Starting phenix.real_space_refine
on Sun Jan 19 14:24:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8izm_35865/01_2025/8izm_35865.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8izm_35865/01_2025/8izm_35865.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.01
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8izm_35865/01_2025/8izm_35865.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8izm_35865/01_2025/8izm_35865.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8izm_35865/01_2025/8izm_35865.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8izm_35865/01_2025/8izm_35865.cif"
  }
  resolution = 3.01
  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=   0.000 sd=   0.053
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 1404 atoms to isotropic.
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      2      6.06       5
     S      81      5.16       5
     C    8105      2.51       5
     N    2182      2.21       5
     O    2372      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 43 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 12742
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 517
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 69, 517
          Classifications: {'peptide': 69}
          Link IDs: {'PTRANS': 3, 'TRANS': 65}
    Chain: "C"
      Number of atoms: 642
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 85, 642
          Classifications: {'peptide': 85}
          Link IDs: {'PTRANS': 4, 'TRANS': 80}
    Chain: "D"
      Number of atoms: 387
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 50, 387
          Classifications: {'peptide': 50}
          Link IDs: {'TRANS': 49}
    Chain: "E"
      Number of atoms: 412
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 412
          Classifications: {'peptide': 54}
          Link IDs: {'TRANS': 53}
    Chain: "A"
      Number of atoms: 10782
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1350, 10782
          Classifications: {'peptide': 1350}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 67, 'TRANS': 1282}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 7
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM  11097  SG  CYS A1187      61.723  18.565  85.241  1.00108.17           S
  ATOM  11122  SG  CYS A1190      63.227  21.089  88.334  1.00128.93           S
  ATOM  10755  SG  CYS A1142      75.237  23.137  70.425  1.00 99.43           S
  ATOM  12460  SG  CYS A1379      73.778  20.648  72.983  1.00109.11           S
  ATOM  12466  SG  CYS A1380      71.860  24.070  72.475  1.00103.98           S

  Time building chain proxies: 8.16, per 1000 atoms: 0.64
  Number of scatterers: 12742
  At special positions: 0
  Unit cell: (104.94, 148.4, 134.09, 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      2     29.99
     S      81     16.00
     O    2372      8.00
     N    2182      7.00
     C    8105      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: 2.82
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A3001 "
        pdb="ZN    ZN A3001 " - pdb=" NE2 HIS A1374 "
        pdb="ZN    ZN A3001 " - pdb=" ND1 HIS A1372 "
        pdb="ZN    ZN A3001 " - pdb=" SG  CYS A1190 "
        pdb="ZN    ZN A3001 " - pdb=" SG  CYS A1187 "
      pdb="  ZN A3002 "
        pdb="ZN    ZN A3002 " - pdb=" SG  CYS A1142 "
        pdb="ZN    ZN A3002 " - pdb=" SG  CYS A1380 "
        pdb="ZN    ZN A3002 " - pdb=" SG  CYS A1379 "
      Number of angles added : 1


  3176 Ramachandran restraints generated.
    1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3070

  Finding SS restraints...
    Secondary structure from input PDB file:
      71 helices and 8 sheets defined
      61.2% alpha, 4.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.37
  Creating SS restraints...
    Processing helix  chain 'B' and resid 218 through 277
      removed outlier: 4.097A  pdb=" N   GLY B 246 " --> pdb=" O   VAL B 242 " (cutoff:3.500A)
      removed outlier: 4.379A  pdb=" N   SER B 247 " --> pdb=" O   LEU B 243 " (cutoff:3.500A)
      removed outlier: 4.260A  pdb=" N   MET B 248 " --> pdb=" O   ALA B 244 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   VAL B 249 " --> pdb=" O   GLN B 245 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   THR B 258 " --> pdb=" O   ASN B 254 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 221 through 272
      removed outlier: 3.788A  pdb=" N   GLY C 227 " --> pdb=" O   ASP C 223 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   MET C 228 " --> pdb=" O   LEU C 224 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   ALA C 230 " --> pdb=" O   ARG C 226 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   ALA C 244 " --> pdb=" O   ASP C 240 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   GLN C 245 " --> pdb=" O   LYS C 241 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   GLY C 246 " --> pdb=" O   VAL C 242 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   SER C 247 " --> pdb=" O   LEU C 243 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   THR C 265 " --> pdb=" O   THR C 261 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 285 through 290
    Processing helix  chain 'D' and resid 219 through 243
      removed outlier: 3.566A  pdb=" N   ARG D 226 " --> pdb=" O   MET D 222 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   ASP D 240 " --> pdb=" O   GLU D 236 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   LYS D 241 " --> pdb=" O   GLN D 237 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   LEU D 243 " --> pdb=" O   VAL D 239 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 244 through 267
      removed outlier: 3.792A  pdb=" N   MET D 248 " --> pdb=" O   ALA D 244 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   THR D 265 " --> pdb=" O   THR D 261 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   ILE D 266 " --> pdb=" O   THR D 262 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 219 through 271
      removed outlier: 3.548A  pdb=" N   LYS E 241 " --> pdb=" O   GLN E 237 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   MET E 248 " --> pdb=" O   ALA E 244 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   GLY E 268 " --> pdb=" O   ALA E 264 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   MET E 269 " --> pdb=" O   THR E 265 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 19 through 30
      removed outlier: 3.629A  pdb=" N   LEU A  23 " --> pdb=" O   VAL A  19 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   GLY A  30 " --> pdb=" O   TYR A  26 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 37 through 42
      removed outlier: 3.700A  pdb=" N   LEU A  41 " --> pdb=" O   GLU A  37 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   GLY A  42 " --> pdb=" O   PRO A  38 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 37 through 42'
    Processing helix  chain 'A' and resid 43 through 47
    Processing helix  chain 'A' and resid 48 through 55
    Processing helix  chain 'A' and resid 56 through 74
    Processing helix  chain 'A' and resid 75 through 79
    Processing helix  chain 'A' and resid 90 through 98
      removed outlier: 4.059A  pdb=" N   LEU A  95 " --> pdb=" O   PRO A  92 " (cutoff:3.500A)
      Proline residue:  A  96  - end of helix
    Processing helix  chain 'A' and resid 108 through 123
      removed outlier: 3.704A  pdb=" N   LEU A 123 " --> pdb=" O   SER A 119 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 124 through 141
    Processing helix  chain 'A' and resid 162 through 172
    Processing helix  chain 'A' and resid 175 through 199
    Processing helix  chain 'A' and resid 237 through 260
    Processing helix  chain 'A' and resid 265 through 285
      removed outlier: 4.394A  pdb=" N   ARG A 269 " --> pdb=" O   PRO A 265 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 305
      removed outlier: 3.914A  pdb=" N   ILE A 291 " --> pdb=" O   LYS A 287 " (cutoff:3.500A)
      removed outlier: 4.088A  pdb=" N   SER A 297 " --> pdb=" O   SER A 293 " (cutoff:3.500A)
      removed outlier: 4.555A  pdb=" N   TYR A 300 " --> pdb=" O   GLU A 296 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 314 through 329
    Processing helix  chain 'A' and resid 335 through 349
      removed outlier: 3.835A  pdb=" N   GLN A 349 " --> pdb=" O   ASP A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 354 through 360
    Processing helix  chain 'A' and resid 361 through 368
      removed outlier: 3.956A  pdb=" N   ILE A 364 " --> pdb=" O   LEU A 361 " (cutoff:3.500A)
      removed outlier: 4.080A  pdb=" N   MET A 365 " --> pdb=" O   LEU A 362 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   ARG A 366 " --> pdb=" O   CYS A 363 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   TRP A 368 " --> pdb=" O   MET A 365 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 374 through 386
      removed outlier: 3.699A  pdb=" N   LYS A 381 " --> pdb=" O   GLN A 377 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   VAL A 382 " --> pdb=" O   ALA A 378 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 394 through 413
    Processing helix  chain 'A' and resid 430 through 439
    Processing helix  chain 'A' and resid 444 through 450
      removed outlier: 3.658A  pdb=" N   LYS A 450 " --> pdb=" O   GLU A 446 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 451 through 456
      removed outlier: 3.536A  pdb=" N   ILE A 455 " --> pdb=" O   ASN A 451 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 488 through 492
      removed outlier: 3.933A  pdb=" N   VAL A 491 " --> pdb=" O   TRP A 488 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 493 through 503
      removed outlier: 3.601A  pdb=" N   ILE A 497 " --> pdb=" O   ARG A 493 " (cutoff:3.500A)
      removed outlier: 4.302A  pdb=" N   GLN A 499 " --> pdb=" O   SER A 495 " (cutoff:3.500A)
      removed outlier: 4.458A  pdb=" N   ARG A 500 " --> pdb=" O   LEU A 496 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 515 through 522
    Processing helix  chain 'A' and resid 527 through 532
    Processing helix  chain 'A' and resid 532 through 537
    Processing helix  chain 'A' and resid 538 through 543
      removed outlier: 3.914A  pdb=" N   ARG A 542 " --> pdb=" O   GLY A 538 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 568 through 585
    Processing helix  chain 'A' and resid 586 through 590
      removed outlier: 3.731A  pdb=" N   MET A 590 " --> pdb=" O   GLY A 587 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 598 through 611
    Processing helix  chain 'A' and resid 672 through 677
      removed outlier: 3.680A  pdb=" N   ASN A 676 " --> pdb=" O   LYS A 672 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 682 through 694
    Processing helix  chain 'A' and resid 700 through 708
      removed outlier: 3.555A  pdb=" N   LEU A 704 " --> pdb=" O   GLU A 700 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   ARG A 708 " --> pdb=" O   LEU A 704 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 749 through 768
      removed outlier: 3.516A  pdb=" N   TRP A 753 " --> pdb=" O   CYS A 749 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 794 through 820
      removed outlier: 4.173A  pdb=" N   LEU A 808 " --> pdb=" O   LYS A 804 " (cutoff:3.500A)
      removed outlier: 4.029A  pdb=" N   PHE A 809 " --> pdb=" O   ALA A 805 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 851 through 858
      removed outlier: 3.822A  pdb=" N   ASN A 855 " --> pdb=" O   GLN A 851 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   LYS A 858 " --> pdb=" O   LYS A 854 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 869 through 887
    Processing helix  chain 'A' and resid 890 through 912
    Processing helix  chain 'A' and resid 920 through 928
    Processing helix  chain 'A' and resid 929 through 939
      removed outlier: 3.577A  pdb=" N   ILE A 933 " --> pdb=" O   HIS A 929 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 940 through 944
    Processing helix  chain 'A' and resid 951 through 955
    Processing helix  chain 'A' and resid 961 through 977
      removed outlier: 3.621A  pdb=" N   SER A 965 " --> pdb=" O   ASP A 961 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 980 through 989
      removed outlier: 3.821A  pdb=" N   LEU A 984 " --> pdb=" O   ASP A 980 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 996 through 1003
      removed outlier: 3.516A  pdb=" N   ALA A1001 " --> pdb=" O   TRP A 997 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   ASP A1003 " --> pdb=" O   THR A 999 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1014 through 1031
    Processing helix  chain 'A' and resid 1043 through 1057
    Processing helix  chain 'A' and resid 1062 through 1073
    Processing helix  chain 'A' and resid 1073 through 1084
    Processing helix  chain 'A' and resid 1088 through 1099
    Processing helix  chain 'A' and resid 1102 through 1111
    Processing helix  chain 'A' and resid 1111 through 1121
    Processing helix  chain 'A' and resid 1131 through 1137
      removed outlier: 3.646A  pdb=" N   LEU A1134 " --> pdb=" O   GLN A1131 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1142 through 1155
    Processing helix  chain 'A' and resid 1155 through 1160
    Processing helix  chain 'A' and resid 1171 through 1176
    Processing helix  chain 'A' and resid 1187 through 1192
    Processing helix  chain 'A' and resid 1242 through 1259
    Processing helix  chain 'A' and resid 1263 through 1268
    Processing helix  chain 'A' and resid 1269 through 1275
    Processing helix  chain 'A' and resid 1280 through 1288
    Processing helix  chain 'A' and resid 1317 through 1321
      removed outlier: 3.658A  pdb=" N   PHE A1320 " --> pdb=" O   PHE A1317 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   VAL A1321 " --> pdb=" O   SER A1318 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1317 through 1321'
    Processing helix  chain 'A' and resid 1338 through 1358
    Processing sheet with id=AA1, first strand: chain 'B' and resid 282 through 283
    Processing sheet with id=AA2, first strand: chain 'C' and resid 274 through 276
      removed outlier: 3.829A  pdb=" N   ILE C 275 " --> pdb=" O   LEU A 392 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   LEU A 392 " --> pdb=" O   ILE C 275 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 89
      removed outlier: 6.075A  pdb=" N   ALA A  87 " --> pdb=" O   LEU A 232 " (cutoff:3.500A)
      removed outlier: 8.166A  pdb=" N   TYR A 234 " --> pdb=" O   ALA A  87 " (cutoff:3.500A)
      removed outlier: 7.727A  pdb=" N   LEU A  89 " --> pdb=" O   TYR A 234 " (cutoff:3.500A)
      removed outlier: 9.550A  pdb=" N   THR A 236 " --> pdb=" O   LEU A  89 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 423 through 424
      removed outlier: 3.646A  pdb=" N   ARG A 459 " --> pdb=" O   THR A 424 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 563 through 566
    Processing sheet with id=AA6, first strand: chain 'A' and resid 780 through 790
    Processing sheet with id=AA7, first strand: chain 'A' and resid 835 through 838
      removed outlier: 3.541A  pdb=" N   PHE A 836 " --> pdb=" O   PHE A 843 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1180 through 1182

    690 hydrogen bonds defined for protein.
    2001 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 4.70

  Time building geometry restraints manager: 3.20 seconds

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

  Histogram of bond lengths:
        1.18 -     1.30: 2116
        1.30 -     1.43: 3115
        1.43 -     1.56: 7612
        1.56 -     1.68: 1
        1.68 -     1.81: 133
  Bond restraints: 12977
  Sorted by residual:
  bond pdb=" C   LYS A 444 "
       pdb=" N   TYR A 445 "
    ideal  model  delta    sigma   weight residual
    1.335  1.445 -0.109 1.34e-02 5.57e+03 6.66e+01
  bond pdb=" C   LEU A 443 "
       pdb=" N   LYS A 444 "
    ideal  model  delta    sigma   weight residual
    1.331  1.436 -0.105 1.37e-02 5.33e+03 5.89e+01
  bond pdb=" C   GLY A 285 "
       pdb=" N   ASP A 286 "
    ideal  model  delta    sigma   weight residual
    1.333  1.428 -0.095 1.49e-02 4.50e+03 4.05e+01
  bond pdb=" C   LYS A 672 "
       pdb=" N   TYR A 673 "
    ideal  model  delta    sigma   weight residual
    1.334  1.245  0.089 1.43e-02 4.89e+03 3.90e+01
  bond pdb=" C   ILE A 364 "
       pdb=" N   MET A 365 "
    ideal  model  delta    sigma   weight residual
    1.334  1.412 -0.078 1.27e-02 6.20e+03 3.73e+01
  ... (remaining 12972 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.39: 16693
        2.39 -     4.78: 775
        4.78 -     7.16: 104
        7.16 -     9.55: 17
        9.55 -    11.94: 2
  Bond angle restraints: 17591
  Sorted by residual:
  angle pdb=" N   ARG A 414 "
        pdb=" CA  ARG A 414 "
        pdb=" C   ARG A 414 "
      ideal   model   delta    sigma   weight residual
     113.72  102.25   11.47 1.52e+00 4.33e-01 5.69e+01
  angle pdb=" C   MET C 228 "
        pdb=" N   ASP C 229 "
        pdb=" CA  ASP C 229 "
      ideal   model   delta    sigma   weight residual
     120.58  132.52  -11.94 1.71e+00 3.42e-01 4.87e+01
  angle pdb=" N   TYR A 412 "
        pdb=" CA  TYR A 412 "
        pdb=" C   TYR A 412 "
      ideal   model   delta    sigma   weight residual
     111.28  103.89    7.39 1.09e+00 8.42e-01 4.59e+01
  angle pdb=" N   SER A 415 "
        pdb=" CA  SER A 415 "
        pdb=" C   SER A 415 "
      ideal   model   delta    sigma   weight residual
     108.45  100.12    8.33 1.26e+00 6.30e-01 4.37e+01
  angle pdb=" N   GLU A 592 "
        pdb=" CA  GLU A 592 "
        pdb=" C   GLU A 592 "
      ideal   model   delta    sigma   weight residual
     111.75  104.45    7.30 1.28e+00 6.10e-01 3.25e+01
  ... (remaining 17586 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.78: 7080
       17.78 -    35.55: 696
       35.55 -    53.33: 143
       53.33 -    71.11: 27
       71.11 -    88.88: 4
  Dihedral angle restraints: 7950
    sinusoidal: 3234
      harmonic: 4716
  Sorted by residual:
  dihedral pdb=" CA  LEU A 849 "
           pdb=" C   LEU A 849 "
           pdb=" N   THR A 850 "
           pdb=" CA  THR A 850 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.63  -22.37     0      5.00e+00 4.00e-02 2.00e+01
  dihedral pdb=" C   ASP A1268 "
           pdb=" N   ASP A1268 "
           pdb=" CA  ASP A1268 "
           pdb=" CB  ASP A1268 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -132.09    9.49     0      2.50e+00 1.60e-01 1.44e+01
  dihedral pdb=" CA  ILE A 820 "
           pdb=" C   ILE A 820 "
           pdb=" N   GLY A 821 "
           pdb=" CA  GLY A 821 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.99   18.01     0      5.00e+00 4.00e-02 1.30e+01
  ... (remaining 7947 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.064: 1686
       0.064 -    0.127: 302
       0.127 -    0.191: 56
       0.191 -    0.255: 12
       0.255 -    0.319: 5
  Chirality restraints: 2061
  Sorted by residual:
  chirality pdb=" CA  MET A 107 "
            pdb=" N   MET A 107 "
            pdb=" C   MET A 107 "
            pdb=" CB  MET A 107 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.83   -0.32 2.00e-01 2.50e+01 2.54e+00
  chirality pdb=" CA  ILE A 830 "
            pdb=" N   ILE A 830 "
            pdb=" C   ILE A 830 "
            pdb=" CB  ILE A 830 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.73   -0.30 2.00e-01 2.50e+01 2.24e+00
  chirality pdb=" CA  ILE A 738 "
            pdb=" N   ILE A 738 "
            pdb=" C   ILE A 738 "
            pdb=" CB  ILE A 738 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.72   -0.29 2.00e-01 2.50e+01 2.09e+00
  ... (remaining 2058 not shown)

  Planarity restraints: 2226
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 443 "   -0.021 2.00e-02 2.50e+03   4.35e-02 1.89e+01
        pdb=" C   LEU A 443 "    0.075 2.00e-02 2.50e+03
        pdb=" O   LEU A 443 "   -0.031 2.00e-02 2.50e+03
        pdb=" N   LYS A 444 "   -0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A1244 "   -0.018 2.00e-02 2.50e+03   3.32e-02 1.10e+01
        pdb=" C   SER A1244 "    0.057 2.00e-02 2.50e+03
        pdb=" O   SER A1244 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   LEU A1245 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A  37 "    0.053 5.00e-02 4.00e+02   8.07e-02 1.04e+01
        pdb=" N   PRO A  38 "   -0.140 5.00e-02 4.00e+02
        pdb=" CA  PRO A  38 "    0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO A  38 "    0.044 5.00e-02 4.00e+02
  ... (remaining 2223 not shown)

  Histogram of nonbonded interaction distances:
        1.51 -     2.19: 8
        2.19 -     2.87: 5196
        2.87 -     3.55: 19262
        3.55 -     4.22: 30921
        4.22 -     4.90: 52655
  Nonbonded interactions: 108042
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU D 255 "
            pdb=" CB  LYS E 260 "
     model   vdw
     1.514 3.440
  nonbonded pdb=" OE2 GLU C 255 "
            pdb=" NZ  LYS D 253 "
     model   vdw
     1.943 3.120
  nonbonded pdb=" OE2 GLU C 255 "
            pdb=" CE  LYS D 253 "
     model   vdw
     1.999 3.440
  nonbonded pdb=" CG2 VAL C 259 "
            pdb=" CD1 LEU D 256 "
     model   vdw
     2.000 3.880
  nonbonded pdb=" O   GLY C 302 "
            pdb=" CE1 HIS A 426 "
     model   vdw
     2.044 3.260
  ... (remaining 108037 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
Found NCS groups:
ncs_group {
  reference = chain 'D'
  selection = (chain 'E' and resid 218 through 267)
}

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:             6.860
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.080
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.700
  Check model and map are aligned:         0.100
  Set scattering table:                    0.130
  Process input model:                     33.270
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.070
  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:             0.010
  Load rotamer database and sin/cos tables:2.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   44.140
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7029
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.114  12977  Z= 0.441
  Angle     :  1.069  11.939  17591  Z= 0.738
  Chirality :  0.054   0.319   2061
  Planarity :  0.006   0.081   2226
  Dihedral  : 14.422  88.883   4880
  Min Nonbonded Distance : 1.514

Molprobity Statistics.
  All-atom Clashscore : 21.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 20.39 %
    Favored  : 78.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.71 (0.20), residues: 1588
  helix: -0.08 (0.17), residues: 890
  sheet: -0.82 (0.55), residues: 81
  loop : -0.82 (0.24), residues: 617

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 488 
 HIS   0.004   0.001   HIS A  60 
 PHE   0.029   0.002   PHE A 520 
 TYR   0.026   0.002   TYR A 550 
 ARG   0.008   0.001   ARG A 814 

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

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

  3176 Ramachandran restraints generated.
    1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3176 Ramachandran restraints generated.
    1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  494 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 480
  time to evaluate  : 1.467 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  248 MET cc_start: 0.6702 (tpp) cc_final: 0.6468 (tpp)
REVERT: C  248 MET cc_start: 0.5793 (mmt) cc_final: 0.5432 (mmt)
REVERT: C  252 ILE cc_start: 0.8366 (mt) cc_final: 0.8053 (mt)
REVERT: A   16 SER cc_start: 0.8457 (p) cc_final: 0.8209 (t)
REVERT: A   66 ILE cc_start: 0.8533 (tt) cc_final: 0.8223 (pt)
REVERT: A   77 LEU cc_start: 0.8509 (mm) cc_final: 0.8284 (mm)
REVERT: A  107 MET cc_start: 0.6246 (ttp) cc_final: 0.5617 (ttp)
REVERT: A  138 GLN cc_start: 0.7847 (tm-30) cc_final: 0.7638 (tm-30)
REVERT: A  174 GLU cc_start: 0.7127 (pt0) cc_final: 0.6722 (pt0)
REVERT: A  184 MET cc_start: 0.7283 (tmm) cc_final: 0.7065 (ttt)
REVERT: A  186 LYS cc_start: 0.8546 (ttpt) cc_final: 0.8200 (ttpp)
REVERT: A  193 ILE cc_start: 0.8403 (mt) cc_final: 0.8181 (mm)
REVERT: A  207 ILE cc_start: 0.7816 (mt) cc_final: 0.7465 (mt)
REVERT: A  255 SER cc_start: 0.7972 (m) cc_final: 0.7708 (p)
REVERT: A  360 GLU cc_start: 0.6726 (mm-30) cc_final: 0.6474 (mm-30)
REVERT: A  420 TRP cc_start: 0.6194 (m-10) cc_final: 0.5963 (m100)
REVERT: A  436 MET cc_start: 0.7575 (mtp) cc_final: 0.6164 (mmm)
REVERT: A  442 GLU cc_start: 0.6073 (tt0) cc_final: 0.5696 (tt0)
REVERT: A  453 LYS cc_start: 0.7852 (mttt) cc_final: 0.7626 (mtpp)
REVERT: A  488 TRP cc_start: 0.8213 (p-90) cc_final: 0.7993 (p-90)
REVERT: A  489 MET cc_start: 0.8107 (mtp) cc_final: 0.7496 (mtt)
REVERT: A  493 ARG cc_start: 0.7232 (ttm170) cc_final: 0.6903 (ttt180)
REVERT: A  523 ASP cc_start: 0.7203 (t0) cc_final: 0.6966 (t0)
REVERT: A  539 GLU cc_start: 0.7323 (tp30) cc_final: 0.6923 (tp30)
REVERT: A  553 LYS cc_start: 0.8337 (tttp) cc_final: 0.7983 (tttp)
REVERT: A  568 THR cc_start: 0.7366 (p) cc_final: 0.6697 (t)
REVERT: A  576 VAL cc_start: 0.7789 (p) cc_final: 0.7522 (m)
REVERT: A  661 ILE cc_start: 0.5475 (OUTLIER) cc_final: 0.5125 (tp)
REVERT: A  674 CYS cc_start: 0.7932 (p) cc_final: 0.7454 (p)
REVERT: A  695 ILE cc_start: 0.8718 (mt) cc_final: 0.8469 (pt)
REVERT: A  701 TRP cc_start: 0.8135 (p-90) cc_final: 0.7838 (p-90)
REVERT: A  801 GLN cc_start: 0.8206 (mm-40) cc_final: 0.7935 (tp40)
REVERT: A  829 THR cc_start: 0.7734 (t) cc_final: 0.7402 (m)
REVERT: A  840 LYS cc_start: 0.8269 (mtpt) cc_final: 0.7810 (mmpt)
REVERT: A  858 LYS cc_start: 0.8313 (ptpt) cc_final: 0.8096 (ptpp)
REVERT: A  866 LEU cc_start: 0.7754 (mm) cc_final: 0.7523 (mt)
REVERT: A  956 ASN cc_start: 0.7315 (p0) cc_final: 0.7072 (p0)
REVERT: A  994 LYS cc_start: 0.8031 (mtmm) cc_final: 0.7830 (mtmm)
REVERT: A 1049 GLU cc_start: 0.7443 (tp30) cc_final: 0.6989 (mm-30)
REVERT: A 1099 ARG cc_start: 0.7861 (ttt-90) cc_final: 0.7628 (ttt180)
REVERT: A 1104 LYS cc_start: 0.8147 (mttt) cc_final: 0.7881 (mttt)
REVERT: A 1105 LYS cc_start: 0.8437 (mmmm) cc_final: 0.7981 (mmmm)
REVERT: A 1176 VAL cc_start: 0.7557 (m) cc_final: 0.7189 (m)
REVERT: A 1372 HIS cc_start: 0.7579 (m170) cc_final: 0.7351 (m170)
  outliers start: 14
  outliers final: 4
  residues processed: 491
  average time/residue: 0.2951
  time to fit residues: 200.9574
Evaluate side-chains
  410 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 405
  time to evaluate  : 1.437 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  265 THR
Chi-restraints excluded: chain B residue  275 ILE
Chi-restraints excluded: chain C residue  266 ILE
Chi-restraints excluded: chain C residue  295 ASP
Chi-restraints excluded: chain A residue  661 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 134 optimal weight:    0.8980
   chunk 120 optimal weight:    2.9990
   chunk 66 optimal weight:    7.9990
   chunk 41 optimal weight:    0.5980
   chunk 81 optimal weight:    3.9990
   chunk 64 optimal weight:    0.9990
   chunk 124 optimal weight:    0.7980
   chunk 48 optimal weight:    1.9990
   chunk 75 optimal weight:    1.9990
   chunk 92 optimal weight:    2.9990
   chunk 144 optimal weight:    0.6980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
B 251 GLN
C 251 GLN
E 234 HIS
E 245 GLN
A  60 HIS
A 172 ASN
A 416 HIS
** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 780 ASN
A 817 ASN
** A 822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 855 ASN
A 905 GLN
A 914 GLN
A1160 ASN
A1177 HIS
A1298 HIS
A1322 HIS

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.149500 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.131590 restraints weight = 22134.454|
|-----------------------------------------------------------------------------|
r_work (start): 0.3789 rms_B_bonded: 2.81
r_work: 0.3662 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3662
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7634
moved from start:          0.3089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062  12977  Z= 0.246
  Angle     :  0.654  11.609  17591  Z= 0.338
  Chirality :  0.044   0.210   2061
  Planarity :  0.005   0.063   2226
  Dihedral  :  4.457  31.085   1742
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 11.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 20.60 %
    Favored  : 75.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.66 (0.21), residues: 1588
  helix:  1.24 (0.17), residues: 885
  sheet: -0.33 (0.55), residues: 89
  loop : -0.54 (0.25), residues: 614

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 677 
 HIS   0.015   0.001   HIS E 234 
 PHE   0.024   0.002   PHE A 717 
 TYR   0.016   0.002   TYR A 895 
 ARG   0.007   0.001   ARG A 514 

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

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

  3176 Ramachandran restraints generated.
    1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3176 Ramachandran restraints generated.
    1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  502 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 449
  time to evaluate  : 1.362 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  234 HIS cc_start: 0.8214 (m90) cc_final: 0.8009 (m90)
REVERT: B  275 ILE cc_start: 0.7587 (OUTLIER) cc_final: 0.7181 (mp)
REVERT: C  248 MET cc_start: 0.6748 (mmt) cc_final: 0.6276 (mmt)
REVERT: C  276 MET cc_start: 0.7478 (ttp) cc_final: 0.7250 (ttp)
REVERT: E  222 MET cc_start: 0.8343 (mmm) cc_final: 0.7876 (mpp)
REVERT: A   15 ASN cc_start: 0.8178 (m-40) cc_final: 0.7837 (m-40)
REVERT: A   50 LYS cc_start: 0.8644 (tttm) cc_final: 0.8380 (ttmm)
REVERT: A   66 ILE cc_start: 0.8587 (tt) cc_final: 0.8299 (pt)
REVERT: A   76 SER cc_start: 0.8260 (p) cc_final: 0.7781 (p)
REVERT: A   77 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8597 (mm)
REVERT: A   94 ILE cc_start: 0.8220 (tt) cc_final: 0.7858 (tp)
REVERT: A  107 MET cc_start: 0.6810 (ttp) cc_final: 0.6133 (ttp)
REVERT: A  137 ASN cc_start: 0.8281 (t0) cc_final: 0.7968 (t0)
REVERT: A  138 GLN cc_start: 0.8567 (tm-30) cc_final: 0.7942 (tm-30)
REVERT: A  184 MET cc_start: 0.8019 (tmm) cc_final: 0.7467 (ttt)
REVERT: A  207 ILE cc_start: 0.8290 (OUTLIER) cc_final: 0.7992 (mt)
REVERT: A  313 LYS cc_start: 0.8555 (tttp) cc_final: 0.8240 (ttmm)
REVERT: A  322 ASN cc_start: 0.7742 (t0) cc_final: 0.7516 (m-40)
REVERT: A  398 MET cc_start: 0.8151 (mmm) cc_final: 0.7928 (mmt)
REVERT: A  420 TRP cc_start: 0.7427 (m-10) cc_final: 0.6659 (m100)
REVERT: A  428 ASN cc_start: 0.7655 (p0) cc_final: 0.7372 (p0)
REVERT: A  442 GLU cc_start: 0.7363 (tt0) cc_final: 0.7094 (tt0)
REVERT: A  444 LYS cc_start: 0.8267 (mttt) cc_final: 0.8029 (mtpp)
REVERT: A  457 MET cc_start: 0.7553 (mpp) cc_final: 0.7051 (mtm)
REVERT: A  494 ARG cc_start: 0.7614 (ttt180) cc_final: 0.7362 (mtt180)
REVERT: A  539 GLU cc_start: 0.7658 (tp30) cc_final: 0.7290 (tp30)
REVERT: A  553 LYS cc_start: 0.8472 (tttp) cc_final: 0.8258 (tttp)
REVERT: A  576 VAL cc_start: 0.8256 (p) cc_final: 0.7912 (m)
REVERT: A  579 GLU cc_start: 0.7458 (mm-30) cc_final: 0.7237 (mm-30)
REVERT: A  661 ILE cc_start: 0.6360 (OUTLIER) cc_final: 0.6089 (tt)
REVERT: A  674 CYS cc_start: 0.8208 (p) cc_final: 0.7857 (m)
REVERT: A  675 LEU cc_start: 0.8785 (mt) cc_final: 0.8570 (mt)
REVERT: A  692 MET cc_start: 0.8369 (mtm) cc_final: 0.8127 (mtp)
REVERT: A  707 MET cc_start: 0.8402 (mtt) cc_final: 0.8186 (mtp)
REVERT: A  801 GLN cc_start: 0.8408 (mm-40) cc_final: 0.8169 (tp40)
REVERT: A  965 SER cc_start: 0.8696 (t) cc_final: 0.8454 (m)
REVERT: A  972 ARG cc_start: 0.8100 (mtt180) cc_final: 0.7824 (mtt180)
REVERT: A  982 TRP cc_start: 0.8010 (p-90) cc_final: 0.7681 (p-90)
REVERT: A 1006 THR cc_start: 0.8341 (m) cc_final: 0.7904 (p)
REVERT: A 1020 LYS cc_start: 0.8531 (mttt) cc_final: 0.8278 (mttm)
REVERT: A 1021 LYS cc_start: 0.8346 (mmtp) cc_final: 0.8129 (mptt)
REVERT: A 1104 LYS cc_start: 0.8549 (mttt) cc_final: 0.8253 (mttt)
REVERT: A 1112 TYR cc_start: 0.8362 (t80) cc_final: 0.8142 (t80)
REVERT: A 1176 VAL cc_start: 0.8046 (m) cc_final: 0.7451 (m)
REVERT: A 1249 LEU cc_start: 0.8544 (mt) cc_final: 0.8283 (mm)
REVERT: A 1282 GLU cc_start: 0.7705 (mp0) cc_final: 0.7258 (mp0)
REVERT: A 1410 ASP cc_start: 0.7937 (p0) cc_final: 0.7516 (p0)
  outliers start: 53
  outliers final: 14
  residues processed: 475
  average time/residue: 0.3073
  time to fit residues: 206.4594
Evaluate side-chains
  427 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 409
  time to evaluate  : 1.622 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  275 ILE
Chi-restraints excluded: chain C residue  262 THR
Chi-restraints excluded: chain E residue  232 LEU
Chi-restraints excluded: chain E residue  253 LYS
Chi-restraints excluded: chain E residue  263 LEU
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  178 SER
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  296 GLU
Chi-restraints excluded: chain A residue  424 THR
Chi-restraints excluded: chain A residue  661 ILE
Chi-restraints excluded: chain A residue  667 THR
Chi-restraints excluded: chain A residue  760 THR
Chi-restraints excluded: chain A residue 1029 GLU
Chi-restraints excluded: chain A residue 1055 LEU
Chi-restraints excluded: chain A residue 1234 SER
Chi-restraints excluded: chain A residue 1365 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 23 optimal weight:    0.7980
   chunk 149 optimal weight:    0.0470
   chunk 4 optimal weight:    2.9990
   chunk 116 optimal weight:    2.9990
   chunk 156 optimal weight:    3.9990
   chunk 5 optimal weight:    5.9990
   chunk 17 optimal weight:    0.9990
   chunk 70 optimal weight:    0.9990
   chunk 6 optimal weight:    9.9990
   chunk 119 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   overall best weight:    0.7684

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

Flipped N/Q/H residues before XYZ refinement:
A 172 ASN
A 438 HIS
A 451 ASN
** A 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1120 ASN
A1322 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.144162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.125440 restraints weight = 21839.566|
|-----------------------------------------------------------------------------|
r_work (start): 0.3719 rms_B_bonded: 2.84
r_work: 0.3584 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3584
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7762
moved from start:          0.4402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  12977  Z= 0.218
  Angle     :  0.611  11.551  17591  Z= 0.315
  Chirality :  0.044   0.318   2061
  Planarity :  0.005   0.057   2226
  Dihedral  :  4.218  32.721   1737
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 11.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 23.31 %
    Favored  : 73.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.02 (0.21), residues: 1588
  helix:  1.55 (0.17), residues: 884
  sheet: -0.30 (0.53), residues: 89
  loop : -0.39 (0.25), residues: 615

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 982 
 HIS   0.004   0.001   HIS A  13 
 PHE   0.017   0.002   PHE A1197 
 TYR   0.012   0.001   TYR A 895 
 ARG   0.006   0.001   ARG A 485 

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

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

  3176 Ramachandran restraints generated.
    1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3176 Ramachandran restraints generated.
    1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  483 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 439
  time to evaluate  : 1.579 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  248 MET cc_start: 0.6468 (tpp) cc_final: 0.6084 (tpp)
REVERT: C  248 MET cc_start: 0.6599 (mmt) cc_final: 0.6323 (mmt)
REVERT: C  276 MET cc_start: 0.7479 (ttp) cc_final: 0.7234 (ttp)
REVERT: E  248 MET cc_start: 0.7352 (mtp) cc_final: 0.6973 (mtp)
REVERT: A   15 ASN cc_start: 0.8206 (m-40) cc_final: 0.7764 (m-40)
REVERT: A   32 LEU cc_start: 0.8738 (mm) cc_final: 0.8534 (mt)
REVERT: A   50 LYS cc_start: 0.8688 (tttm) cc_final: 0.8432 (ttmm)
REVERT: A   66 ILE cc_start: 0.8623 (tt) cc_final: 0.8354 (pt)
REVERT: A   69 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7645 (mm-30)
REVERT: A  107 MET cc_start: 0.6837 (ttp) cc_final: 0.6120 (ttp)
REVERT: A  137 ASN cc_start: 0.8323 (t0) cc_final: 0.8051 (t0)
REVERT: A  138 GLN cc_start: 0.8482 (tm-30) cc_final: 0.8210 (tm-30)
REVERT: A  184 MET cc_start: 0.7984 (tmm) cc_final: 0.7501 (ttt)
REVERT: A  207 ILE cc_start: 0.8316 (mt) cc_final: 0.8098 (mt)
REVERT: A  225 TYR cc_start: 0.8056 (t80) cc_final: 0.7716 (t80)
REVERT: A  279 ASP cc_start: 0.8126 (m-30) cc_final: 0.7894 (m-30)
REVERT: A  360 GLU cc_start: 0.7490 (mm-30) cc_final: 0.7223 (mm-30)
REVERT: A  366 ARG cc_start: 0.8463 (mmt90) cc_final: 0.8138 (mmt90)
REVERT: A  394 PHE cc_start: 0.7867 (t80) cc_final: 0.7412 (t80)
REVERT: A  428 ASN cc_start: 0.8097 (p0) cc_final: 0.7787 (p0)
REVERT: A  437 ARG cc_start: 0.8028 (ttp80) cc_final: 0.7547 (ttt180)
REVERT: A  442 GLU cc_start: 0.7817 (tt0) cc_final: 0.7526 (tt0)
REVERT: A  457 MET cc_start: 0.8130 (mpp) cc_final: 0.7697 (mtm)
REVERT: A  494 ARG cc_start: 0.7691 (ttt180) cc_final: 0.7384 (mtt180)
REVERT: A  503 ASP cc_start: 0.7921 (m-30) cc_final: 0.7615 (m-30)
REVERT: A  539 GLU cc_start: 0.7669 (tp30) cc_final: 0.7320 (tp30)
REVERT: A  550 TYR cc_start: 0.8656 (m-80) cc_final: 0.8434 (m-80)
REVERT: A  553 LYS cc_start: 0.8514 (tttp) cc_final: 0.8312 (tttp)
REVERT: A  555 LYS cc_start: 0.8428 (mttp) cc_final: 0.7876 (mttt)
REVERT: A  579 GLU cc_start: 0.7470 (mm-30) cc_final: 0.7242 (mm-30)
REVERT: A  674 CYS cc_start: 0.8331 (p) cc_final: 0.8006 (m)
REVERT: A  707 MET cc_start: 0.8463 (mtt) cc_final: 0.8214 (mtp)
REVERT: A  801 GLN cc_start: 0.8394 (mm-40) cc_final: 0.8085 (tp40)
REVERT: A  883 ARG cc_start: 0.8182 (mpt180) cc_final: 0.7803 (mpt180)
REVERT: A  886 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8278 (mt-10)
REVERT: A  965 SER cc_start: 0.8790 (t) cc_final: 0.8432 (p)
REVERT: A  996 LYS cc_start: 0.8572 (mttm) cc_final: 0.8174 (mtmm)
REVERT: A 1006 THR cc_start: 0.8652 (m) cc_final: 0.8203 (p)
REVERT: A 1020 LYS cc_start: 0.8585 (mttt) cc_final: 0.8282 (mttp)
REVERT: A 1021 LYS cc_start: 0.8463 (mmtp) cc_final: 0.8201 (mmtm)
REVERT: A 1049 GLU cc_start: 0.8229 (tp30) cc_final: 0.8007 (tp30)
REVERT: A 1112 TYR cc_start: 0.8454 (t80) cc_final: 0.8175 (t80)
REVERT: A 1174 GLU cc_start: 0.8280 (tt0) cc_final: 0.7601 (tt0)
REVERT: A 1207 ARG cc_start: 0.7422 (ttm110) cc_final: 0.7194 (ttm170)
REVERT: A 1282 GLU cc_start: 0.7733 (mp0) cc_final: 0.7234 (mp0)
REVERT: A 1403 GLN cc_start: 0.8531 (mm110) cc_final: 0.8299 (mm110)
  outliers start: 44
  outliers final: 15
  residues processed: 459
  average time/residue: 0.2879
  time to fit residues: 183.8501
Evaluate side-chains
  414 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 399
  time to evaluate  : 1.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  225 LEU
Chi-restraints excluded: chain C residue  228 MET
Chi-restraints excluded: chain C residue  252 ILE
Chi-restraints excluded: chain D residue  232 LEU
Chi-restraints excluded: chain A residue  174 GLU
Chi-restraints excluded: chain A residue  178 SER
Chi-restraints excluded: chain A residue  296 GLU
Chi-restraints excluded: chain A residue  424 THR
Chi-restraints excluded: chain A residue  667 THR
Chi-restraints excluded: chain A residue  739 VAL
Chi-restraints excluded: chain A residue  946 LEU
Chi-restraints excluded: chain A residue 1029 GLU
Chi-restraints excluded: chain A residue 1055 LEU
Chi-restraints excluded: chain A residue 1274 SER
Chi-restraints excluded: chain A residue 1396 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 126 optimal weight:    2.9990
   chunk 143 optimal weight:    0.7980
   chunk 140 optimal weight:    0.9980
   chunk 3 optimal weight:    0.7980
   chunk 149 optimal weight:    0.8980
   chunk 86 optimal weight:    0.2980
   chunk 23 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 110 optimal weight:    0.4980
   chunk 22 optimal weight:    4.9990
   chunk 12 optimal weight:    0.5980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 245 GLN
D 245 GLN
A 105 GLN
A 122 ASN
A 172 ASN
A 229 HIS
A 438 HIS
A 451 ASN
** A 822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 920 GLN
A1120 ASN
A1322 HIS

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.142806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.124334 restraints weight = 21492.980|
|-----------------------------------------------------------------------------|
r_work (start): 0.3707 rms_B_bonded: 2.80
r_work: 0.3576 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3576
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7769
moved from start:          0.4976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12977  Z= 0.187
  Angle     :  0.601  11.265  17591  Z= 0.306
  Chirality :  0.043   0.231   2061
  Planarity :  0.005   0.054   2226
  Dihedral  :  4.082  24.023   1733
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 11.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 26.17 %
    Favored  : 71.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.14 (0.21), residues: 1588
  helix:  1.60 (0.17), residues: 893
  sheet: -0.07 (0.55), residues: 89
  loop : -0.32 (0.25), residues: 606

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 982 
 HIS   0.006   0.001   HIS B 234 
 PHE   0.020   0.001   PHE A1197 
 TYR   0.014   0.001   TYR A 679 
 ARG   0.007   0.001   ARG A 742 

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

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

  3176 Ramachandran restraints generated.
    1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3176 Ramachandran restraints generated.
    1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  453 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 415
  time to evaluate  : 1.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  248 MET cc_start: 0.6426 (tpp) cc_final: 0.6052 (tpp)
REVERT: B  274 LYS cc_start: 0.7966 (OUTLIER) cc_final: 0.7721 (mmtp)
REVERT: C  228 MET cc_start: 0.5444 (mmm) cc_final: 0.5243 (mmt)
REVERT: C  276 MET cc_start: 0.7336 (ttp) cc_final: 0.7063 (ttp)
REVERT: D  221 ILE cc_start: 0.8385 (tp) cc_final: 0.8048 (tp)
REVERT: E  222 MET cc_start: 0.8181 (mmm) cc_final: 0.7775 (mpp)
REVERT: E  248 MET cc_start: 0.7450 (mtp) cc_final: 0.7099 (mtp)
REVERT: A   50 LYS cc_start: 0.8708 (tttm) cc_final: 0.8428 (ttmm)
REVERT: A   64 LYS cc_start: 0.8466 (ttpp) cc_final: 0.8258 (ttpp)
REVERT: A   66 ILE cc_start: 0.8578 (tt) cc_final: 0.8299 (pt)
REVERT: A   69 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7600 (mm-30)
REVERT: A   94 ILE cc_start: 0.8148 (tt) cc_final: 0.7811 (tp)
REVERT: A  107 MET cc_start: 0.6806 (ttp) cc_final: 0.6046 (ttp)
REVERT: A  137 ASN cc_start: 0.8338 (t0) cc_final: 0.8095 (t0)
REVERT: A  138 GLN cc_start: 0.8466 (tm-30) cc_final: 0.8045 (tm-30)
REVERT: A  184 MET cc_start: 0.8018 (tmm) cc_final: 0.7478 (ttt)
REVERT: A  207 ILE cc_start: 0.8364 (OUTLIER) cc_final: 0.8120 (mt)
REVERT: A  214 LEU cc_start: 0.8565 (tp) cc_final: 0.8363 (tt)
REVERT: A  279 ASP cc_start: 0.8106 (m-30) cc_final: 0.7865 (m-30)
REVERT: A  360 GLU cc_start: 0.7483 (mm-30) cc_final: 0.7175 (mm-30)
REVERT: A  366 ARG cc_start: 0.8440 (mmt90) cc_final: 0.8104 (mmt90)
REVERT: A  394 PHE cc_start: 0.8084 (t80) cc_final: 0.7789 (t80)
REVERT: A  428 ASN cc_start: 0.8095 (p0) cc_final: 0.7885 (p0)
REVERT: A  437 ARG cc_start: 0.8106 (ttp80) cc_final: 0.7675 (ttt180)
REVERT: A  442 GLU cc_start: 0.7838 (tt0) cc_final: 0.7580 (tt0)
REVERT: A  457 MET cc_start: 0.8057 (mpp) cc_final: 0.7739 (mtm)
REVERT: A  499 GLN cc_start: 0.8345 (tp40) cc_final: 0.7824 (tp40)
REVERT: A  503 ASP cc_start: 0.7901 (m-30) cc_final: 0.7459 (m-30)
REVERT: A  539 GLU cc_start: 0.7656 (tp30) cc_final: 0.7316 (tp30)
REVERT: A  553 LYS cc_start: 0.8544 (tttp) cc_final: 0.8328 (tttm)
REVERT: A  579 GLU cc_start: 0.7521 (mm-30) cc_final: 0.7300 (mm-30)
REVERT: A  659 PHE cc_start: 0.5974 (OUTLIER) cc_final: 0.5770 (m-10)
REVERT: A  710 THR cc_start: 0.8719 (m) cc_final: 0.8154 (p)
REVERT: A  797 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7699 (mm-30)
REVERT: A  801 GLN cc_start: 0.8327 (mm-40) cc_final: 0.8018 (tp40)
REVERT: A  826 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7679 (mp0)
REVERT: A  883 ARG cc_start: 0.8214 (mpt180) cc_final: 0.7750 (mpt180)
REVERT: A  886 GLU cc_start: 0.8462 (mt-10) cc_final: 0.8141 (mt-10)
REVERT: A  933 ILE cc_start: 0.8806 (mt) cc_final: 0.8589 (mp)
REVERT: A  965 SER cc_start: 0.8774 (t) cc_final: 0.8447 (m)
REVERT: A  996 LYS cc_start: 0.8510 (mttm) cc_final: 0.8181 (mtmm)
REVERT: A 1006 THR cc_start: 0.8674 (m) cc_final: 0.8208 (p)
REVERT: A 1021 LYS cc_start: 0.8450 (mmtp) cc_final: 0.8175 (mmtm)
REVERT: A 1030 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.8474 (mtp85)
REVERT: A 1041 SER cc_start: 0.8484 (t) cc_final: 0.8273 (t)
REVERT: A 1112 TYR cc_start: 0.8434 (t80) cc_final: 0.8180 (t80)
REVERT: A 1141 THR cc_start: 0.8761 (m) cc_final: 0.8182 (p)
REVERT: A 1174 GLU cc_start: 0.8253 (tt0) cc_final: 0.7647 (tt0)
REVERT: A 1249 LEU cc_start: 0.8564 (mt) cc_final: 0.8324 (mm)
REVERT: A 1282 GLU cc_start: 0.7800 (mp0) cc_final: 0.7314 (mp0)
REVERT: A 1320 PHE cc_start: 0.7747 (m-10) cc_final: 0.7501 (m-10)
REVERT: A 1393 LEU cc_start: 0.8159 (tp) cc_final: 0.7948 (tt)
  outliers start: 38
  outliers final: 20
  residues processed: 431
  average time/residue: 0.2896
  time to fit residues: 173.8898
Evaluate side-chains
  420 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 396
  time to evaluate  : 1.444 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  274 LYS
Chi-restraints excluded: chain C residue  225 LEU
Chi-restraints excluded: chain C residue  252 ILE
Chi-restraints excluded: chain D residue  232 LEU
Chi-restraints excluded: chain E residue  249 VAL
Chi-restraints excluded: chain A residue    7 ILE
Chi-restraints excluded: chain A residue  178 SER
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  218 THR
Chi-restraints excluded: chain A residue  296 GLU
Chi-restraints excluded: chain A residue  384 GLU
Chi-restraints excluded: chain A residue  420 TRP
Chi-restraints excluded: chain A residue  424 THR
Chi-restraints excluded: chain A residue  659 PHE
Chi-restraints excluded: chain A residue  667 THR
Chi-restraints excluded: chain A residue  840 LYS
Chi-restraints excluded: chain A residue  946 LEU
Chi-restraints excluded: chain A residue 1029 GLU
Chi-restraints excluded: chain A residue 1030 ARG
Chi-restraints excluded: chain A residue 1055 LEU
Chi-restraints excluded: chain A residue 1234 SER
Chi-restraints excluded: chain A residue 1235 MET
Chi-restraints excluded: chain A residue 1354 ILE
Chi-restraints excluded: chain A residue 1389 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 99 optimal weight:    0.5980
   chunk 50 optimal weight:    0.9990
   chunk 131 optimal weight:    0.0370
   chunk 28 optimal weight:    2.9990
   chunk 137 optimal weight:    0.9990
   chunk 4 optimal weight:    4.9990
   chunk 21 optimal weight:    3.9990
   chunk 22 optimal weight:    5.9990
   chunk 84 optimal weight:    3.9990
   chunk 15 optimal weight:    0.8980
   chunk 106 optimal weight:    1.9990
   overall best weight:    0.7062

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

Flipped N/Q/H residues before XYZ refinement:
** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 245 GLN
A 172 ASN
A 451 ASN
** A 822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1120 ASN
A1322 HIS
** A1328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.141198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.122729 restraints weight = 21627.630|
|-----------------------------------------------------------------------------|
r_work (start): 0.3684 rms_B_bonded: 2.82
r_work: 0.3550 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3550
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
moved from start:          0.5377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12977  Z= 0.203
  Angle     :  0.597  10.395  17591  Z= 0.305
  Chirality :  0.043   0.226   2061
  Planarity :  0.005   0.052   2226
  Dihedral  :  4.052  23.829   1733
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 10.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 25.26 %
    Favored  : 71.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.16 (0.21), residues: 1588
  helix:  1.61 (0.18), residues: 895
  sheet:  0.01 (0.59), residues: 81
  loop : -0.32 (0.25), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 982 
 HIS   0.008   0.001   HIS B 234 
 PHE   0.023   0.002   PHE A1197 
 TYR   0.017   0.001   TYR A 447 
 ARG   0.006   0.000   ARG A1219 

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

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

  3176 Ramachandran restraints generated.
    1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3176 Ramachandran restraints generated.
    1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  466 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 413
  time to evaluate  : 1.443 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  248 MET cc_start: 0.6460 (tpp) cc_final: 0.6069 (tpp)
REVERT: C  276 MET cc_start: 0.7341 (ttp) cc_final: 0.7066 (ttp)
REVERT: D  245 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.8302 (pm20)
REVERT: E  222 MET cc_start: 0.8256 (mmm) cc_final: 0.7836 (mpp)
REVERT: A   66 ILE cc_start: 0.8554 (tt) cc_final: 0.8284 (pt)
REVERT: A   69 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7580 (mm-30)
REVERT: A   94 ILE cc_start: 0.8134 (tt) cc_final: 0.7769 (tp)
REVERT: A  104 ARG cc_start: 0.7755 (OUTLIER) cc_final: 0.7453 (ttm110)
REVERT: A  107 MET cc_start: 0.6882 (ttp) cc_final: 0.6090 (ttp)
REVERT: A  137 ASN cc_start: 0.8353 (t0) cc_final: 0.8129 (t0)
REVERT: A  138 GLN cc_start: 0.8462 (tm-30) cc_final: 0.8232 (tm-30)
REVERT: A  165 GLU cc_start: 0.7905 (mp0) cc_final: 0.7071 (mp0)
REVERT: A  184 MET cc_start: 0.7993 (tmm) cc_final: 0.7473 (ttt)
REVERT: A  207 ILE cc_start: 0.8411 (OUTLIER) cc_final: 0.8173 (mt)
REVERT: A  279 ASP cc_start: 0.8157 (m-30) cc_final: 0.7923 (m-30)
REVERT: A  286 ASP cc_start: 0.7703 (p0) cc_final: 0.7479 (p0)
REVERT: A  313 LYS cc_start: 0.8516 (tttp) cc_final: 0.8294 (tttm)
REVERT: A  337 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7532 (mt-10)
REVERT: A  360 GLU cc_start: 0.7542 (mm-30) cc_final: 0.7205 (mm-30)
REVERT: A  366 ARG cc_start: 0.8461 (mmt90) cc_final: 0.8080 (mmt90)
REVERT: A  428 ASN cc_start: 0.8167 (p0) cc_final: 0.7936 (p0)
REVERT: A  437 ARG cc_start: 0.8255 (ttp80) cc_final: 0.7830 (ttt180)
REVERT: A  442 GLU cc_start: 0.7862 (tt0) cc_final: 0.7643 (tt0)
REVERT: A  457 MET cc_start: 0.8338 (mpp) cc_final: 0.8003 (mtm)
REVERT: A  489 MET cc_start: 0.8426 (mtp) cc_final: 0.8117 (ttm)
REVERT: A  495 SER cc_start: 0.8560 (OUTLIER) cc_final: 0.8353 (p)
REVERT: A  499 GLN cc_start: 0.8396 (tp40) cc_final: 0.7807 (tp40)
REVERT: A  503 ASP cc_start: 0.7902 (m-30) cc_final: 0.7460 (m-30)
REVERT: A  539 GLU cc_start: 0.7674 (tp30) cc_final: 0.7332 (tp30)
REVERT: A  550 TYR cc_start: 0.8597 (m-80) cc_final: 0.8388 (m-80)
REVERT: A  553 LYS cc_start: 0.8588 (tttp) cc_final: 0.8368 (tttm)
REVERT: A  555 LYS cc_start: 0.8377 (mttp) cc_final: 0.7670 (mttt)
REVERT: A  579 GLU cc_start: 0.7462 (mm-30) cc_final: 0.7232 (mm-30)
REVERT: A  601 LYS cc_start: 0.7235 (mtmt) cc_final: 0.6929 (mtmt)
REVERT: A  659 PHE cc_start: 0.6275 (OUTLIER) cc_final: 0.5949 (m-10)
REVERT: A  710 THR cc_start: 0.8673 (m) cc_final: 0.8161 (p)
REVERT: A  738 ILE cc_start: 0.8060 (OUTLIER) cc_final: 0.7690 (mt)
REVERT: A  797 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7716 (mm-30)
REVERT: A  883 ARG cc_start: 0.8165 (mpt180) cc_final: 0.7739 (mpt180)
REVERT: A  886 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8207 (mt-10)
REVERT: A  933 ILE cc_start: 0.8818 (mt) cc_final: 0.8598 (mp)
REVERT: A  965 SER cc_start: 0.8759 (t) cc_final: 0.8444 (m)
REVERT: A  996 LYS cc_start: 0.8393 (mttm) cc_final: 0.8127 (mtmm)
REVERT: A 1006 THR cc_start: 0.8731 (m) cc_final: 0.8287 (p)
REVERT: A 1021 LYS cc_start: 0.8473 (mmtp) cc_final: 0.8191 (mmtm)
REVERT: A 1030 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.7946 (ttm110)
REVERT: A 1112 TYR cc_start: 0.8463 (t80) cc_final: 0.8179 (t80)
REVERT: A 1141 THR cc_start: 0.8763 (m) cc_final: 0.8472 (t)
REVERT: A 1174 GLU cc_start: 0.8369 (tt0) cc_final: 0.8035 (tt0)
REVERT: A 1196 LYS cc_start: 0.7723 (mmmt) cc_final: 0.7420 (mmmt)
REVERT: A 1249 LEU cc_start: 0.8574 (mt) cc_final: 0.8317 (mm)
REVERT: A 1282 GLU cc_start: 0.7911 (mp0) cc_final: 0.7327 (mp0)
REVERT: A 1373 LEU cc_start: 0.7578 (tp) cc_final: 0.7369 (mp)
REVERT: A 1393 LEU cc_start: 0.8326 (tp) cc_final: 0.8114 (tt)
REVERT: A 1403 GLN cc_start: 0.8555 (mm110) cc_final: 0.8304 (mm110)
  outliers start: 53
  outliers final: 28
  residues processed: 434
  average time/residue: 0.2933
  time to fit residues: 176.5362
Evaluate side-chains
  438 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 403
  time to evaluate  : 1.500 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  225 LEU
Chi-restraints excluded: chain D residue  232 LEU
Chi-restraints excluded: chain D residue  245 GLN
Chi-restraints excluded: chain D residue  263 LEU
Chi-restraints excluded: chain E residue  249 VAL
Chi-restraints excluded: chain A residue  104 ARG
Chi-restraints excluded: chain A residue  174 GLU
Chi-restraints excluded: chain A residue  178 SER
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  218 THR
Chi-restraints excluded: chain A residue  246 MET
Chi-restraints excluded: chain A residue  296 GLU
Chi-restraints excluded: chain A residue  385 SER
Chi-restraints excluded: chain A residue  420 TRP
Chi-restraints excluded: chain A residue  424 THR
Chi-restraints excluded: chain A residue  444 LYS
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  495 SER
Chi-restraints excluded: chain A residue  659 PHE
Chi-restraints excluded: chain A residue  667 THR
Chi-restraints excluded: chain A residue  725 GLN
Chi-restraints excluded: chain A residue  738 ILE
Chi-restraints excluded: chain A residue  840 LYS
Chi-restraints excluded: chain A residue  866 LEU
Chi-restraints excluded: chain A residue  876 ASN
Chi-restraints excluded: chain A residue  946 LEU
Chi-restraints excluded: chain A residue 1029 GLU
Chi-restraints excluded: chain A residue 1030 ARG
Chi-restraints excluded: chain A residue 1234 SER
Chi-restraints excluded: chain A residue 1235 MET
Chi-restraints excluded: chain A residue 1263 GLU
Chi-restraints excluded: chain A residue 1354 ILE
Chi-restraints excluded: chain A residue 1381 ILE
Chi-restraints excluded: chain A residue 1389 VAL
Chi-restraints excluded: chain A residue 1396 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 80 optimal weight:    0.6980
   chunk 64 optimal weight:    0.7980
   chunk 137 optimal weight:    0.6980
   chunk 139 optimal weight:    0.5980
   chunk 90 optimal weight:    0.2980
   chunk 93 optimal weight:    0.7980
   chunk 134 optimal weight:    0.9990
   chunk 150 optimal weight:    4.9990
   chunk 143 optimal weight:    0.0980
   chunk 30 optimal weight:    0.6980
   chunk 54 optimal weight:    1.9990
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 245 GLN
A 172 ASN
A 451 ASN
** A 822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 823 HIS
A1120 ASN
A1322 HIS
A1328 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.143158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.124766 restraints weight = 21849.407|
|-----------------------------------------------------------------------------|
r_work (start): 0.3693 rms_B_bonded: 2.79
r_work: 0.3561 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3561
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7794
moved from start:          0.5595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  12977  Z= 0.175
  Angle     :  0.602  10.845  17591  Z= 0.304
  Chirality :  0.042   0.232   2061
  Planarity :  0.005   0.051   2226
  Dihedral  :  4.022  23.914   1733
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 11.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 25.68 %
    Favored  : 70.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.20 (0.21), residues: 1588
  helix:  1.65 (0.18), residues: 893
  sheet:  0.10 (0.60), residues: 81
  loop : -0.32 (0.25), residues: 614

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  79 
 HIS   0.008   0.001   HIS B 234 
 PHE   0.022   0.001   PHE A1197 
 TYR   0.017   0.001   TYR A 679 
 ARG   0.009   0.001   ARG A 742 

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

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

  3176 Ramachandran restraints generated.
    1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3176 Ramachandran restraints generated.
    1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  457 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 409
  time to evaluate  : 1.424 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  248 MET cc_start: 0.6412 (tpp) cc_final: 0.6023 (tpp)
REVERT: C  276 MET cc_start: 0.7231 (ttp) cc_final: 0.6942 (ttp)
REVERT: E  222 MET cc_start: 0.8178 (mmm) cc_final: 0.7787 (mpp)
REVERT: A   66 ILE cc_start: 0.8554 (tt) cc_final: 0.8286 (pt)
REVERT: A   69 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7555 (mm-30)
REVERT: A   94 ILE cc_start: 0.8131 (tt) cc_final: 0.7762 (tp)
REVERT: A  104 ARG cc_start: 0.7713 (OUTLIER) cc_final: 0.7415 (ttm110)
REVERT: A  137 ASN cc_start: 0.8360 (t0) cc_final: 0.8134 (t0)
REVERT: A  138 GLN cc_start: 0.8458 (tm-30) cc_final: 0.8242 (tm-30)
REVERT: A  165 GLU cc_start: 0.7919 (mp0) cc_final: 0.7093 (mp0)
REVERT: A  179 VAL cc_start: 0.8412 (OUTLIER) cc_final: 0.8192 (p)
REVERT: A  279 ASP cc_start: 0.8191 (m-30) cc_final: 0.7958 (m-30)
REVERT: A  286 ASP cc_start: 0.7720 (p0) cc_final: 0.7505 (p0)
REVERT: A  313 LYS cc_start: 0.8534 (tttp) cc_final: 0.8283 (tttm)
REVERT: A  337 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7566 (mt-10)
REVERT: A  360 GLU cc_start: 0.7550 (mm-30) cc_final: 0.7229 (mm-30)
REVERT: A  366 ARG cc_start: 0.8464 (mmt90) cc_final: 0.8081 (mmt90)
REVERT: A  428 ASN cc_start: 0.8213 (p0) cc_final: 0.7995 (p0)
REVERT: A  437 ARG cc_start: 0.8259 (ttp80) cc_final: 0.7932 (ttt180)
REVERT: A  442 GLU cc_start: 0.7850 (tt0) cc_final: 0.7577 (tt0)
REVERT: A  457 MET cc_start: 0.8307 (mpp) cc_final: 0.8003 (mtm)
REVERT: A  489 MET cc_start: 0.8346 (mtp) cc_final: 0.8138 (ttm)
REVERT: A  499 GLN cc_start: 0.8383 (tp40) cc_final: 0.7803 (tp40)
REVERT: A  503 ASP cc_start: 0.7863 (m-30) cc_final: 0.7426 (m-30)
REVERT: A  539 GLU cc_start: 0.7670 (tp30) cc_final: 0.7327 (tp30)
REVERT: A  553 LYS cc_start: 0.8596 (tttp) cc_final: 0.8381 (tttm)
REVERT: A  555 LYS cc_start: 0.8345 (mttp) cc_final: 0.7615 (mttt)
REVERT: A  579 GLU cc_start: 0.7458 (mm-30) cc_final: 0.7232 (mm-30)
REVERT: A  601 LYS cc_start: 0.7289 (mtmt) cc_final: 0.6974 (mtmt)
REVERT: A  659 PHE cc_start: 0.6374 (OUTLIER) cc_final: 0.5931 (m-10)
REVERT: A  661 ILE cc_start: 0.7153 (mt) cc_final: 0.6845 (tt)
REVERT: A  710 THR cc_start: 0.8651 (m) cc_final: 0.8159 (p)
REVERT: A  730 THR cc_start: 0.8609 (m) cc_final: 0.8176 (p)
REVERT: A  797 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7660 (mm-30)
REVERT: A  883 ARG cc_start: 0.8162 (mpt180) cc_final: 0.7607 (mpt180)
REVERT: A  886 GLU cc_start: 0.8450 (mt-10) cc_final: 0.8166 (mt-10)
REVERT: A  933 ILE cc_start: 0.8820 (mt) cc_final: 0.8605 (mp)
REVERT: A  965 SER cc_start: 0.8761 (t) cc_final: 0.8463 (m)
REVERT: A  996 LYS cc_start: 0.8348 (mttm) cc_final: 0.8058 (mtmm)
REVERT: A 1006 THR cc_start: 0.8734 (m) cc_final: 0.8315 (p)
REVERT: A 1021 LYS cc_start: 0.8435 (mmtp) cc_final: 0.8162 (mmtm)
REVERT: A 1030 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.8483 (mtp85)
REVERT: A 1105 LYS cc_start: 0.8459 (mmmm) cc_final: 0.8259 (mmtm)
REVERT: A 1112 TYR cc_start: 0.8459 (t80) cc_final: 0.8191 (t80)
REVERT: A 1118 SER cc_start: 0.8847 (t) cc_final: 0.8582 (p)
REVERT: A 1141 THR cc_start: 0.8757 (m) cc_final: 0.8491 (t)
REVERT: A 1143 SER cc_start: 0.8477 (p) cc_final: 0.8243 (m)
REVERT: A 1174 GLU cc_start: 0.8345 (tt0) cc_final: 0.7974 (tt0)
REVERT: A 1196 LYS cc_start: 0.7733 (mmmt) cc_final: 0.7429 (mmmt)
REVERT: A 1249 LEU cc_start: 0.8582 (mt) cc_final: 0.8324 (mm)
REVERT: A 1267 GLN cc_start: 0.8222 (mm-40) cc_final: 0.7981 (mm-40)
REVERT: A 1282 GLU cc_start: 0.7934 (mp0) cc_final: 0.7329 (mp0)
REVERT: A 1403 GLN cc_start: 0.8549 (mm110) cc_final: 0.8284 (mm110)
  outliers start: 48
  outliers final: 28
  residues processed: 430
  average time/residue: 0.2838
  time to fit residues: 170.6517
Evaluate side-chains
  437 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 405
  time to evaluate  : 1.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  225 LEU
Chi-restraints excluded: chain D residue  225 LEU
Chi-restraints excluded: chain D residue  232 LEU
Chi-restraints excluded: chain D residue  263 LEU
Chi-restraints excluded: chain E residue  249 VAL
Chi-restraints excluded: chain A residue  104 ARG
Chi-restraints excluded: chain A residue  174 GLU
Chi-restraints excluded: chain A residue  178 SER
Chi-restraints excluded: chain A residue  179 VAL
Chi-restraints excluded: chain A residue  218 THR
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  296 GLU
Chi-restraints excluded: chain A residue  384 GLU
Chi-restraints excluded: chain A residue  385 SER
Chi-restraints excluded: chain A residue  420 TRP
Chi-restraints excluded: chain A residue  424 THR
Chi-restraints excluded: chain A residue  495 SER
Chi-restraints excluded: chain A residue  609 MET
Chi-restraints excluded: chain A residue  659 PHE
Chi-restraints excluded: chain A residue  667 THR
Chi-restraints excluded: chain A residue  840 LYS
Chi-restraints excluded: chain A residue  866 LEU
Chi-restraints excluded: chain A residue  876 ASN
Chi-restraints excluded: chain A residue  946 LEU
Chi-restraints excluded: chain A residue  978 CYS
Chi-restraints excluded: chain A residue 1029 GLU
Chi-restraints excluded: chain A residue 1030 ARG
Chi-restraints excluded: chain A residue 1046 GLU
Chi-restraints excluded: chain A residue 1234 SER
Chi-restraints excluded: chain A residue 1354 ILE
Chi-restraints excluded: chain A residue 1389 VAL
Chi-restraints excluded: chain A residue 1396 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 58 optimal weight:    0.7980
   chunk 118 optimal weight:    2.9990
   chunk 82 optimal weight:    5.9990
   chunk 98 optimal weight:    4.9990
   chunk 32 optimal weight:    2.9990
   chunk 154 optimal weight:    7.9990
   chunk 150 optimal weight:    1.9990
   chunk 142 optimal weight:    8.9990
   chunk 83 optimal weight:    3.9990
   chunk 70 optimal weight:    0.0470
   chunk 42 optimal weight:    0.8980
   overall best weight:    1.3482

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

Flipped N/Q/H residues before XYZ refinement:
** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 245 GLN
A 172 ASN
A 451 ASN
** A 822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1120 ASN
A1322 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.137963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.119268 restraints weight = 21649.438|
|-----------------------------------------------------------------------------|
r_work (start): 0.3600 rms_B_bonded: 2.83
r_work: 0.3461 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3461
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.5940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  12977  Z= 0.291
  Angle     :  0.645  10.969  17591  Z= 0.331
  Chirality :  0.045   0.235   2061
  Planarity :  0.005   0.053   2226
  Dihedral  :  4.242  26.090   1733
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 12.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 25.75 %
    Favored  : 70.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.98 (0.21), residues: 1588
  helix:  1.45 (0.17), residues: 895
  sheet: -0.03 (0.58), residues: 81
  loop : -0.39 (0.25), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 182 
 HIS   0.008   0.001   HIS B 234 
 PHE   0.022   0.002   PHE A1197 
 TYR   0.031   0.002   TYR A 225 
 ARG   0.010   0.001   ARG A 742 

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

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

  3176 Ramachandran restraints generated.
    1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3176 Ramachandran restraints generated.
    1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  490 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 441
  time to evaluate  : 1.479 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  248 MET cc_start: 0.6780 (tpp) cc_final: 0.6343 (tpp)
REVERT: C  276 MET cc_start: 0.7256 (ttp) cc_final: 0.6922 (ttp)
REVERT: E  222 MET cc_start: 0.8247 (mmm) cc_final: 0.7785 (mpp)
REVERT: E  232 LEU cc_start: 0.9157 (pp) cc_final: 0.8933 (pp)
REVERT: A   27 ILE cc_start: 0.8641 (pt) cc_final: 0.8345 (mt)
REVERT: A   62 ARG cc_start: 0.8677 (mtm-85) cc_final: 0.8428 (mtt180)
REVERT: A   68 VAL cc_start: 0.9021 (t) cc_final: 0.8709 (m)
REVERT: A   69 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7502 (mm-30)
REVERT: A   94 ILE cc_start: 0.8173 (tt) cc_final: 0.7790 (tp)
REVERT: A  137 ASN cc_start: 0.8402 (t0) cc_final: 0.8191 (t0)
REVERT: A  138 GLN cc_start: 0.8455 (tm-30) cc_final: 0.8203 (tm-30)
REVERT: A  184 MET cc_start: 0.7676 (OUTLIER) cc_final: 0.7026 (tmm)
REVERT: A  279 ASP cc_start: 0.8275 (m-30) cc_final: 0.8068 (m-30)
REVERT: A  337 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7679 (mt-10)
REVERT: A  360 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7176 (mm-30)
REVERT: A  366 ARG cc_start: 0.8384 (mmt90) cc_final: 0.8001 (mmt90)
REVERT: A  436 MET cc_start: 0.8709 (mmm) cc_final: 0.8448 (mtp)
REVERT: A  437 ARG cc_start: 0.8318 (ttp80) cc_final: 0.8002 (ttt180)
REVERT: A  442 GLU cc_start: 0.7960 (tt0) cc_final: 0.7700 (tt0)
REVERT: A  524 ASP cc_start: 0.8098 (t0) cc_final: 0.7822 (t0)
REVERT: A  539 GLU cc_start: 0.7708 (tp30) cc_final: 0.7364 (tp30)
REVERT: A  550 TYR cc_start: 0.8730 (m-80) cc_final: 0.8290 (m-80)
REVERT: A  555 LYS cc_start: 0.8418 (mttp) cc_final: 0.7759 (mttt)
REVERT: A  579 GLU cc_start: 0.7569 (mm-30) cc_final: 0.7282 (mm-30)
REVERT: A  601 LYS cc_start: 0.7422 (mtmt) cc_final: 0.7069 (mtmt)
REVERT: A  659 PHE cc_start: 0.6599 (OUTLIER) cc_final: 0.6119 (m-10)
REVERT: A  661 ILE cc_start: 0.7500 (mt) cc_final: 0.7229 (tt)
REVERT: A  674 CYS cc_start: 0.8408 (p) cc_final: 0.7973 (m)
REVERT: A  710 THR cc_start: 0.8725 (m) cc_final: 0.8252 (p)
REVERT: A  730 THR cc_start: 0.8624 (m) cc_final: 0.8195 (p)
REVERT: A  738 ILE cc_start: 0.8072 (OUTLIER) cc_final: 0.7840 (mp)
REVERT: A  764 SER cc_start: 0.8675 (m) cc_final: 0.8357 (p)
REVERT: A  797 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7699 (mm-30)
REVERT: A  883 ARG cc_start: 0.8120 (mpt180) cc_final: 0.7642 (mpt180)
REVERT: A  886 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8249 (mt-10)
REVERT: A  898 ASN cc_start: 0.8531 (t0) cc_final: 0.8320 (t0)
REVERT: A  965 SER cc_start: 0.8779 (t) cc_final: 0.8491 (m)
REVERT: A  996 LYS cc_start: 0.8332 (mttm) cc_final: 0.8068 (mtmm)
REVERT: A 1006 THR cc_start: 0.8822 (m) cc_final: 0.8339 (p)
REVERT: A 1021 LYS cc_start: 0.8486 (mmtp) cc_final: 0.8211 (mmtm)
REVERT: A 1030 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.8473 (mtp85)
REVERT: A 1141 THR cc_start: 0.8755 (m) cc_final: 0.8480 (t)
REVERT: A 1143 SER cc_start: 0.8498 (p) cc_final: 0.8264 (m)
REVERT: A 1174 GLU cc_start: 0.8410 (tt0) cc_final: 0.8041 (tt0)
REVERT: A 1196 LYS cc_start: 0.7742 (mmmt) cc_final: 0.7426 (mmmt)
REVERT: A 1221 PRO cc_start: 0.8037 (Cg_endo) cc_final: 0.7734 (Cg_exo)
REVERT: A 1249 LEU cc_start: 0.8604 (mt) cc_final: 0.8334 (mm)
REVERT: A 1265 SER cc_start: 0.8596 (m) cc_final: 0.8187 (p)
REVERT: A 1267 GLN cc_start: 0.8295 (mm-40) cc_final: 0.8076 (mm-40)
REVERT: A 1282 GLU cc_start: 0.7897 (mp0) cc_final: 0.7319 (mp0)
  outliers start: 49
  outliers final: 33
  residues processed: 461
  average time/residue: 0.2897
  time to fit residues: 185.9976
Evaluate side-chains
  461 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 424
  time to evaluate  : 1.496 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  225 LEU
Chi-restraints excluded: chain D residue  232 LEU
Chi-restraints excluded: chain D residue  245 GLN
Chi-restraints excluded: chain D residue  263 LEU
Chi-restraints excluded: chain A residue  174 GLU
Chi-restraints excluded: chain A residue  178 SER
Chi-restraints excluded: chain A residue  184 MET
Chi-restraints excluded: chain A residue  218 THR
Chi-restraints excluded: chain A residue  246 MET
Chi-restraints excluded: chain A residue  296 GLU
Chi-restraints excluded: chain A residue  310 ILE
Chi-restraints excluded: chain A residue  336 GLU
Chi-restraints excluded: chain A residue  384 GLU
Chi-restraints excluded: chain A residue  385 SER
Chi-restraints excluded: chain A residue  420 TRP
Chi-restraints excluded: chain A residue  424 THR
Chi-restraints excluded: chain A residue  458 LEU
Chi-restraints excluded: chain A residue  495 SER
Chi-restraints excluded: chain A residue  609 MET
Chi-restraints excluded: chain A residue  659 PHE
Chi-restraints excluded: chain A residue  667 THR
Chi-restraints excluded: chain A residue  725 GLN
Chi-restraints excluded: chain A residue  738 ILE
Chi-restraints excluded: chain A residue  786 THR
Chi-restraints excluded: chain A residue  840 LYS
Chi-restraints excluded: chain A residue  866 LEU
Chi-restraints excluded: chain A residue  946 LEU
Chi-restraints excluded: chain A residue  978 CYS
Chi-restraints excluded: chain A residue 1029 GLU
Chi-restraints excluded: chain A residue 1030 ARG
Chi-restraints excluded: chain A residue 1118 SER
Chi-restraints excluded: chain A residue 1169 THR
Chi-restraints excluded: chain A residue 1234 SER
Chi-restraints excluded: chain A residue 1263 GLU
Chi-restraints excluded: chain A residue 1354 ILE
Chi-restraints excluded: chain A residue 1389 VAL
Chi-restraints excluded: chain A residue 1396 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 53 optimal weight:    0.9990
   chunk 77 optimal weight:    0.0010
   chunk 3 optimal weight:    1.9990
   chunk 54 optimal weight:    0.6980
   chunk 127 optimal weight:    0.8980
   chunk 156 optimal weight:    0.7980
   chunk 92 optimal weight:    0.9990
   chunk 111 optimal weight:    1.9990
   chunk 121 optimal weight:    0.7980
   chunk 62 optimal weight:    0.4980
   chunk 33 optimal weight:    0.4980
   overall best weight:    0.4986

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

Flipped N/Q/H residues before XYZ refinement:
** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 245 GLN
E 245 GLN
A 395 GLN
A 416 HIS
** A 822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1120 ASN
A1322 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.140042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.121629 restraints weight = 21529.197|
|-----------------------------------------------------------------------------|
r_work (start): 0.3671 rms_B_bonded: 2.78
r_work: 0.3541 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3541
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7819
moved from start:          0.6095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  12977  Z= 0.184
  Angle     :  0.637  12.048  17591  Z= 0.321
  Chirality :  0.043   0.240   2061
  Planarity :  0.005   0.051   2226
  Dihedral  :  4.139  25.236   1733
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 11.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 27.56 %
    Favored  : 69.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.04 (0.21), residues: 1588
  helix:  1.51 (0.18), residues: 896
  sheet: -0.10 (0.55), residues: 91
  loop : -0.37 (0.25), residues: 601

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 982 
 HIS   0.008   0.001   HIS B 234 
 PHE   0.022   0.001   PHE A1197 
 TYR   0.031   0.001   TYR A 225 
 ARG   0.013   0.001   ARG A  78 

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

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

  3176 Ramachandran restraints generated.
    1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3176 Ramachandran restraints generated.
    1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  465 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 422
  time to evaluate  : 1.543 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  248 MET cc_start: 0.6533 (tpp) cc_final: 0.6139 (tpp)
REVERT: C  276 MET cc_start: 0.7101 (ttp) cc_final: 0.6813 (ttp)
REVERT: E  232 LEU cc_start: 0.9107 (pp) cc_final: 0.8606 (pp)
REVERT: A   27 ILE cc_start: 0.8639 (pt) cc_final: 0.8348 (mt)
REVERT: A   68 VAL cc_start: 0.8986 (t) cc_final: 0.8704 (m)
REVERT: A   69 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7431 (mm-30)
REVERT: A   94 ILE cc_start: 0.8128 (tt) cc_final: 0.7736 (tp)
REVERT: A  137 ASN cc_start: 0.8383 (t0) cc_final: 0.8157 (t0)
REVERT: A  138 GLN cc_start: 0.8457 (tm-30) cc_final: 0.8238 (tm-30)
REVERT: A  165 GLU cc_start: 0.7983 (mp0) cc_final: 0.7106 (mp0)
REVERT: A  172 ASN cc_start: 0.8300 (m-40) cc_final: 0.8021 (m-40)
REVERT: A  184 MET cc_start: 0.7505 (OUTLIER) cc_final: 0.7028 (tmm)
REVERT: A  279 ASP cc_start: 0.8227 (m-30) cc_final: 0.8022 (m-30)
REVERT: A  337 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7653 (mt-10)
REVERT: A  360 GLU cc_start: 0.7535 (mm-30) cc_final: 0.7124 (mm-30)
REVERT: A  366 ARG cc_start: 0.8390 (mmt90) cc_final: 0.7997 (mmt90)
REVERT: A  428 ASN cc_start: 0.8398 (p0) cc_final: 0.8184 (p0)
REVERT: A  437 ARG cc_start: 0.8272 (ttp80) cc_final: 0.7956 (ttt180)
REVERT: A  442 GLU cc_start: 0.7867 (tt0) cc_final: 0.7625 (tt0)
REVERT: A  489 MET cc_start: 0.8396 (mtp) cc_final: 0.8071 (ttm)
REVERT: A  524 ASP cc_start: 0.8016 (t0) cc_final: 0.7727 (t0)
REVERT: A  539 GLU cc_start: 0.7650 (tp30) cc_final: 0.7307 (tp30)
REVERT: A  550 TYR cc_start: 0.8666 (m-80) cc_final: 0.8216 (m-80)
REVERT: A  579 GLU cc_start: 0.7483 (mm-30) cc_final: 0.7218 (mm-30)
REVERT: A  601 LYS cc_start: 0.7348 (mtmt) cc_final: 0.7006 (mtmt)
REVERT: A  659 PHE cc_start: 0.6596 (OUTLIER) cc_final: 0.6077 (m-10)
REVERT: A  661 ILE cc_start: 0.7432 (mt) cc_final: 0.7179 (tt)
REVERT: A  695 ILE cc_start: 0.8906 (mt) cc_final: 0.8648 (pt)
REVERT: A  710 THR cc_start: 0.8712 (m) cc_final: 0.8228 (p)
REVERT: A  730 THR cc_start: 0.8569 (OUTLIER) cc_final: 0.8149 (p)
REVERT: A  738 ILE cc_start: 0.8018 (OUTLIER) cc_final: 0.7669 (mt)
REVERT: A  764 SER cc_start: 0.8607 (m) cc_final: 0.8344 (p)
REVERT: A  797 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7674 (mm-30)
REVERT: A  883 ARG cc_start: 0.8171 (mpt180) cc_final: 0.7659 (mpt180)
REVERT: A  886 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8202 (mt-10)
REVERT: A  898 ASN cc_start: 0.8482 (t0) cc_final: 0.8277 (t0)
REVERT: A  965 SER cc_start: 0.8723 (t) cc_final: 0.8447 (m)
REVERT: A  996 LYS cc_start: 0.8307 (mttm) cc_final: 0.7993 (mtmm)
REVERT: A 1006 THR cc_start: 0.8803 (m) cc_final: 0.8377 (p)
REVERT: A 1021 LYS cc_start: 0.8422 (mmtp) cc_final: 0.8155 (mmtm)
REVERT: A 1141 THR cc_start: 0.8718 (m) cc_final: 0.8467 (t)
REVERT: A 1143 SER cc_start: 0.8499 (p) cc_final: 0.8274 (m)
REVERT: A 1174 GLU cc_start: 0.8401 (tt0) cc_final: 0.8056 (tt0)
REVERT: A 1196 LYS cc_start: 0.7735 (mmmt) cc_final: 0.7444 (mmmt)
REVERT: A 1249 LEU cc_start: 0.8535 (mt) cc_final: 0.8265 (mm)
REVERT: A 1265 SER cc_start: 0.8534 (m) cc_final: 0.8156 (p)
REVERT: A 1267 GLN cc_start: 0.8263 (mm-40) cc_final: 0.8033 (mm-40)
REVERT: A 1282 GLU cc_start: 0.7891 (mp0) cc_final: 0.7304 (mp0)
REVERT: A 1393 LEU cc_start: 0.8590 (tp) cc_final: 0.8383 (tt)
  outliers start: 43
  outliers final: 23
  residues processed: 441
  average time/residue: 0.2978
  time to fit residues: 185.9007
Evaluate side-chains
  440 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 413
  time to evaluate  : 1.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  225 LEU
Chi-restraints excluded: chain D residue  232 LEU
Chi-restraints excluded: chain D residue  245 GLN
Chi-restraints excluded: chain D residue  263 LEU
Chi-restraints excluded: chain A residue  174 GLU
Chi-restraints excluded: chain A residue  178 SER
Chi-restraints excluded: chain A residue  184 MET
Chi-restraints excluded: chain A residue  218 THR
Chi-restraints excluded: chain A residue  246 MET
Chi-restraints excluded: chain A residue  296 GLU
Chi-restraints excluded: chain A residue  384 GLU
Chi-restraints excluded: chain A residue  385 SER
Chi-restraints excluded: chain A residue  395 GLN
Chi-restraints excluded: chain A residue  420 TRP
Chi-restraints excluded: chain A residue  424 THR
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  659 PHE
Chi-restraints excluded: chain A residue  667 THR
Chi-restraints excluded: chain A residue  700 GLU
Chi-restraints excluded: chain A residue  730 THR
Chi-restraints excluded: chain A residue  738 ILE
Chi-restraints excluded: chain A residue  840 LYS
Chi-restraints excluded: chain A residue  856 VAL
Chi-restraints excluded: chain A residue  866 LEU
Chi-restraints excluded: chain A residue  946 LEU
Chi-restraints excluded: chain A residue 1029 GLU
Chi-restraints excluded: chain A residue 1389 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 68 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9990
   chunk 123 optimal weight:    0.5980
   chunk 70 optimal weight:    0.7980
   chunk 121 optimal weight:    1.9990
   chunk 10 optimal weight:    0.6980
   chunk 48 optimal weight:    3.9990
   chunk 34 optimal weight:    0.6980
   chunk 99 optimal weight:    1.9990
   chunk 107 optimal weight:    0.9990
   chunk 134 optimal weight:    1.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 245 GLN
A   5 ASN
A 395 GLN
** A 822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1120 ASN
A1322 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.139390 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.120846 restraints weight = 21630.668|
|-----------------------------------------------------------------------------|
r_work (start): 0.3613 rms_B_bonded: 2.79
r_work: 0.3474 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3474
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7843
moved from start:          0.6220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  12977  Z= 0.218
  Angle     :  0.664  12.466  17591  Z= 0.340
  Chirality :  0.045   0.245   2061
  Planarity :  0.005   0.051   2226
  Dihedral  :  4.120  25.219   1733
  Min Nonbonded Distance : 2.325

Molprobity Statistics.
  All-atom Clashscore : 11.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 27.91 %
    Favored  : 69.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.96 (0.21), residues: 1588
  helix:  1.43 (0.17), residues: 900
  sheet: -0.17 (0.55), residues: 91
  loop : -0.36 (0.25), residues: 597

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 982 
 HIS   0.007   0.001   HIS B 234 
 PHE   0.020   0.001   PHE A1197 
 TYR   0.032   0.002   TYR A 225 
 ARG   0.011   0.001   ARG A  78 

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

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

  3176 Ramachandran restraints generated.
    1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3176 Ramachandran restraints generated.
    1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  443 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 409
  time to evaluate  : 1.390 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  248 MET cc_start: 0.6739 (tpp) cc_final: 0.6294 (tpp)
REVERT: C  276 MET cc_start: 0.7087 (ttp) cc_final: 0.6790 (ttp)
REVERT: A   27 ILE cc_start: 0.8609 (pt) cc_final: 0.8312 (mt)
REVERT: A   62 ARG cc_start: 0.8619 (mtm-85) cc_final: 0.8382 (mtt180)
REVERT: A   68 VAL cc_start: 0.8983 (t) cc_final: 0.8724 (m)
REVERT: A   69 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7322 (mm-30)
REVERT: A   94 ILE cc_start: 0.8131 (tt) cc_final: 0.7735 (tp)
REVERT: A  107 MET cc_start: 0.7185 (mmm) cc_final: 0.6511 (mmp)
REVERT: A  137 ASN cc_start: 0.8423 (t0) cc_final: 0.8207 (t0)
REVERT: A  138 GLN cc_start: 0.8483 (tm-30) cc_final: 0.8249 (tm-30)
REVERT: A  165 GLU cc_start: 0.8045 (mp0) cc_final: 0.7153 (mp0)
REVERT: A  172 ASN cc_start: 0.8313 (m-40) cc_final: 0.8056 (m-40)
REVERT: A  184 MET cc_start: 0.7600 (OUTLIER) cc_final: 0.7036 (tmm)
REVERT: A  279 ASP cc_start: 0.8251 (m-30) cc_final: 0.8042 (m-30)
REVERT: A  337 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7705 (mt-10)
REVERT: A  360 GLU cc_start: 0.7562 (mm-30) cc_final: 0.7135 (mm-30)
REVERT: A  366 ARG cc_start: 0.8304 (mmt90) cc_final: 0.7916 (mmt90)
REVERT: A  428 ASN cc_start: 0.8435 (p0) cc_final: 0.8184 (p0)
REVERT: A  431 LYS cc_start: 0.7976 (mtmm) cc_final: 0.7513 (mtmm)
REVERT: A  437 ARG cc_start: 0.8296 (ttp80) cc_final: 0.8006 (ttt180)
REVERT: A  442 GLU cc_start: 0.7995 (tt0) cc_final: 0.7734 (tt0)
REVERT: A  489 MET cc_start: 0.8386 (mtp) cc_final: 0.8138 (ttm)
REVERT: A  524 ASP cc_start: 0.8121 (t0) cc_final: 0.7834 (t0)
REVERT: A  539 GLU cc_start: 0.7700 (tp30) cc_final: 0.7355 (tp30)
REVERT: A  550 TYR cc_start: 0.8708 (m-80) cc_final: 0.8240 (m-80)
REVERT: A  555 LYS cc_start: 0.8368 (mttp) cc_final: 0.7752 (mttt)
REVERT: A  556 GLU cc_start: 0.7667 (tp30) cc_final: 0.7455 (tp30)
REVERT: A  579 GLU cc_start: 0.7564 (mm-30) cc_final: 0.7270 (mm-30)
REVERT: A  601 LYS cc_start: 0.7426 (mtmt) cc_final: 0.7068 (mtmt)
REVERT: A  659 PHE cc_start: 0.6656 (OUTLIER) cc_final: 0.6147 (m-10)
REVERT: A  661 ILE cc_start: 0.7500 (mt) cc_final: 0.7186 (tt)
REVERT: A  695 ILE cc_start: 0.8921 (mt) cc_final: 0.8670 (pt)
REVERT: A  710 THR cc_start: 0.8714 (m) cc_final: 0.8241 (p)
REVERT: A  730 THR cc_start: 0.8612 (OUTLIER) cc_final: 0.8178 (p)
REVERT: A  738 ILE cc_start: 0.8010 (OUTLIER) cc_final: 0.7666 (mt)
REVERT: A  764 SER cc_start: 0.8645 (m) cc_final: 0.8359 (p)
REVERT: A  797 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7670 (mm-30)
REVERT: A  883 ARG cc_start: 0.8163 (mpt180) cc_final: 0.7620 (mpt180)
REVERT: A  886 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8194 (mt-10)
REVERT: A  898 ASN cc_start: 0.8472 (t0) cc_final: 0.8257 (t0)
REVERT: A  920 GLN cc_start: 0.8271 (mt0) cc_final: 0.8054 (mt0)
REVERT: A  965 SER cc_start: 0.8770 (t) cc_final: 0.8473 (m)
REVERT: A  996 LYS cc_start: 0.8276 (mttm) cc_final: 0.7952 (mtmm)
REVERT: A 1006 THR cc_start: 0.8814 (m) cc_final: 0.8361 (p)
REVERT: A 1021 LYS cc_start: 0.8415 (mmtp) cc_final: 0.8141 (mmtm)
REVERT: A 1141 THR cc_start: 0.8729 (m) cc_final: 0.8469 (t)
REVERT: A 1143 SER cc_start: 0.8492 (p) cc_final: 0.8257 (m)
REVERT: A 1174 GLU cc_start: 0.8402 (tt0) cc_final: 0.8048 (tt0)
REVERT: A 1196 LYS cc_start: 0.7718 (mmmt) cc_final: 0.7434 (mmmt)
REVERT: A 1249 LEU cc_start: 0.8575 (mt) cc_final: 0.8308 (mm)
REVERT: A 1265 SER cc_start: 0.8541 (m) cc_final: 0.8161 (p)
REVERT: A 1267 GLN cc_start: 0.8253 (mm-40) cc_final: 0.8033 (mm-40)
REVERT: A 1282 GLU cc_start: 0.7875 (mp0) cc_final: 0.7319 (mp0)
REVERT: A 1393 LEU cc_start: 0.8620 (tp) cc_final: 0.8359 (tt)
  outliers start: 34
  outliers final: 27
  residues processed: 423
  average time/residue: 0.2915
  time to fit residues: 173.0346
Evaluate side-chains
  441 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 410
  time to evaluate  : 1.573 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  225 LEU
Chi-restraints excluded: chain D residue  232 LEU
Chi-restraints excluded: chain D residue  245 GLN
Chi-restraints excluded: chain D residue  263 LEU
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue  174 GLU
Chi-restraints excluded: chain A residue  184 MET
Chi-restraints excluded: chain A residue  218 THR
Chi-restraints excluded: chain A residue  246 MET
Chi-restraints excluded: chain A residue  296 GLU
Chi-restraints excluded: chain A residue  384 GLU
Chi-restraints excluded: chain A residue  385 SER
Chi-restraints excluded: chain A residue  395 GLN
Chi-restraints excluded: chain A residue  420 TRP
Chi-restraints excluded: chain A residue  424 THR
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  659 PHE
Chi-restraints excluded: chain A residue  667 THR
Chi-restraints excluded: chain A residue  700 GLU
Chi-restraints excluded: chain A residue  730 THR
Chi-restraints excluded: chain A residue  738 ILE
Chi-restraints excluded: chain A residue  840 LYS
Chi-restraints excluded: chain A residue  866 LEU
Chi-restraints excluded: chain A residue  946 LEU
Chi-restraints excluded: chain A residue 1029 GLU
Chi-restraints excluded: chain A residue 1046 GLU
Chi-restraints excluded: chain A residue 1169 THR
Chi-restraints excluded: chain A residue 1263 GLU
Chi-restraints excluded: chain A residue 1354 ILE
Chi-restraints excluded: chain A residue 1389 VAL
Chi-restraints excluded: chain A residue 1396 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 65 optimal weight:    0.4980
   chunk 49 optimal weight:    0.5980
   chunk 78 optimal weight:    0.0980
   chunk 12 optimal weight:    0.7980
   chunk 33 optimal weight:    0.6980
   chunk 144 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 152 optimal weight:    0.9980
   chunk 53 optimal weight:    2.9990
   chunk 13 optimal weight:   10.0000
   chunk 143 optimal weight:    0.8980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
D 245 GLN
** A   5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 510 GLN
** A 822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1120 ASN
A1322 HIS

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 = 0.139813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.121435 restraints weight = 21717.585|
|-----------------------------------------------------------------------------|
r_work (start): 0.3641 rms_B_bonded: 2.80
r_work: 0.3502 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3502
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
moved from start:          0.6310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  12977  Z= 0.197
  Angle     :  0.676  15.813  17591  Z= 0.342
  Chirality :  0.044   0.249   2061
  Planarity :  0.005   0.077   2226
  Dihedral  :  4.119  23.843   1733
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 11.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 28.60 %
    Favored  : 69.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.98 (0.21), residues: 1588
  helix:  1.43 (0.17), residues: 901
  sheet: -0.20 (0.55), residues: 91
  loop : -0.33 (0.25), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 982 
 HIS   0.012   0.001   HIS A 229 
 PHE   0.020   0.001   PHE A1197 
 TYR   0.048   0.002   TYR A 679 
 ARG   0.012   0.001   ARG B 231 

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

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

  3176 Ramachandran restraints generated.
    1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3176 Ramachandran restraints generated.
    1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  442 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 409
  time to evaluate  : 2.609 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  248 MET cc_start: 0.6724 (tpp) cc_final: 0.6280 (tpp)
REVERT: C  276 MET cc_start: 0.7044 (ttp) cc_final: 0.6735 (ttp)
REVERT: E  222 MET cc_start: 0.8147 (mmm) cc_final: 0.7538 (mpp)
REVERT: A   27 ILE cc_start: 0.8607 (pt) cc_final: 0.8320 (mt)
REVERT: A   62 ARG cc_start: 0.8611 (mtm-85) cc_final: 0.8261 (mtm110)
REVERT: A   68 VAL cc_start: 0.8974 (t) cc_final: 0.8726 (m)
REVERT: A   69 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7249 (mm-30)
REVERT: A   94 ILE cc_start: 0.8111 (tt) cc_final: 0.7709 (tp)
REVERT: A  137 ASN cc_start: 0.8431 (t0) cc_final: 0.8218 (t0)
REVERT: A  138 GLN cc_start: 0.8481 (tm-30) cc_final: 0.8260 (tm-30)
REVERT: A  165 GLU cc_start: 0.8028 (mp0) cc_final: 0.7148 (mp0)
REVERT: A  172 ASN cc_start: 0.8296 (m-40) cc_final: 0.8044 (m-40)
REVERT: A  184 MET cc_start: 0.7612 (OUTLIER) cc_final: 0.7128 (tmm)
REVERT: A  279 ASP cc_start: 0.8261 (m-30) cc_final: 0.8049 (m-30)
REVERT: A  332 ASN cc_start: 0.8817 (m-40) cc_final: 0.8574 (t0)
REVERT: A  337 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7695 (mt-10)
REVERT: A  360 GLU cc_start: 0.7560 (mm-30) cc_final: 0.7131 (mm-30)
REVERT: A  366 ARG cc_start: 0.8304 (mmt90) cc_final: 0.7904 (mmt90)
REVERT: A  431 LYS cc_start: 0.7971 (mtmm) cc_final: 0.7489 (mtmm)
REVERT: A  437 ARG cc_start: 0.8288 (ttp80) cc_final: 0.8005 (ttt180)
REVERT: A  489 MET cc_start: 0.8363 (mtp) cc_final: 0.8135 (ttm)
REVERT: A  524 ASP cc_start: 0.8120 (t0) cc_final: 0.7830 (t0)
REVERT: A  539 GLU cc_start: 0.7662 (tp30) cc_final: 0.7317 (tp30)
REVERT: A  550 TYR cc_start: 0.8692 (m-80) cc_final: 0.8218 (m-80)
REVERT: A  555 LYS cc_start: 0.8362 (mttp) cc_final: 0.7694 (mttt)
REVERT: A  556 GLU cc_start: 0.7675 (tp30) cc_final: 0.7471 (tp30)
REVERT: A  579 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7251 (mm-30)
REVERT: A  601 LYS cc_start: 0.7433 (mtmt) cc_final: 0.7074 (mtmt)
REVERT: A  659 PHE cc_start: 0.6666 (OUTLIER) cc_final: 0.6080 (m-10)
REVERT: A  661 ILE cc_start: 0.7492 (mt) cc_final: 0.7191 (tt)
REVERT: A  695 ILE cc_start: 0.8921 (mt) cc_final: 0.8694 (pt)
REVERT: A  710 THR cc_start: 0.8692 (m) cc_final: 0.8210 (p)
REVERT: A  730 THR cc_start: 0.8593 (OUTLIER) cc_final: 0.8167 (p)
REVERT: A  738 ILE cc_start: 0.7983 (OUTLIER) cc_final: 0.7631 (mt)
REVERT: A  764 SER cc_start: 0.8625 (m) cc_final: 0.8346 (p)
REVERT: A  797 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7675 (mm-30)
REVERT: A  798 LYS cc_start: 0.8552 (ttpt) cc_final: 0.8258 (mtmt)
REVERT: A  883 ARG cc_start: 0.8153 (mpt180) cc_final: 0.7623 (mpt180)
REVERT: A  886 GLU cc_start: 0.8479 (mt-10) cc_final: 0.8120 (mt-10)
REVERT: A  901 MET cc_start: 0.8283 (mmm) cc_final: 0.7987 (mtt)
REVERT: A  920 GLN cc_start: 0.8298 (mt0) cc_final: 0.8070 (mt0)
REVERT: A  965 SER cc_start: 0.8767 (t) cc_final: 0.8468 (m)
REVERT: A  996 LYS cc_start: 0.8275 (mttm) cc_final: 0.7952 (mtmm)
REVERT: A 1006 THR cc_start: 0.8778 (m) cc_final: 0.8357 (p)
REVERT: A 1021 LYS cc_start: 0.8404 (mmtp) cc_final: 0.8138 (mmtm)
REVERT: A 1046 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7360 (pm20)
REVERT: A 1105 LYS cc_start: 0.8493 (mmtm) cc_final: 0.8062 (mmmm)
REVERT: A 1118 SER cc_start: 0.8861 (t) cc_final: 0.8607 (p)
REVERT: A 1143 SER cc_start: 0.8491 (p) cc_final: 0.8269 (m)
REVERT: A 1174 GLU cc_start: 0.8389 (tt0) cc_final: 0.8048 (tt0)
REVERT: A 1196 LYS cc_start: 0.7696 (mmmt) cc_final: 0.7419 (mmmt)
REVERT: A 1249 LEU cc_start: 0.8570 (mt) cc_final: 0.8323 (mm)
REVERT: A 1265 SER cc_start: 0.8538 (m) cc_final: 0.8153 (p)
REVERT: A 1267 GLN cc_start: 0.8232 (mm-40) cc_final: 0.8015 (mm-40)
REVERT: A 1282 GLU cc_start: 0.7859 (mp0) cc_final: 0.7303 (mp0)
REVERT: A 1393 LEU cc_start: 0.8621 (tp) cc_final: 0.8374 (tt)
  outliers start: 33
  outliers final: 25
  residues processed: 420
  average time/residue: 0.3315
  time to fit residues: 195.9894
Evaluate side-chains
  434 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 404
  time to evaluate  : 1.754 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  232 LEU
Chi-restraints excluded: chain D residue  245 GLN
Chi-restraints excluded: chain D residue  263 LEU
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue  174 GLU
Chi-restraints excluded: chain A residue  184 MET
Chi-restraints excluded: chain A residue  218 THR
Chi-restraints excluded: chain A residue  246 MET
Chi-restraints excluded: chain A residue  296 GLU
Chi-restraints excluded: chain A residue  384 GLU
Chi-restraints excluded: chain A residue  420 TRP
Chi-restraints excluded: chain A residue  424 THR
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  553 LYS
Chi-restraints excluded: chain A residue  659 PHE
Chi-restraints excluded: chain A residue  667 THR
Chi-restraints excluded: chain A residue  700 GLU
Chi-restraints excluded: chain A residue  730 THR
Chi-restraints excluded: chain A residue  738 ILE
Chi-restraints excluded: chain A residue  840 LYS
Chi-restraints excluded: chain A residue  866 LEU
Chi-restraints excluded: chain A residue  876 ASN
Chi-restraints excluded: chain A residue  946 LEU
Chi-restraints excluded: chain A residue 1029 GLU
Chi-restraints excluded: chain A residue 1046 GLU
Chi-restraints excluded: chain A residue 1091 ILE
Chi-restraints excluded: chain A residue 1263 GLU
Chi-restraints excluded: chain A residue 1354 ILE
Chi-restraints excluded: chain A residue 1389 VAL
Chi-restraints excluded: chain A residue 1396 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 140 optimal weight:    0.0370
   chunk 62 optimal weight:    0.6980
   chunk 95 optimal weight:    0.5980
   chunk 134 optimal weight:    1.9990
   chunk 131 optimal weight:    0.0010
   chunk 130 optimal weight:    0.7980
   chunk 17 optimal weight:    5.9990
   chunk 110 optimal weight:    0.7980
   chunk 14 optimal weight:    0.2980
   chunk 28 optimal weight:    1.9990
   chunk 108 optimal weight:    0.8980
   overall best weight:    0.3264

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

Flipped N/Q/H residues before XYZ refinement:
B 237 GLN
D 245 GLN
** A 898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1322 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.146808 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.127951 restraints weight = 21450.597|
|-----------------------------------------------------------------------------|
r_work (start): 0.3662 rms_B_bonded: 2.87
r_work: 0.3516 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3516
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7809
moved from start:          0.6406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  12977  Z= 0.176
  Angle     :  0.682  18.755  17591  Z= 0.341
  Chirality :  0.044   0.248   2061
  Planarity :  0.005   0.077   2226
  Dihedral  :  4.057  24.677   1733
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 11.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 28.46 %
    Favored  : 69.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.02 (0.21), residues: 1588
  helix:  1.48 (0.18), residues: 905
  sheet: -0.25 (0.55), residues: 91
  loop : -0.36 (0.25), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 982 
 HIS   0.012   0.001   HIS A 229 
 PHE   0.019   0.001   PHE A1197 
 TYR   0.039   0.001   TYR A 679 
 ARG   0.011   0.001   ARG A  78 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7246.50 seconds
wall clock time: 130 minutes 27.94 seconds (7827.94 seconds total)