (mm-30)
REVERT: A  807 LYS cc_start: 0.7931 (mtmm) cc_final: 0.7577 (mttp)
REVERT: A  824 ARG cc_start: 0.7580 (mtp85) cc_final: 0.6750 (mtm110)
REVERT: A  895 LYS cc_start: 0.7193 (pttp) cc_final: 0.6828 (ptmt)
REVERT: A  959 LYS cc_start: 0.8159 (mttt) cc_final: 0.7718 (mtmt)
REVERT: A  967 ASP cc_start: 0.7940 (m-30) cc_final: 0.7533 (m-30)
REVERT: A  971 ASN cc_start: 0.7654 (t0) cc_final: 0.6940 (p0)
REVERT: A 1000 GLN cc_start: 0.8175 (mt0) cc_final: 0.7832 (mt0)
REVERT: A 1097 ASP cc_start: 0.7624 (m-30) cc_final: 0.7010 (p0)
REVERT: A 1143 GLU cc_start: 0.7978 (pt0) cc_final: 0.7081 (mm-30)
REVERT: A 1155 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7712 (tp30)
REVERT: A 1255 THR cc_start: 0.6198 (m) cc_final: 0.5739 (p)
REVERT: A 1366 ASN cc_start: 0.8617 (p0) cc_final: 0.8334 (p0)
REVERT: A 1389 ASP cc_start: 0.8126 (p0) cc_final: 0.7919 (p0)
REVERT: A 1403 GLU cc_start: 0.7661 (pm20) cc_final: 0.7164 (mm-30)
REVERT: B  166 LYS cc_start: 0.7862 (ttpp) cc_final: 0.7634 (tttm)
REVERT: B  194 LYS cc_start: 0.7280 (mptt) cc_final: 0.6476 (pttp)
REVERT: B  211 LYS cc_start: 0.7419 (tttt) cc_final: 0.7078 (tttp)
REVERT: C  154 GLU cc_start: 0.8221 (tp30) cc_final: 0.7779 (tp30)
REVERT: D  113 MET cc_start: 0.5435 (pmm) cc_final: 0.4565 (mtt)
REVERT: E  113 MET cc_start: 0.5915 (mmp) cc_final: 0.5363 (mtp)
  outliers start: 2
  outliers final: 1
  residues processed: 294
  average time/residue: 1.3968
  time to fit residues: 445.5026
Evaluate side-chains
  210 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 210
  time to evaluate  : 1.450 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 141 optimal weight:    6.9990
   chunk 127 optimal weight:    5.9990
   chunk 70 optimal weight:    0.6980
   chunk 43 optimal weight:   10.0000
   chunk 85 optimal weight:    2.9990
   chunk 68 optimal weight:    2.9990
   chunk 131 optimal weight:    6.9990
   chunk 50 optimal weight:    0.0980
   chunk 80 optimal weight:    3.9990
   chunk 98 optimal weight:    6.9990
   chunk 152 optimal weight:    8.9990
   overall best weight:    2.1586

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

Flipped N/Q/H residues before XYZ refinement:
A 335 HIS
A 360 GLN
A 395 HIS
A 509 ASN
A 575 ASN
A1048 GLN
A1141 GLN
A1158 ASN
A1270 ASN
A1303 HIS
A1312 ASN
A1322 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 = 0.3885 r_free = 0.3885 target = 0.162277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.124356 restraints weight = 15776.558|
|-----------------------------------------------------------------------------|
r_work (start): 0.3444 rms_B_bonded: 2.03
r_work: 0.3252 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3124 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8374
moved from start:          0.1897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  13942  Z= 0.179
  Angle     :  0.644   9.788  18893  Z= 0.339
  Chirality :  0.044   0.155   2108
  Planarity :  0.005   0.048   2404
  Dihedral  :  4.907  30.283   1836
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 3.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  :  9.51 %
    Favored  : 88.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

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:  0.27 (0.20), residues: 1682
  helix:  1.09 (0.18), residues: 867
  sheet:  1.02 (0.52), residues: 85
  loop : -1.03 (0.22), residues: 730

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  76 
 HIS   0.007   0.001   HIS A 705 
 PHE   0.020   0.002   PHE A 372 
 TYR   0.022   0.002   TYR A 430 
 ARG   0.008   0.001   ARG A 855 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06688 (  684)
  hydrogen bonds       : angle       4.65028 ( 1932)
  metal coordination   : bond        0.00193 (    3)
  covalent geometry    : bond        0.00421 (13939)
  covalent geometry    : angle       0.64407 (18893)

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

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

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 219
  time to evaluate  : 1.603 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 ASP cc_start: 0.7959 (t0) cc_final: 0.7013 (p0)
REVERT: A   17 ILE cc_start: 0.8209 (OUTLIER) cc_final: 0.7672 (mp)
REVERT: A   41 ARG cc_start: 0.7713 (mmm160) cc_final: 0.7488 (mpt180)
REVERT: A   75 ILE cc_start: 0.8033 (mm) cc_final: 0.7809 (pt)
REVERT: A   92 ASP cc_start: 0.8168 (m-30) cc_final: 0.7786 (OUTLIER)
REVERT: A   95 LYS cc_start: 0.8149 (tppt) cc_final: 0.7779 (pttm)
REVERT: A  104 LYS cc_start: 0.8712 (tttp) cc_final: 0.8441 (ttmt)
REVERT: A  196 LYS cc_start: 0.7485 (mptt) cc_final: 0.7069 (mmtm)
REVERT: A  229 GLU cc_start: 0.7537 (mm-30) cc_final: 0.7276 (tt0)
REVERT: A  390 ASP cc_start: 0.7350 (m-30) cc_final: 0.6997 (t70)
REVERT: A  536 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7210 (tp30)
REVERT: A  540 LYS cc_start: 0.7948 (mmtt) cc_final: 0.7744 (mppt)
REVERT: A  564 ARG cc_start: 0.8357 (mtp180) cc_final: 0.7479 (mpt180)
REVERT: A  603 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7781 (mm-30)
REVERT: A  628 ARG cc_start: 0.8687 (tpt-90) cc_final: 0.8341 (mmt90)
REVERT: A  742 VAL cc_start: 0.8246 (t) cc_final: 0.7953 (p)
REVERT: A  778 GLU cc_start: 0.8383 (tp30) cc_final: 0.8133 (tp30)
REVERT: A  791 LYS cc_start: 0.7840 (mtpp) cc_final: 0.7473 (tttp)
REVERT: A  794 GLU cc_start: 0.8225 (mp0) cc_final: 0.7969 (mp0)
REVERT: A  824 ARG cc_start: 0.7817 (mtp85) cc_final: 0.7355 (mtm-85)
REVERT: A  869 MET cc_start: 0.8494 (tpt) cc_final: 0.8124 (tpt)
REVERT: A  895 LYS cc_start: 0.7835 (pttp) cc_final: 0.7526 (ptmt)
REVERT: A  959 LYS cc_start: 0.8130 (mttt) cc_final: 0.7720 (mtmt)
REVERT: A 1000 GLN cc_start: 0.8183 (mt0) cc_final: 0.7926 (mt0)
REVERT: A 1097 ASP cc_start: 0.7548 (m-30) cc_final: 0.7215 (p0)
REVERT: A 1104 GLU cc_start: 0.7541 (mm-30) cc_final: 0.7011 (mp0)
REVERT: A 1143 GLU cc_start: 0.8002 (pt0) cc_final: 0.7663 (mt-10)
REVERT: A 1155 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7941 (tp30)
REVERT: A 1255 THR cc_start: 0.6005 (m) cc_final: 0.5739 (p)
REVERT: A 1366 ASN cc_start: 0.8549 (p0) cc_final: 0.8331 (p0)
REVERT: A 1374 ASN cc_start: 0.8021 (m-40) cc_final: 0.7615 (m110)
REVERT: A 1401 ASP cc_start: 0.7460 (OUTLIER) cc_final: 0.7254 (p0)
REVERT: B  194 LYS cc_start: 0.7892 (mptt) cc_final: 0.7363 (ttpp)
REVERT: C  113 MET cc_start: 0.3490 (ppp) cc_final: 0.3174 (ptp)
REVERT: C  154 GLU cc_start: 0.8229 (tp30) cc_final: 0.7954 (tp30)
  outliers start: 37
  outliers final: 16
  residues processed: 237
  average time/residue: 1.2691
  time to fit residues: 328.8624
Evaluate side-chains
  209 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 191
  time to evaluate  : 1.663 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 ILE
Chi-restraints excluded: chain A residue  428 SER
Chi-restraints excluded: chain A residue  504 SER
Chi-restraints excluded: chain A residue  532 ASN
Chi-restraints excluded: chain A residue  536 GLU
Chi-restraints excluded: chain A residue  640 ASN
Chi-restraints excluded: chain A residue  753 SER
Chi-restraints excluded: chain A residue  851 THR
Chi-restraints excluded: chain A residue  985 THR
Chi-restraints excluded: chain A residue 1248 VAL
Chi-restraints excluded: chain A residue 1254 VAL
Chi-restraints excluded: chain A residue 1266 ILE
Chi-restraints excluded: chain A residue 1337 SER
Chi-restraints excluded: chain A residue 1396 LEU
Chi-restraints excluded: chain A residue 1401 ASP
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain C residue  135 VAL
Chi-restraints excluded: chain D residue  113 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 89 optimal weight:    0.9990
   chunk 53 optimal weight:    3.9990
   chunk 32 optimal weight:    4.9990
   chunk 150 optimal weight:    0.9990
   chunk 83 optimal weight:    6.9990
   chunk 120 optimal weight:    7.9990
   chunk 138 optimal weight:    8.9990
   chunk 67 optimal weight:    0.7980
   chunk 108 optimal weight:    0.0980
   chunk 15 optimal weight:    3.9990
   chunk 8 optimal weight:    3.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1048 GLN
A1158 ASN
A1270 ASN
A1322 ASN
A1338 ASN
C 161 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.163498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.125805 restraints weight = 15775.842|
|-----------------------------------------------------------------------------|
r_work (start): 0.3442 rms_B_bonded: 2.03
r_work: 0.3255 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3125 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8308
moved from start:          0.2479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  13942  Z= 0.130
  Angle     :  0.539   8.735  18893  Z= 0.284
  Chirality :  0.041   0.153   2108
  Planarity :  0.004   0.047   2404
  Dihedral  :  4.497  27.014   1836
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 3.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 11.84 %
    Favored  : 85.64 %
  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:  0.65 (0.20), residues: 1682
  helix:  1.44 (0.18), residues: 866
  sheet:  1.23 (0.49), residues: 90
  loop : -0.91 (0.22), residues: 726

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 261 
 HIS   0.005   0.001   HIS A 154 
 PHE   0.016   0.002   PHE A 372 
 TYR   0.013   0.001   TYR A 803 
 ARG   0.004   0.000   ARG A 855 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05413 (  684)
  hydrogen bonds       : angle       4.24510 ( 1932)
  metal coordination   : bond        0.00102 (    3)
  covalent geometry    : bond        0.00292 (13939)
  covalent geometry    : angle       0.53935 (18893)

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

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

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 200
  time to evaluate  : 1.463 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 ASP cc_start: 0.8013 (t0) cc_final: 0.6917 (p0)
REVERT: A   41 ARG cc_start: 0.7650 (mmm160) cc_final: 0.7340 (mpt180)
REVERT: A   92 ASP cc_start: 0.8115 (m-30) cc_final: 0.7685 (t70)
REVERT: A   95 LYS cc_start: 0.8184 (tppt) cc_final: 0.7785 (pttm)
REVERT: A  123 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8445 (mt)
REVERT: A  196 LYS cc_start: 0.7461 (mptt) cc_final: 0.6961 (mmtm)
REVERT: A  229 GLU cc_start: 0.7456 (mm-30) cc_final: 0.7100 (tt0)
REVERT: A  289 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.7802 (ttm)
REVERT: A  390 ASP cc_start: 0.7348 (m-30) cc_final: 0.6980 (t70)
REVERT: A  536 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.6903 (tp30)
REVERT: A  540 LYS cc_start: 0.7885 (mmtt) cc_final: 0.7645 (mppt)
REVERT: A  564 ARG cc_start: 0.8401 (mtp180) cc_final: 0.8075 (mtm180)
REVERT: A  581 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7203 (tp30)
REVERT: A  628 ARG cc_start: 0.8593 (tpt-90) cc_final: 0.8309 (mmt90)
REVERT: A  693 ASN cc_start: 0.6798 (t0) cc_final: 0.6595 (t0)
REVERT: A  742 VAL cc_start: 0.8126 (t) cc_final: 0.7887 (p)
REVERT: A  778 GLU cc_start: 0.8338 (tp30) cc_final: 0.8101 (tp30)
REVERT: A  785 TYR cc_start: 0.8919 (OUTLIER) cc_final: 0.8238 (m-80)
REVERT: A  794 GLU cc_start: 0.8186 (mp0) cc_final: 0.7803 (mp0)
REVERT: A  824 ARG cc_start: 0.7930 (mtp85) cc_final: 0.7368 (mtm180)
REVERT: A  832 ILE cc_start: 0.7677 (mt) cc_final: 0.7368 (mm)
REVERT: A  894 LYS cc_start: 0.8740 (mtpp) cc_final: 0.8310 (mmtt)
REVERT: A  895 LYS cc_start: 0.7598 (pttp) cc_final: 0.7269 (ptmt)
REVERT: A  959 LYS cc_start: 0.8095 (mttt) cc_final: 0.7652 (mtmt)
REVERT: A 1000 GLN cc_start: 0.8156 (mt0) cc_final: 0.7834 (mt0)
REVERT: A 1040 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.7355 (mtt-85)
REVERT: A 1104 GLU cc_start: 0.7468 (mm-30) cc_final: 0.6964 (mt-10)
REVERT: A 1155 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7842 (tp30)
REVERT: A 1306 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.7538 (ppp)
REVERT: A 1366 ASN cc_start: 0.8502 (p0) cc_final: 0.8301 (p0)
REVERT: A 1385 TYR cc_start: 0.7492 (m-80) cc_final: 0.7239 (m-10)
REVERT: A 1387 TYR cc_start: 0.8128 (t80) cc_final: 0.7648 (t80)
REVERT: B  194 LYS cc_start: 0.7894 (mptt) cc_final: 0.7305 (ttpp)
REVERT: C  113 MET cc_start: 0.3363 (ppp) cc_final: 0.3076 (ptp)
REVERT: C  154 GLU cc_start: 0.8265 (tp30) cc_final: 0.7849 (tp30)
  outliers start: 38
  outliers final: 15
  residues processed: 222
  average time/residue: 1.2136
  time to fit residues: 295.6013
Evaluate side-chains
  206 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 185
  time to evaluate  : 1.673 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 ARG
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain A residue  187 ASP
Chi-restraints excluded: chain A residue  289 MET
Chi-restraints excluded: chain A residue  504 SER
Chi-restraints excluded: chain A residue  532 ASN
Chi-restraints excluded: chain A residue  536 GLU
Chi-restraints excluded: chain A residue  634 THR
Chi-restraints excluded: chain A residue  746 ASN
Chi-restraints excluded: chain A residue  753 SER
Chi-restraints excluded: chain A residue  785 TYR
Chi-restraints excluded: chain A residue  851 THR
Chi-restraints excluded: chain A residue  900 SER
Chi-restraints excluded: chain A residue 1040 ARG
Chi-restraints excluded: chain A residue 1188 ASN
Chi-restraints excluded: chain A residue 1248 VAL
Chi-restraints excluded: chain A residue 1254 VAL
Chi-restraints excluded: chain A residue 1266 ILE
Chi-restraints excluded: chain A residue 1306 MET
Chi-restraints excluded: chain A residue 1337 SER
Chi-restraints excluded: chain C residue  135 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 90 optimal weight:    3.9990
   chunk 151 optimal weight:    3.9990
   chunk 41 optimal weight:    6.9990
   chunk 138 optimal weight:    8.9990
   chunk 103 optimal weight:    0.9980
   chunk 59 optimal weight:    6.9990
   chunk 145 optimal weight:    9.9990
   chunk 164 optimal weight:    9.9990
   chunk 160 optimal weight:    4.9990
   chunk 15 optimal weight:    4.9990
   chunk 26 optimal weight:    4.9990
   overall best weight:    3.7988

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

Flipped N/Q/H residues before XYZ refinement:
A 375 GLN
A 994 ASN
A1048 GLN
A1158 ASN
A1256 GLN
A1270 ASN
A1287 HIS
A1322 ASN
A1374 ASN
C 161 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.157783 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.120002 restraints weight = 15771.705|
|-----------------------------------------------------------------------------|
r_work (start): 0.3365 rms_B_bonded: 1.98
r_work: 0.3173 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3043 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8414
moved from start:          0.2894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.053  13942  Z= 0.256
  Angle     :  0.670  10.571  18893  Z= 0.348
  Chirality :  0.047   0.164   2108
  Planarity :  0.005   0.051   2404
  Dihedral  :  4.887  31.042   1836
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 12.23 %
    Favored  : 83.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

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:  0.28 (0.20), residues: 1682
  helix:  1.05 (0.18), residues: 865
  sheet:  1.33 (0.52), residues: 91
  loop : -1.00 (0.22), residues: 726

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 108 
 HIS   0.007   0.002   HIS A 154 
 PHE   0.025   0.003   PHE A 414 
 TYR   0.023   0.002   TYR A 803 
 ARG   0.006   0.001   ARG A 855 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07746 (  684)
  hydrogen bonds       : angle       4.48290 ( 1932)
  metal coordination   : bond        0.00582 (    3)
  covalent geometry    : bond        0.00642 (13939)
  covalent geometry    : angle       0.66969 (18893)

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

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

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 182
  time to evaluate  : 1.465 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 ILE cc_start: 0.8226 (OUTLIER) cc_final: 0.7699 (mp)
REVERT: A   41 ARG cc_start: 0.7798 (mmm160) cc_final: 0.7473 (mpt180)
REVERT: A   51 ARG cc_start: 0.8281 (ptm160) cc_final: 0.7741 (ptt-90)
REVERT: A  196 LYS cc_start: 0.7430 (mptt) cc_final: 0.6959 (mmtm)
REVERT: A  229 GLU cc_start: 0.7417 (mm-30) cc_final: 0.6998 (tt0)
REVERT: A  289 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.8031 (ttm)
REVERT: A  390 ASP cc_start: 0.7435 (m-30) cc_final: 0.7076 (t70)
REVERT: A  536 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7263 (tp30)
REVERT: A  540 LYS cc_start: 0.8153 (mmtt) cc_final: 0.7931 (mppt)
REVERT: A  564 ARG cc_start: 0.8491 (mtp180) cc_final: 0.8132 (mtm180)
REVERT: A  581 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7177 (tp30)
REVERT: A  605 LYS cc_start: 0.6614 (mtpm) cc_final: 0.6361 (mmmt)
REVERT: A  696 ASN cc_start: 0.7723 (t0) cc_final: 0.7365 (m110)
REVERT: A  770 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7714 (mp)
REVERT: A  778 GLU cc_start: 0.8423 (tp30) cc_final: 0.8120 (tp30)
REVERT: A  785 TYR cc_start: 0.9138 (OUTLIER) cc_final: 0.8453 (m-80)
REVERT: A  791 LYS cc_start: 0.7813 (mtpp) cc_final: 0.7454 (mtpp)
REVERT: A  794 GLU cc_start: 0.8405 (mp0) cc_final: 0.8115 (mp0)
REVERT: A  820 LYS cc_start: 0.8970 (ptmm) cc_final: 0.8718 (ptmm)
REVERT: A  824 ARG cc_start: 0.8024 (mtp85) cc_final: 0.7378 (mtm180)
REVERT: A  894 LYS cc_start: 0.8815 (mtpp) cc_final: 0.8323 (mmtt)
REVERT: A  895 LYS cc_start: 0.7616 (pttp) cc_final: 0.7281 (ptmt)
REVERT: A  927 ASN cc_start: 0.8675 (m110) cc_final: 0.8300 (m-40)
REVERT: A  959 LYS cc_start: 0.8069 (mttt) cc_final: 0.7658 (mtmt)
REVERT: A  962 LEU cc_start: 0.7588 (mt) cc_final: 0.7329 (pp)
REVERT: A 1040 ARG cc_start: 0.8913 (OUTLIER) cc_final: 0.7617 (mtt-85)
REVERT: A 1104 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7062 (mt-10)
REVERT: A 1155 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7846 (tp30)
REVERT: A 1366 ASN cc_start: 0.8521 (p0) cc_final: 0.8320 (p0)
REVERT: A 1385 TYR cc_start: 0.7444 (m-80) cc_final: 0.7180 (m-10)
REVERT: B  124 MET cc_start: 0.7790 (mmm) cc_final: 0.7551 (mmm)
REVERT: B  194 LYS cc_start: 0.7902 (mptt) cc_final: 0.7321 (ttpp)
REVERT: C  113 MET cc_start: 0.3605 (ppp) cc_final: 0.3279 (ptp)
REVERT: C  154 GLU cc_start: 0.8327 (tp30) cc_final: 0.7988 (tp30)
  outliers start: 57
  outliers final: 26
  residues processed: 217
  average time/residue: 1.2853
  time to fit residues: 304.2527
Evaluate side-chains
  208 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 176
  time to evaluate  : 1.555 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 ILE
Chi-restraints excluded: chain A residue   53 ARG
Chi-restraints excluded: chain A residue  178 THR
Chi-restraints excluded: chain A residue  195 VAL
Chi-restraints excluded: chain A residue  289 MET
Chi-restraints excluded: chain A residue  339 LEU
Chi-restraints excluded: chain A residue  428 SER
Chi-restraints excluded: chain A residue  504 SER
Chi-restraints excluded: chain A residue  532 ASN
Chi-restraints excluded: chain A residue  536 GLU
Chi-restraints excluded: chain A residue  634 THR
Chi-restraints excluded: chain A residue  640 ASN
Chi-restraints excluded: chain A residue  745 ASP
Chi-restraints excluded: chain A residue  746 ASN
Chi-restraints excluded: chain A residue  753 SER
Chi-restraints excluded: chain A residue  770 LEU
Chi-restraints excluded: chain A residue  785 TYR
Chi-restraints excluded: chain A residue  851 THR
Chi-restraints excluded: chain A residue  900 SER
Chi-restraints excluded: chain A residue  985 THR
Chi-restraints excluded: chain A residue 1040 ARG
Chi-restraints excluded: chain A residue 1097 ASP
Chi-restraints excluded: chain A residue 1109 THR
Chi-restraints excluded: chain A residue 1188 ASN
Chi-restraints excluded: chain A residue 1241 LEU
Chi-restraints excluded: chain A residue 1254 VAL
Chi-restraints excluded: chain A residue 1266 ILE
Chi-restraints excluded: chain B residue  113 MET
Chi-restraints excluded: chain B residue  141 THR
Chi-restraints excluded: chain B residue  267 THR
Chi-restraints excluded: chain C residue  135 VAL
Chi-restraints excluded: chain D residue  113 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 144 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 21 optimal weight:    7.9990
   chunk 166 optimal weight:    8.9990
   chunk 105 optimal weight:    7.9990
   chunk 125 optimal weight:    0.1980
   chunk 51 optimal weight:    0.0040
   chunk 120 optimal weight:    7.9990
   chunk 156 optimal weight:    9.9990
   chunk 97 optimal weight:    5.9990
   chunk 31 optimal weight:    2.9990
   overall best weight:    2.0398

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

Flipped N/Q/H residues before XYZ refinement:
** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 764 GLN
A 994 ASN
A1048 GLN
A1158 ASN
A1322 ASN
A1374 ASN
C 161 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.160504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.122993 restraints weight = 15675.037|
|-----------------------------------------------------------------------------|
r_work (start): 0.3403 rms_B_bonded: 2.00
r_work: 0.3213 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3083 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8368
moved from start:          0.3077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  13942  Z= 0.154
  Angle     :  0.558   9.503  18893  Z= 0.292
  Chirality :  0.042   0.159   2108
  Planarity :  0.004   0.051   2404
  Dihedral  :  4.599  29.837   1836
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 3.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 14.36 %
    Favored  : 82.71 %
  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:  0.49 (0.20), residues: 1682
  helix:  1.24 (0.18), residues: 874
  sheet:  1.06 (0.50), residues: 97
  loop : -0.93 (0.22), residues: 711

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 108 
 HIS   0.005   0.001   HIS A 154 
 PHE   0.019   0.002   PHE A 414 
 TYR   0.018   0.001   TYR A 803 
 ARG   0.003   0.000   ARG A 628 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05829 (  684)
  hydrogen bonds       : angle       4.26760 ( 1932)
  metal coordination   : bond        0.00150 (    3)
  covalent geometry    : bond        0.00366 (13939)
  covalent geometry    : angle       0.55784 (18893)

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

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

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 180
  time to evaluate  : 1.551 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 ILE cc_start: 0.8195 (OUTLIER) cc_final: 0.7664 (mp)
REVERT: A   41 ARG cc_start: 0.7769 (mmm160) cc_final: 0.7351 (mmt180)
REVERT: A   51 ARG cc_start: 0.8285 (ptm160) cc_final: 0.7785 (ptt-90)
REVERT: A  196 LYS cc_start: 0.7425 (mptt) cc_final: 0.6925 (mmtm)
REVERT: A  217 ARG cc_start: 0.7427 (mpt180) cc_final: 0.7212 (mpt180)
REVERT: A  229 GLU cc_start: 0.7385 (mm-30) cc_final: 0.6993 (tt0)
REVERT: A  390 ASP cc_start: 0.7454 (m-30) cc_final: 0.7108 (t70)
REVERT: A  536 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7235 (tp30)
REVERT: A  542 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8083 (mm-30)
REVERT: A  564 ARG cc_start: 0.8451 (mtp180) cc_final: 0.8139 (mtm180)
REVERT: A  581 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7159 (tp30)
REVERT: A  696 ASN cc_start: 0.7657 (t0) cc_final: 0.7284 (m110)
REVERT: A  770 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7664 (mp)
REVERT: A  778 GLU cc_start: 0.8413 (tp30) cc_final: 0.8124 (tp30)
REVERT: A  794 GLU cc_start: 0.8397 (mp0) cc_final: 0.8188 (mp0)
REVERT: A  824 ARG cc_start: 0.7999 (mtp85) cc_final: 0.7347 (mtm180)
REVERT: A  895 LYS cc_start: 0.7561 (pttp) cc_final: 0.7245 (ptmt)
REVERT: A  925 TYR cc_start: 0.9091 (OUTLIER) cc_final: 0.8009 (p90)
REVERT: A  927 ASN cc_start: 0.8650 (m110) cc_final: 0.8287 (m-40)
REVERT: A  959 LYS cc_start: 0.8043 (mttt) cc_final: 0.7631 (mtmt)
REVERT: A  962 LEU cc_start: 0.7605 (mt) cc_final: 0.7359 (pp)
REVERT: A 1000 GLN cc_start: 0.8222 (mt0) cc_final: 0.7732 (mt0)
REVERT: A 1104 GLU cc_start: 0.7549 (mm-30) cc_final: 0.6999 (mt-10)
REVERT: A 1143 GLU cc_start: 0.7851 (pt0) cc_final: 0.7376 (mt-10)
REVERT: A 1155 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7873 (tp30)
REVERT: A 1403 GLU cc_start: 0.7146 (mm-30) cc_final: 0.6905 (pt0)
REVERT: B  132 ASP cc_start: 0.8344 (t0) cc_final: 0.7894 (t70)
REVERT: B  194 LYS cc_start: 0.7857 (mptt) cc_final: 0.7300 (ttpp)
REVERT: C  113 MET cc_start: 0.3591 (ppp) cc_final: 0.3255 (ptp)
REVERT: C  124 MET cc_start: 0.6217 (ttp) cc_final: 0.5980 (ttm)
REVERT: C  127 MET cc_start: 0.6965 (mmt) cc_final: 0.6275 (mmp)
REVERT: C  154 GLU cc_start: 0.8264 (tp30) cc_final: 0.7935 (tp30)
  outliers start: 44
  outliers final: 21
  residues processed: 207
  average time/residue: 1.2511
  time to fit residues: 284.6606
Evaluate side-chains
  200 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 174
  time to evaluate  : 1.585 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 ILE
Chi-restraints excluded: chain A residue   53 ARG
Chi-restraints excluded: chain A residue  195 VAL
Chi-restraints excluded: chain A residue  339 LEU
Chi-restraints excluded: chain A residue  428 SER
Chi-restraints excluded: chain A residue  483 ILE
Chi-restraints excluded: chain A residue  504 SER
Chi-restraints excluded: chain A residue  532 ASN
Chi-restraints excluded: chain A residue  536 GLU
Chi-restraints excluded: chain A residue  542 GLU
Chi-restraints excluded: chain A residue  640 ASN
Chi-restraints excluded: chain A residue  743 MET
Chi-restraints excluded: chain A residue  746 ASN
Chi-restraints excluded: chain A residue  753 SER
Chi-restraints excluded: chain A residue  770 LEU
Chi-restraints excluded: chain A residue  851 THR
Chi-restraints excluded: chain A residue  925 TYR
Chi-restraints excluded: chain A residue 1097 ASP
Chi-restraints excluded: chain A residue 1109 THR
Chi-restraints excluded: chain A residue 1188 ASN
Chi-restraints excluded: chain A residue 1248 VAL
Chi-restraints excluded: chain A residue 1254 VAL
Chi-restraints excluded: chain A residue 1396 LEU
Chi-restraints excluded: chain B residue  113 MET
Chi-restraints excluded: chain C residue  135 VAL
Chi-restraints excluded: chain D residue  113 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 22 optimal weight:    4.9990
   chunk 14 optimal weight:    1.9990
   chunk 131 optimal weight:    7.9990
   chunk 127 optimal weight:    6.9990
   chunk 41 optimal weight:    5.9990
   chunk 54 optimal weight:    2.9990
   chunk 27 optimal weight:    4.9990
   chunk 100 optimal weight:    3.9990
   chunk 138 optimal weight:    8.9990
   chunk 163 optimal weight:    0.0980
   chunk 35 optimal weight:    2.9990
   overall best weight:    2.4188

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

Flipped N/Q/H residues before XYZ refinement:
A 693 ASN
** A 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1048 GLN
A1270 ASN
A1322 ASN
C 161 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.159600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.121732 restraints weight = 15879.447|
|-----------------------------------------------------------------------------|
r_work (start): 0.3387 rms_B_bonded: 2.02
r_work: 0.3196 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3064 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3064
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8385
moved from start:          0.3236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  13942  Z= 0.177
  Angle     :  0.579   9.619  18893  Z= 0.302
  Chirality :  0.043   0.159   2108
  Planarity :  0.005   0.051   2404
  Dihedral  :  4.578  30.257   1836
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 3.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 15.03 %
    Favored  : 81.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

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:  0.47 (0.20), residues: 1682
  helix:  1.21 (0.18), residues: 874
  sheet:  1.15 (0.51), residues: 97
  loop : -0.94 (0.22), residues: 711

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 108 
 HIS   0.006   0.001   HIS A 154 
 PHE   0.023   0.002   PHE A 414 
 TYR   0.019   0.002   TYR A 803 
 ARG   0.003   0.000   ARG B 271 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06337 (  684)
  hydrogen bonds       : angle       4.29007 ( 1932)
  metal coordination   : bond        0.00334 (    3)
  covalent geometry    : bond        0.00431 (13939)
  covalent geometry    : angle       0.57935 (18893)

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

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

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 167
  time to evaluate  : 1.814 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 ILE cc_start: 0.8212 (OUTLIER) cc_final: 0.7687 (mp)
REVERT: A   41 ARG cc_start: 0.7822 (mmm160) cc_final: 0.7367 (mmt180)
REVERT: A   51 ARG cc_start: 0.8255 (ptm160) cc_final: 0.7736 (ptt-90)
REVERT: A  196 LYS cc_start: 0.7494 (mptt) cc_final: 0.6977 (mmtm)
REVERT: A  229 GLU cc_start: 0.7410 (mm-30) cc_final: 0.6971 (tt0)
REVERT: A  289 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.7733 (ttm)
REVERT: A  345 ASP cc_start: 0.6873 (p0) cc_final: 0.6670 (t0)
REVERT: A  390 ASP cc_start: 0.7461 (m-30) cc_final: 0.7116 (t70)
REVERT: A  431 LYS cc_start: 0.7623 (tptp) cc_final: 0.7266 (mptt)
REVERT: A  536 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7341 (tp30)
REVERT: A  542 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8098 (mm-30)
REVERT: A  581 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7190 (tp30)
REVERT: A  696 ASN cc_start: 0.7686 (t0) cc_final: 0.7411 (m110)
REVERT: A  770 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7680 (mp)
REVERT: A  778 GLU cc_start: 0.8412 (tp30) cc_final: 0.8195 (mm-30)
REVERT: A  785 TYR cc_start: 0.9100 (OUTLIER) cc_final: 0.8474 (m-80)
REVERT: A  791 LYS cc_start: 0.7720 (mtpp) cc_final: 0.7392 (mtpp)
REVERT: A  794 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8097 (mp0)
REVERT: A  824 ARG cc_start: 0.8017 (mtp85) cc_final: 0.7355 (mtm180)
REVERT: A  895 LYS cc_start: 0.7510 (pttp) cc_final: 0.7171 (ptmt)
REVERT: A  925 TYR cc_start: 0.9101 (OUTLIER) cc_final: 0.7963 (p90)
REVERT: A  927 ASN cc_start: 0.8640 (m110) cc_final: 0.8287 (m-40)
REVERT: A  959 LYS cc_start: 0.8059 (mttt) cc_final: 0.7620 (mtmt)
REVERT: A  962 LEU cc_start: 0.7633 (mt) cc_final: 0.7379 (pp)
REVERT: A 1104 GLU cc_start: 0.7578 (mm-30) cc_final: 0.7043 (mt-10)
REVERT: A 1143 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7370 (mt-10)
REVERT: A 1155 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7838 (tp30)
REVERT: A 1246 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7328 (mm-30)
REVERT: A 1403 GLU cc_start: 0.7131 (mm-30) cc_final: 0.6902 (pt0)
REVERT: B  124 MET cc_start: 0.7809 (mmm) cc_final: 0.7608 (mmm)
REVERT: B  132 ASP cc_start: 0.8349 (t0) cc_final: 0.7894 (t70)
REVERT: B  194 LYS cc_start: 0.7866 (mptt) cc_final: 0.7334 (ttpp)
REVERT: B  254 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.8108 (tt0)
REVERT: C  113 MET cc_start: 0.3663 (ppp) cc_final: 0.3296 (ptp)
REVERT: C  124 MET cc_start: 0.6205 (ttp) cc_final: 0.5975 (ttm)
REVERT: C  154 GLU cc_start: 0.8263 (tp30) cc_final: 0.7966 (tp30)
  outliers start: 47
  outliers final: 25
  residues processed: 195
  average time/residue: 1.2495
  time to fit residues: 267.0056
Evaluate side-chains
  197 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 163
  time to evaluate  : 1.531 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 ILE
Chi-restraints excluded: chain A residue   53 ARG
Chi-restraints excluded: chain A residue  195 VAL
Chi-restraints excluded: chain A residue  199 ILE
Chi-restraints excluded: chain A residue  289 MET
Chi-restraints excluded: chain A residue  339 LEU
Chi-restraints excluded: chain A residue  428 SER
Chi-restraints excluded: chain A residue  430 TYR
Chi-restraints excluded: chain A residue  483 ILE
Chi-restraints excluded: chain A residue  504 SER
Chi-restraints excluded: chain A residue  536 GLU
Chi-restraints excluded: chain A residue  542 GLU
Chi-restraints excluded: chain A residue  634 THR
Chi-restraints excluded: chain A residue  640 ASN
Chi-restraints excluded: chain A residue  743 MET
Chi-restraints excluded: chain A residue  746 ASN
Chi-restraints excluded: chain A residue  753 SER
Chi-restraints excluded: chain A residue  770 LEU
Chi-restraints excluded: chain A residue  785 TYR
Chi-restraints excluded: chain A residue  851 THR
Chi-restraints excluded: chain A residue  890 ILE
Chi-restraints excluded: chain A residue  925 TYR
Chi-restraints excluded: chain A residue 1097 ASP
Chi-restraints excluded: chain A residue 1109 THR
Chi-restraints excluded: chain A residue 1143 GLU
Chi-restraints excluded: chain A residue 1188 ASN
Chi-restraints excluded: chain A residue 1252 LEU
Chi-restraints excluded: chain A residue 1254 VAL
Chi-restraints excluded: chain A residue 1396 LEU
Chi-restraints excluded: chain B residue  113 MET
Chi-restraints excluded: chain B residue  141 THR
Chi-restraints excluded: chain B residue  254 GLN
Chi-restraints excluded: chain C residue  135 VAL
Chi-restraints excluded: chain D residue  113 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 71 optimal weight:    0.9990
   chunk 61 optimal weight:    0.6980
   chunk 66 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 41 optimal weight:    0.7980
   chunk 75 optimal weight:    8.9990
   chunk 36 optimal weight:    4.9990
   chunk 13 optimal weight:    3.9990
   chunk 9 optimal weight:    0.7980
   chunk 112 optimal weight:    0.7980
   chunk 154 optimal weight:    4.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** A 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1048 GLN
A1158 ASN
A1322 ASN
C 161 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.164077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.126497 restraints weight = 15719.559|
|-----------------------------------------------------------------------------|
r_work (start): 0.3453 rms_B_bonded: 2.00
r_work: 0.3270 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3140 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8303
moved from start:          0.3387

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  13942  Z= 0.106
  Angle     :  0.500   8.312  18893  Z= 0.261
  Chirality :  0.039   0.159   2108
  Planarity :  0.004   0.050   2404
  Dihedral  :  4.218  26.791   1836
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 3.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 16.29 %
    Favored  : 81.58 %
  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:  0.88 (0.21), residues: 1682
  helix:  1.58 (0.18), residues: 873
  sheet:  1.18 (0.50), residues: 97
  loop : -0.76 (0.22), residues: 712

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  76 
 HIS   0.003   0.001   HIS A 154 
 PHE   0.014   0.001   PHE A 414 
 TYR   0.015   0.001   TYR A 237 
 ARG   0.007   0.000   ARG A1057 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04350 (  684)
  hydrogen bonds       : angle       4.07546 ( 1932)
  metal coordination   : bond        0.00199 (    3)
  covalent geometry    : bond        0.00228 (13939)
  covalent geometry    : angle       0.50016 (18893)

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

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

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 184
  time to evaluate  : 1.630 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 ARG cc_start: 0.7750 (mmm160) cc_final: 0.7300 (mmp-170)
REVERT: A   51 ARG cc_start: 0.8208 (ptm160) cc_final: 0.7711 (ptt-90)
REVERT: A   77 ASP cc_start: 0.7828 (t70) cc_final: 0.7572 (t0)
REVERT: A  196 LYS cc_start: 0.7461 (mptt) cc_final: 0.6946 (mmtm)
REVERT: A  229 GLU cc_start: 0.7361 (mm-30) cc_final: 0.7050 (tt0)
REVERT: A  431 LYS cc_start: 0.7636 (tptp) cc_final: 0.7278 (mptt)
REVERT: A  536 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7150 (tp30)
REVERT: A  542 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.8037 (mm-30)
REVERT: A  581 GLU cc_start: 0.7590 (mt-10) cc_final: 0.7147 (tp30)
REVERT: A  696 ASN cc_start: 0.7622 (t0) cc_final: 0.7365 (m110)
REVERT: A  778 GLU cc_start: 0.8393 (tp30) cc_final: 0.8089 (tp30)
REVERT: A  791 LYS cc_start: 0.7634 (mtpp) cc_final: 0.7095 (mttt)
REVERT: A  822 MET cc_start: 0.9075 (tpt) cc_final: 0.8837 (tpt)
REVERT: A  824 ARG cc_start: 0.7983 (mtp85) cc_final: 0.7338 (mtm180)
REVERT: A  895 LYS cc_start: 0.7351 (pttp) cc_final: 0.7027 (ptmt)
REVERT: A  925 TYR cc_start: 0.9098 (OUTLIER) cc_final: 0.7872 (p90)
REVERT: A  927 ASN cc_start: 0.8562 (m110) cc_final: 0.8170 (m-40)
REVERT: A  959 LYS cc_start: 0.8061 (mttt) cc_final: 0.7639 (mtmt)
REVERT: A  962 LEU cc_start: 0.7579 (mt) cc_final: 0.7340 (pp)
REVERT: A 1000 GLN cc_start: 0.8191 (mt0) cc_final: 0.7700 (mt0)
REVERT: A 1104 GLU cc_start: 0.7532 (mm-30) cc_final: 0.6973 (mt-10)
REVERT: A 1143 GLU cc_start: 0.7837 (pt0) cc_final: 0.7371 (mt-10)
REVERT: A 1155 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7851 (tp30)
REVERT: A 1246 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7329 (mm-30)
REVERT: A 1282 ASN cc_start: 0.7610 (m110) cc_final: 0.7281 (m110)
REVERT: B  194 LYS cc_start: 0.7852 (mptt) cc_final: 0.7240 (ttpp)
REVERT: C  113 MET cc_start: 0.3674 (ppp) cc_final: 0.3322 (ptp)
REVERT: C  154 GLU cc_start: 0.8252 (tp30) cc_final: 0.7851 (tp30)
  outliers start: 32
  outliers final: 15
  residues processed: 203
  average time/residue: 1.2258
  time to fit residues: 273.6854
Evaluate side-chains
  191 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 173
  time to evaluate  : 1.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  178 THR
Chi-restraints excluded: chain A residue  195 VAL
Chi-restraints excluded: chain A residue  483 ILE
Chi-restraints excluded: chain A residue  504 SER
Chi-restraints excluded: chain A residue  532 ASN
Chi-restraints excluded: chain A residue  536 GLU
Chi-restraints excluded: chain A residue  542 GLU
Chi-restraints excluded: chain A residue  640 ASN
Chi-restraints excluded: chain A residue  753 SER
Chi-restraints excluded: chain A residue  925 TYR
Chi-restraints excluded: chain A residue 1095 LEU
Chi-restraints excluded: chain A residue 1097 ASP
Chi-restraints excluded: chain A residue 1252 LEU
Chi-restraints excluded: chain A residue 1396 LEU
Chi-restraints excluded: chain B residue  113 MET
Chi-restraints excluded: chain B residue  141 THR
Chi-restraints excluded: chain C residue  135 VAL
Chi-restraints excluded: chain D residue  113 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 104 optimal weight:    8.9990
   chunk 125 optimal weight:    5.9990
   chunk 156 optimal weight:    9.9990
   chunk 131 optimal weight:    8.9990
   chunk 49 optimal weight:    4.9990
   chunk 80 optimal weight:    0.8980
   chunk 115 optimal weight:    0.9990
   chunk 82 optimal weight:    8.9990
   chunk 98 optimal weight:    0.9990
   chunk 52 optimal weight:    8.9990
   chunk 106 optimal weight:    0.7980
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
** A 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1048 GLN
C 161 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.161282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.123410 restraints weight = 15663.275|
|-----------------------------------------------------------------------------|
r_work (start): 0.3414 rms_B_bonded: 2.00
r_work: 0.3229 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3098 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8357
moved from start:          0.3392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  13942  Z= 0.142
  Angle     :  0.538   8.882  18893  Z= 0.279
  Chirality :  0.041   0.157   2108
  Planarity :  0.004   0.050   2404
  Dihedral  :  4.267  27.964   1836
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 3.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 17.02 %
    Favored  : 81.05 %
  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:  0.83 (0.20), residues: 1682
  helix:  1.53 (0.18), residues: 873
  sheet:  1.23 (0.50), residues: 97
  loop : -0.77 (0.22), residues: 712

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 261 
 HIS   0.005   0.001   HIS A 154 
 PHE   0.020   0.002   PHE A 414 
 TYR   0.016   0.001   TYR A 803 
 ARG   0.005   0.000   ARG A 628 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05417 (  684)
  hydrogen bonds       : angle       4.13064 ( 1932)
  metal coordination   : bond        0.00256 (    3)
  covalent geometry    : bond        0.00335 (13939)
  covalent geometry    : angle       0.53753 (18893)

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

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

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 175
  time to evaluate  : 1.686 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 ARG cc_start: 0.7785 (mmm160) cc_final: 0.7358 (mmt180)
REVERT: A   51 ARG cc_start: 0.8241 (ptm160) cc_final: 0.7732 (ptt-90)
REVERT: A  196 LYS cc_start: 0.7497 (mptt) cc_final: 0.6984 (mmtm)
REVERT: A  229 GLU cc_start: 0.7378 (mm-30) cc_final: 0.7031 (tt0)
REVERT: A  390 ASP cc_start: 0.7417 (m-30) cc_final: 0.7093 (t70)
REVERT: A  431 LYS cc_start: 0.7676 (tptp) cc_final: 0.7336 (mptt)
REVERT: A  536 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7252 (tp30)
REVERT: A  542 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8081 (mm-30)
REVERT: A  581 GLU cc_start: 0.7642 (mt-10) cc_final: 0.7195 (tp30)
REVERT: A  696 ASN cc_start: 0.7653 (t0) cc_final: 0.7365 (m110)
REVERT: A  778 GLU cc_start: 0.8416 (tp30) cc_final: 0.8213 (mm-30)
REVERT: A  791 LYS cc_start: 0.7680 (mtpp) cc_final: 0.7478 (mtpp)
REVERT: A  824 ARG cc_start: 0.8029 (mtp85) cc_final: 0.7359 (mtm180)
REVERT: A  895 LYS cc_start: 0.7360 (pttp) cc_final: 0.7038 (ptmt)
REVERT: A  925 TYR cc_start: 0.9102 (OUTLIER) cc_final: 0.7896 (p90)
REVERT: A  927 ASN cc_start: 0.8565 (m110) cc_final: 0.8202 (m-40)
REVERT: A  959 LYS cc_start: 0.8054 (mttt) cc_final: 0.7589 (mtmt)
REVERT: A  962 LEU cc_start: 0.7625 (mt) cc_final: 0.7388 (pp)
REVERT: A 1073 MET cc_start: 0.6755 (tpt) cc_final: 0.6520 (tpt)
REVERT: A 1104 GLU cc_start: 0.7569 (mm-30) cc_final: 0.6996 (mt-10)
REVERT: A 1143 GLU cc_start: 0.7837 (pt0) cc_final: 0.7371 (mt-10)
REVERT: A 1155 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7869 (tp30)
REVERT: A 1246 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7322 (mm-30)
REVERT: B  194 LYS cc_start: 0.7891 (mptt) cc_final: 0.7325 (ttpp)
REVERT: B  254 GLN cc_start: 0.8375 (tt0) cc_final: 0.8170 (tt0)
REVERT: C  113 MET cc_start: 0.3547 (ppp) cc_final: 0.3190 (ptp)
REVERT: C  154 GLU cc_start: 0.8268 (tp30) cc_final: 0.7853 (tp30)
  outliers start: 29
  outliers final: 19
  residues processed: 194
  average time/residue: 1.1786
  time to fit residues: 251.6061
Evaluate side-chains
  194 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 172
  time to evaluate  : 1.497 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  195 VAL
Chi-restraints excluded: chain A residue  483 ILE
Chi-restraints excluded: chain A residue  504 SER
Chi-restraints excluded: chain A residue  532 ASN
Chi-restraints excluded: chain A residue  536 GLU
Chi-restraints excluded: chain A residue  542 GLU
Chi-restraints excluded: chain A residue  640 ASN
Chi-restraints excluded: chain A residue  746 ASN
Chi-restraints excluded: chain A residue  753 SER
Chi-restraints excluded: chain A residue  851 THR
Chi-restraints excluded: chain A residue  925 TYR
Chi-restraints excluded: chain A residue  985 THR
Chi-restraints excluded: chain A residue 1095 LEU
Chi-restraints excluded: chain A residue 1097 ASP
Chi-restraints excluded: chain A residue 1188 ASN
Chi-restraints excluded: chain A residue 1252 LEU
Chi-restraints excluded: chain A residue 1396 LEU
Chi-restraints excluded: chain B residue  113 MET
Chi-restraints excluded: chain B residue  141 THR
Chi-restraints excluded: chain C residue  135 VAL
Chi-restraints excluded: chain D residue  113 MET
Chi-restraints excluded: chain D residue  134 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 6 optimal weight:    0.6980
   chunk 140 optimal weight:    7.9990
   chunk 166 optimal weight:   20.0000
   chunk 95 optimal weight:    5.9990
   chunk 43 optimal weight:    9.9990
   chunk 101 optimal weight:    0.9990
   chunk 160 optimal weight:    0.8980
   chunk 59 optimal weight:    6.9990
   chunk 142 optimal weight:    9.9990
   chunk 9 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
A 395 HIS
** A 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1048 GLN
C 161 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.162350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.124573 restraints weight = 15610.496|
|-----------------------------------------------------------------------------|
r_work (start): 0.3429 rms_B_bonded: 2.03
r_work: 0.3245 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3115 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3115
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8335
moved from start:          0.3451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  13942  Z= 0.122
  Angle     :  0.528  12.215  18893  Z= 0.271
  Chirality :  0.040   0.157   2108
  Planarity :  0.004   0.050   2404
  Dihedral  :  4.207  27.599   1836
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 3.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 17.62 %
    Favored  : 80.59 %
  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:  0.91 (0.21), residues: 1682
  helix:  1.61 (0.18), residues: 873
  sheet:  1.26 (0.50), residues: 97
  loop : -0.75 (0.22), residues: 712

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   0.017   0.001   PHE A 414 
 TYR   0.015   0.001   TYR A 803 
 ARG   0.004   0.000   ARG A 564 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04932 (  684)
  hydrogen bonds       : angle       4.08878 ( 1932)
  metal coordination   : bond        0.00130 (    3)
  covalent geometry    : bond        0.00280 (13939)
  covalent geometry    : angle       0.52791 (18893)

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

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

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 169
  time to evaluate  : 1.682 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 ILE cc_start: 0.8109 (OUTLIER) cc_final: 0.7557 (mp)
REVERT: A   41 ARG cc_start: 0.7790 (mmm160) cc_final: 0.7352 (mmt180)
REVERT: A   51 ARG cc_start: 0.8238 (ptm160) cc_final: 0.7726 (ptt-90)
REVERT: A  196 LYS cc_start: 0.7449 (mptt) cc_final: 0.6936 (mmtm)
REVERT: A  229 GLU cc_start: 0.7363 (mm-30) cc_final: 0.7035 (tt0)
REVERT: A  431 LYS cc_start: 0.7686 (tptp) cc_final: 0.7337 (mptt)
REVERT: A  536 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7334 (tp30)
REVERT: A  542 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8055 (mm-30)
REVERT: A  564 ARG cc_start: 0.8374 (mmm-85) cc_final: 0.8150 (mmm-85)
REVERT: A  581 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7203 (tp30)
REVERT: A  696 ASN cc_start: 0.7625 (t0) cc_final: 0.7340 (m110)
REVERT: A  778 GLU cc_start: 0.8423 (tp30) cc_final: 0.8209 (mm-30)
REVERT: A  824 ARG cc_start: 0.8020 (mtp85) cc_final: 0.7346 (mtm180)
REVERT: A  895 LYS cc_start: 0.7339 (pttp) cc_final: 0.7022 (ptmt)
REVERT: A  925 TYR cc_start: 0.9113 (OUTLIER) cc_final: 0.7845 (p90)
REVERT: A  927 ASN cc_start: 0.8550 (m110) cc_final: 0.8185 (m-40)
REVERT: A  959 LYS cc_start: 0.8056 (mttt) cc_final: 0.7594 (mtmt)
REVERT: A  962 LEU cc_start: 0.7634 (mt) cc_final: 0.7393 (pp)
REVERT: A  997 ILE cc_start: 0.7628 (tp) cc_final: 0.7388 (tp)
REVERT: A 1073 MET cc_start: 0.6687 (tpt) cc_final: 0.6454 (tpt)
REVERT: A 1104 GLU cc_start: 0.7545 (mm-30) cc_final: 0.6973 (mt-10)
REVERT: A 1143 GLU cc_start: 0.7841 (pt0) cc_final: 0.7377 (mt-10)
REVERT: A 1155 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7855 (tp30)
REVERT: A 1246 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7324 (mm-30)
REVERT: B  194 LYS cc_start: 0.7908 (mptt) cc_final: 0.7296 (ttpp)
REVERT: B  254 GLN cc_start: 0.8352 (tt0) cc_final: 0.8147 (tt0)
REVERT: C  113 MET cc_start: 0.3534 (ppp) cc_final: 0.3174 (ptp)
REVERT: C  154 GLU cc_start: 0.8250 (tp30) cc_final: 0.7860 (tp30)
  outliers start: 27
  outliers final: 20
  residues processed: 188
  average time/residue: 1.2095
  time to fit residues: 251.0866
Evaluate side-chains
  192 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 168
  time to evaluate  : 1.565 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 ILE
Chi-restraints excluded: chain A residue  195 VAL
Chi-restraints excluded: chain A residue  428 SER
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  483 ILE
Chi-restraints excluded: chain A residue  504 SER
Chi-restraints excluded: chain A residue  532 ASN
Chi-restraints excluded: chain A residue  536 GLU
Chi-restraints excluded: chain A residue  542 GLU
Chi-restraints excluded: chain A residue  640 ASN
Chi-restraints excluded: chain A residue  746 ASN
Chi-restraints excluded: chain A residue  753 SER
Chi-restraints excluded: chain A residue  851 THR
Chi-restraints excluded: chain A residue  925 TYR
Chi-restraints excluded: chain A residue  985 THR
Chi-restraints excluded: chain A residue 1095 LEU
Chi-restraints excluded: chain A residue 1097 ASP
Chi-restraints excluded: chain A residue 1252 LEU
Chi-restraints excluded: chain A residue 1396 LEU
Chi-restraints excluded: chain B residue  113 MET
Chi-restraints excluded: chain B residue  141 THR
Chi-restraints excluded: chain C residue  135 VAL
Chi-restraints excluded: chain D residue  113 MET
Chi-restraints excluded: chain D residue  134 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 153 optimal weight:   20.0000
   chunk 106 optimal weight:    4.9990
   chunk 105 optimal weight:    8.9990
   chunk 9 optimal weight:    0.8980
   chunk 22 optimal weight:    0.8980
   chunk 73 optimal weight:    9.9990
   chunk 69 optimal weight:    4.9990
   chunk 12 optimal weight:    5.9990
   chunk 94 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 74 optimal weight:   10.0000
   overall best weight:    2.5384

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

Flipped N/Q/H residues before XYZ refinement:
A 395 HIS
** A 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1048 GLN
A1158 ASN
C 161 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.159525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.121857 restraints weight = 15658.714|
|-----------------------------------------------------------------------------|
r_work (start): 0.3391 rms_B_bonded: 1.97
r_work: 0.3203 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3072 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8381
moved from start:          0.3465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  13942  Z= 0.180
  Angle     :  0.589  13.339  18893  Z= 0.302
  Chirality :  0.043   0.156   2108
  Planarity :  0.005   0.050   2404
  Dihedral  :  4.420  29.748   1836
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 3.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 17.62 %
    Favored  : 80.52 %
  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:  0.68 (0.20), residues: 1682
  helix:  1.40 (0.18), residues: 871
  sheet:  1.21 (0.51), residues: 97
  loop : -0.84 (0.22), residues: 714

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 108 
 HIS   0.006   0.001   HIS A 154 
 PHE   0.023   0.002   PHE A 414 
 TYR   0.018   0.002   TYR A 803 
 ARG   0.005   0.000   ARG A 564 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06273 (  684)
  hydrogen bonds       : angle       4.23707 ( 1932)
  metal coordination   : bond        0.00492 (    3)
  covalent geometry    : bond        0.00438 (13939)
  covalent geometry    : angle       0.58883 (18893)

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

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

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 173
  time to evaluate  : 1.460 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 ILE cc_start: 0.8209 (OUTLIER) cc_final: 0.7675 (mp)
REVERT: A   41 ARG cc_start: 0.7788 (mmm160) cc_final: 0.7346 (mmt180)
REVERT: A   51 ARG cc_start: 0.8223 (ptm160) cc_final: 0.7706 (ptt-90)
REVERT: A  196 LYS cc_start: 0.7450 (mptt) cc_final: 0.6956 (mmtm)
REVERT: A  217 ARG cc_start: 0.7392 (mpt180) cc_final: 0.7133 (mpt180)
REVERT: A  390 ASP cc_start: 0.7426 (m-30) cc_final: 0.7103 (t70)
REVERT: A  431 LYS cc_start: 0.7679 (tptp) cc_final: 0.7329 (mptt)
REVERT: A  536 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7330 (tp30)
REVERT: A  542 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8096 (mm-30)
REVERT: A  564 ARG cc_start: 0.8353 (mtm-85) cc_final: 0.8114 (mmm-85)
REVERT: A  581 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7187 (tp30)
REVERT: A  605 LYS cc_start: 0.6584 (mtpm) cc_final: 0.6311 (mmmt)
REVERT: A  696 ASN cc_start: 0.7753 (t0) cc_final: 0.7418 (m110)
REVERT: A  778 GLU cc_start: 0.8432 (tp30) cc_final: 0.8227 (mm-30)
REVERT: A  791 LYS cc_start: 0.8002 (mtpp) cc_final: 0.7407 (mttt)
REVERT: A  824 ARG cc_start: 0.8033 (mtp85) cc_final: 0.7351 (mtm180)
REVERT: A  895 LYS cc_start: 0.7399 (pttp) cc_final: 0.7076 (ptmt)
REVERT: A  925 TYR cc_start: 0.9100 (OUTLIER) cc_final: 0.7814 (p90)
REVERT: A  927 ASN cc_start: 0.8550 (m110) cc_final: 0.8202 (m-40)
REVERT: A  959 LYS cc_start: 0.8024 (mttt) cc_final: 0.7605 (mtmt)
REVERT: A 1104 GLU cc_start: 0.7589 (mm-30) cc_final: 0.7018 (mt-10)
REVERT: A 1143 GLU cc_start: 0.7862 (pt0) cc_final: 0.7383 (mt-10)
REVERT: A 1155 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7847 (tp30)
REVERT: A 1246 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7305 (mm-30)
REVERT: A 1282 ASN cc_start: 0.7693 (m110) cc_final: 0.7377 (m110)
REVERT: B  194 LYS cc_start: 0.7919 (mptt) cc_final: 0.7377 (ttpp)
REVERT: B  254 GLN cc_start: 0.8419 (tt0) cc_final: 0.8211 (tt0)
REVERT: C  113 MET cc_start: 0.3552 (ppp) cc_final: 0.3190 (ptp)
REVERT: C  154 GLU cc_start: 0.8265 (tp30) cc_final: 0.7848 (tp30)
  outliers start: 28
  outliers final: 19
  residues processed: 192
  average time/residue: 1.2666
  time to fit residues: 266.5493
Evaluate side-chains
  194 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 171
  time to evaluate  : 1.649 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 ILE
Chi-restraints excluded: chain A residue  195 VAL
Chi-restraints excluded: chain A residue  199 ILE
Chi-restraints excluded: chain A residue  428 SER
Chi-restraints excluded: chain A residue  483 ILE
Chi-restraints excluded: chain A residue  504 SER
Chi-restraints excluded: chain A residue  536 GLU
Chi-restraints excluded: chain A residue  542 GLU
Chi-restraints excluded: chain A residue  640 ASN
Chi-restraints excluded: chain A residue  746 ASN
Chi-restraints excluded: chain A residue  753 SER
Chi-restraints excluded: chain A residue  851 THR
Chi-restraints excluded: chain A residue  925 TYR
Chi-restraints excluded: chain A residue  985 THR
Chi-restraints excluded: chain A residue  992 ARG
Chi-restraints excluded: chain A residue 1095 LEU
Chi-restraints excluded: chain A residue 1097 ASP
Chi-restraints excluded: chain A residue 1252 LEU
Chi-restraints excluded: chain A residue 1396 LEU
Chi-restraints excluded: chain B residue  113 MET
Chi-restraints excluded: chain B residue  141 THR
Chi-restraints excluded: chain C residue  135 VAL
Chi-restraints excluded: chain D residue  113 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 82 optimal weight:    7.9990
   chunk 156 optimal weight:    8.9990
   chunk 52 optimal weight:    4.9990
   chunk 110 optimal weight:    5.9990
   chunk 41 optimal weight:    5.9990
   chunk 130 optimal weight:    0.0070
   chunk 1 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 99 optimal weight:    1.9990
   chunk 119 optimal weight:    0.9990
   chunk 87 optimal weight:    0.0980
   overall best weight:    0.8202

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

Flipped N/Q/H residues before XYZ refinement:
A 395 HIS
** A 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1048 GLN
C 161 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.163412 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.125783 restraints weight = 15790.334|
|-----------------------------------------------------------------------------|
r_work (start): 0.3437 rms_B_bonded: 2.05
r_work: 0.3255 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3124 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8311
moved from start:          0.3590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  13942  Z= 0.107
  Angle     :  0.519  13.811  18893  Z= 0.266
  Chirality :  0.040   0.156   2108
  Planarity :  0.004   0.049   2404
  Dihedral  :  4.143  26.893   1836
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 3.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 17.49 %
    Favored  : 80.59 %
  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 (0.21), residues: 1682
  helix:  1.71 (0.18), residues: 862
  sheet:  1.23 (0.50), residues: 97
  loop : -0.73 (0.22), residues: 723

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   0.015   0.001   PHE A 529 
 TYR   0.013   0.001   TYR A 237 
 ARG   0.004   0.000   ARG A 217 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04449 (  684)
  hydrogen bonds       : angle       4.08074 ( 1932)
  metal coordination   : bond        0.00264 (    3)
  covalent geometry    : bond        0.00233 (13939)
  covalent geometry    : angle       0.51890 (18893)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 10082.40 seconds
wall clock time: 173 minutes 55.66 seconds (10435.66 seconds total)