Starting phenix.real_space_refine
on Fri Sep 19 00:37:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7s5z_24844/09_2025/7s5z_24844.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7s5z_24844/09_2025/7s5z_24844.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7s5z_24844/09_2025/7s5z_24844.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7s5z_24844/09_2025/7s5z_24844.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7s5z_24844/09_2025/7s5z_24844.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7s5z_24844/09_2025/7s5z_24844.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.005 sd=   0.078
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       5      5.49       5
     Mg      2      5.21       5
     S     121      5.16       5
     C   13673      2.51       5
     N    3597      2.21       5
     O    3750      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 111 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 21148
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2519
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 321, 2519
          Classifications: {'peptide': 321}
          Link IDs: {'PTRANS': 13, 'TRANS': 307}
    Chain: "E"
      Number of atoms: 11012
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1403, 11012
          Classifications: {'peptide': 1403}
          Incomplete info: {'truncation_to_alanine': 20}
          Link IDs: {'PTRANS': 42, 'TRANS': 1360}
          Chain breaks: 7
          Unresolved non-hydrogen bonds: 75
          Unresolved non-hydrogen angles: 94
          Unresolved non-hydrogen dihedrals: 58
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'ARG:plan': 3, 'PHE:plan': 1, 'ASP:plan': 3, 'GLU:plan': 5, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 53
    Chain: "E"
      Number of atoms: 60
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 60
          Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
  Restraints were copied for chains:
    B, C, D
  Time building chain proxies: 4.63, per 1000 atoms: 0.22
  Number of scatterers: 21148
  At special positions: 0
  Unit cell: (130, 154.7, 141.7, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S     121     16.00
     P       5     15.00
     Mg      2     11.99
     O    3750      8.00
     N    3597      7.00
     C   13673      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 110 " - pdb=" SG  CYS A 142 " distance=2.03
    Simple disulfide: pdb=" C   CYS D 344 " - pdb=" SG  CYS D 344 " distance=2.89
    Simple disulfide: pdb=" SG  CYS B 110 " - pdb=" SG  CYS B 142 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 110 " - pdb=" SG  CYS C 142 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 110 " - pdb=" SG  CYS D 142 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.88
  Conformation dependent library (CDL) restraints added in 916.4 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  5326 Ramachandran restraints generated.
    2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  5070

  Finding SS restraints...
    Secondary structure from input PDB file:
      93 helices and 31 sheets defined
      51.9% alpha, 15.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.84
  Creating SS restraints...
    Processing helix  chain 'A' and resid 52 through 57
    Processing helix  chain 'A' and resid 58 through 65
      removed outlier: 4.131A  pdb=" N   THR A  62 " --> pdb=" O   ASP A  58 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 67 through 97
    Processing helix  chain 'A' and resid 116 through 129
    Processing helix  chain 'A' and resid 142 through 173
    Processing helix  chain 'A' and resid 176 through 179
    Processing helix  chain 'A' and resid 271 through 275
      removed outlier: 3.527A  pdb=" N   LEU A 275 " --> pdb=" O   PRO A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 309
      No H-bonds generated for 'chain 'A' and resid 307 through 309'
    Processing helix  chain 'A' and resid 330 through 333
    Processing helix  chain 'A' and resid 345 through 350
      removed outlier: 3.794A  pdb=" N   ASP A 350 " --> pdb=" O   ALA A 346 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 52 through 57
    Processing helix  chain 'B' and resid 58 through 65
      removed outlier: 4.132A  pdb=" N   THR B  62 " --> pdb=" O   ASP B  58 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 67 through 97
    Processing helix  chain 'B' and resid 116 through 129
    Processing helix  chain 'B' and resid 142 through 173
    Processing helix  chain 'B' and resid 176 through 179
    Processing helix  chain 'B' and resid 271 through 275
      removed outlier: 3.528A  pdb=" N   LEU B 275 " --> pdb=" O   PRO B 272 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 307 through 309
      No H-bonds generated for 'chain 'B' and resid 307 through 309'
    Processing helix  chain 'B' and resid 330 through 333
    Processing helix  chain 'B' and resid 345 through 350
      removed outlier: 3.794A  pdb=" N   ASP B 350 " --> pdb=" O   ALA B 346 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 52 through 57
    Processing helix  chain 'C' and resid 58 through 65
      removed outlier: 4.131A  pdb=" N   THR C  62 " --> pdb=" O   ASP C  58 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 67 through 97
    Processing helix  chain 'C' and resid 116 through 129
    Processing helix  chain 'C' and resid 142 through 173
    Processing helix  chain 'C' and resid 176 through 179
    Processing helix  chain 'C' and resid 271 through 275
      removed outlier: 3.528A  pdb=" N   LEU C 275 " --> pdb=" O   PRO C 272 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 307 through 309
      No H-bonds generated for 'chain 'C' and resid 307 through 309'
    Processing helix  chain 'C' and resid 330 through 333
    Processing helix  chain 'C' and resid 345 through 350
      removed outlier: 3.793A  pdb=" N   ASP C 350 " --> pdb=" O   ALA C 346 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 52 through 57
    Processing helix  chain 'D' and resid 58 through 65
      removed outlier: 4.131A  pdb=" N   THR D  62 " --> pdb=" O   ASP D  58 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 67 through 97
    Processing helix  chain 'D' and resid 116 through 129
    Processing helix  chain 'D' and resid 142 through 173
    Processing helix  chain 'D' and resid 176 through 179
    Processing helix  chain 'D' and resid 271 through 275
      removed outlier: 3.527A  pdb=" N   LEU D 275 " --> pdb=" O   PRO D 272 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 307 through 309
      No H-bonds generated for 'chain 'D' and resid 307 through 309'
    Processing helix  chain 'D' and resid 330 through 333
    Processing helix  chain 'D' and resid 345 through 350
      removed outlier: 3.793A  pdb=" N   ASP D 350 " --> pdb=" O   ALA D 346 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 13 through 17
      removed outlier: 3.617A  pdb=" N   ARG E  17 " --> pdb=" O   ALA E  14 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 25 through 52
      removed outlier: 3.563A  pdb=" N   VAL E  35 " --> pdb=" O   ALA E  31 " (cutoff:3.500A)
      Proline residue:  E  36  - end of helix
      Proline residue:  E  46  - end of helix
      removed outlier: 3.526A  pdb=" N   TRP E  52 " --> pdb=" O   LEU E  48 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 71 through 97
      removed outlier: 3.648A  pdb=" N   ASP E  97 " --> pdb=" O   GLY E  93 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 108 through 131
    Processing helix  chain 'E' and resid 137 through 162
    Processing helix  chain 'E' and resid 167 through 193
      removed outlier: 3.697A  pdb=" N   CYS E 171 " --> pdb=" O   GLN E 167 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 224 through 231
    Processing helix  chain 'E' and resid 233 through 240
      removed outlier: 4.214A  pdb=" N   PHE E 237 " --> pdb=" O   TRP E 233 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 262 through 275
      removed outlier: 5.837A  pdb=" N   LEU E 267 " --> pdb=" O   ASN E 263 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   ALA E 273 " --> pdb=" O   GLU E 269 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 285 through 310
      removed outlier: 5.631A  pdb=" N   ARG E 298 " --> pdb=" O   HIS E 294 " (cutoff:3.500A)
      removed outlier: 6.206A  pdb=" N   ARG E 299 " --> pdb=" O   ALA E 295 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 316 through 328
    Processing helix  chain 'E' and resid 348 through 355
    Processing helix  chain 'E' and resid 355 through 402
      removed outlier: 3.796A  pdb=" N   LEU E 359 " --> pdb=" O   ASN E 355 " (cutoff:3.500A)
      removed outlier: 4.001A  pdb=" N   THR E 394 " --> pdb=" O   GLY E 390 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   HIS E 402 " --> pdb=" O   ASN E 398 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 404 through 410
      removed outlier: 4.154A  pdb=" N   LEU E 408 " --> pdb=" O   SER E 404 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 414 through 435
      removed outlier: 5.293A  pdb=" N   ASN E 427 " --> pdb=" O   ALA E 423 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 435 through 456
      removed outlier: 3.629A  pdb=" N   LEU E 439 " --> pdb=" O   LEU E 435 " (cutoff:3.500A)
      Proline residue:  E 443  - end of helix
      removed outlier: 3.600A  pdb=" N   ILE E 456 " --> pdb=" O   LEU E 452 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 459 through 506
      removed outlier: 3.617A  pdb=" N   ILE E 463 " --> pdb=" O   VAL E 459 " (cutoff:3.500A)
      removed outlier: 5.315A  pdb=" N   VAL E 467 " --> pdb=" O   ILE E 463 " (cutoff:3.500A)
      removed outlier: 5.591A  pdb=" N   ILE E 468 " --> pdb=" O   GLY E 464 " (cutoff:3.500A)
      removed outlier: 4.110A  pdb=" N   ILE E 469 " --> pdb=" O   ALA E 465 " (cutoff:3.500A)
      Proline residue:  E 473  - end of helix
      removed outlier: 3.636A  pdb=" N   TYR E 476 " --> pdb=" O   ALA E 472 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   GLU E 491 " --> pdb=" O   ARG E 487 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 506 through 513
    Processing helix  chain 'E' and resid 515 through 549
      removed outlier: 3.530A  pdb=" N   SER E 533 " --> pdb=" O   LYS E 529 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   ALA E 536 " --> pdb=" O   THR E 532 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 550 through 565
    Processing helix  chain 'E' and resid 573 through 589
      removed outlier: 3.623A  pdb=" N   ALA E 577 " --> pdb=" O   SER E 573 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 593 through 616
    Processing helix  chain 'E' and resid 719 through 728
      removed outlier: 3.620A  pdb=" N   LEU E 724 " --> pdb=" O   LYS E 720 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 783 through 790
    Processing helix  chain 'E' and resid 795 through 806
    Processing helix  chain 'E' and resid 808 through 815
    Processing helix  chain 'E' and resid 817 through 821
      removed outlier: 3.666A  pdb=" N   GLN E 820 " --> pdb=" O   HIS E 817 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   THR E 821 " --> pdb=" O   GLY E 818 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 817 through 821'
    Processing helix  chain 'E' and resid 832 through 845
    Processing helix  chain 'E' and resid 861 through 871
    Processing helix  chain 'E' and resid 890 through 897
      removed outlier: 3.696A  pdb=" N   TYR E 893 " --> pdb=" O   LYS E 890 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   LEU E 894 " --> pdb=" O   LEU E 891 " (cutoff:3.500A)
      Proline residue:  E 895  - end of helix
      No H-bonds generated for 'chain 'E' and resid 890 through 897'
    Processing helix  chain 'E' and resid 913 through 920
    Processing helix  chain 'E' and resid 921 through 933
    Processing helix  chain 'E' and resid 998 through 1009
      removed outlier: 4.096A  pdb=" N   ALA E1002 " --> pdb=" O   TRP E 998 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 1009 through 1038
    Processing helix  chain 'E' and resid 1066 through 1098
      removed outlier: 3.666A  pdb=" N   VAL E1070 " --> pdb=" O   MET E1066 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 1100 through 1107
    Processing helix  chain 'E' and resid 1109 through 1116
      removed outlier: 3.676A  pdb=" N   PHE E1113 " --> pdb=" O   PRO E1109 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 1117 through 1135
      removed outlier: 3.563A  pdb=" N   ILE E1121 " --> pdb=" O   PRO E1117 " (cutoff:3.500A)
      removed outlier: 4.984A  pdb=" N   CYS E1129 " --> pdb=" O   PHE E1125 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 1135 through 1161
      removed outlier: 3.544A  pdb=" N   SER E1146 " --> pdb=" O   CYS E1142 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   LEU E1148 " --> pdb=" O   SER E1144 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   LEU E1149 " --> pdb=" O   ARG E1145 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 1164 through 1210
      Proline residue:  E1170  - end of helix
      removed outlier: 4.470A  pdb=" N   VAL E1184 " --> pdb=" O   LYS E1180 " (cutoff:3.500A)
      removed outlier: 4.919A  pdb=" N   ALA E1185 " --> pdb=" O   TYR E1181 " (cutoff:3.500A)
      Proline residue:  E1199  - end of helix
      removed outlier: 3.568A  pdb=" N   GLU E1209 " --> pdb=" O   ALA E1205 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   GLY E1210 " --> pdb=" O   GLU E1206 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 1210 through 1217
    Processing helix  chain 'E' and resid 1219 through 1273
      removed outlier: 3.613A  pdb=" N   PHE E1223 " --> pdb=" O   TYR E1219 " (cutoff:3.500A)
      removed outlier: 4.029A  pdb=" N   VAL E1260 " --> pdb=" O   GLY E1256 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   HIS E1273 " --> pdb=" O   SER E1269 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 1279 through 1320
      removed outlier: 5.342A  pdb=" N   ASN E1296 " --> pdb=" O   SER E1292 " (cutoff:3.500A)
      removed outlier: 4.810A  pdb=" N   TRP E1297 " --> pdb=" O   ASN E1293 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   ALA E1311 " --> pdb=" O   LEU E1307 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   VAL E1312 " --> pdb=" O   GLN E1308 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   LYS E1320 " --> pdb=" O   HIS E1316 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 1384 through 1393
      removed outlier: 3.859A  pdb=" N   SER E1389 " --> pdb=" O   LYS E1385 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 1414 through 1421
    Processing helix  chain 'E' and resid 1436 through 1441
    Processing helix  chain 'E' and resid 1447 through 1457
    Processing helix  chain 'E' and resid 1460 through 1467
    Processing helix  chain 'E' and resid 1483 through 1498
      removed outlier: 4.137A  pdb=" N   ARG E1498 " --> pdb=" O   ARG E1494 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 1513 through 1524
    Processing helix  chain 'E' and resid 1539 through 1544
      removed outlier: 3.913A  pdb=" N   ILE E1543 " --> pdb=" O   ARG E1539 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 1562 through 1568
    Processing helix  chain 'E' and resid 1572 through 1582
    Processing sheet with id=AA1, first strand: chain 'A' and resid 181 through 183
      removed outlier: 3.670A  pdb=" N   VAL A 202 " --> pdb=" O   LEU A 255 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   LEU A 255 " --> pdb=" O   VAL A 202 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 181 through 183
    Processing sheet with id=AA3, first strand: chain 'A' and resid 210 through 211
      removed outlier: 4.395A  pdb=" N   MET A 217 " --> pdb=" O   ILE A 238 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   ARG A 221 " --> pdb=" O   HIS A 234 " (cutoff:3.500A)
      removed outlier: 5.121A  pdb=" N   THR A 223 " --> pdb=" O   PRO A 232 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 210 through 211
    Processing sheet with id=AA5, first strand: chain 'A' and resid 313 through 315
    Processing sheet with id=AA6, first strand: chain 'A' and resid 319 through 322
    Processing sheet with id=AA7, first strand: chain 'B' and resid 47 through 49
      removed outlier: 6.577A  pdb=" N   HIS E  60 " --> pdb=" O   LYS B  47 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 181 through 183
      removed outlier: 3.670A  pdb=" N   VAL B 202 " --> pdb=" O   LEU B 255 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   LEU B 255 " --> pdb=" O   VAL B 202 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 181 through 183
    Processing sheet with id=AB1, first strand: chain 'B' and resid 210 through 211
      removed outlier: 4.395A  pdb=" N   MET B 217 " --> pdb=" O   ILE B 238 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   ARG B 221 " --> pdb=" O   HIS B 234 " (cutoff:3.500A)
      removed outlier: 5.121A  pdb=" N   THR B 223 " --> pdb=" O   PRO B 232 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 210 through 211
    Processing sheet with id=AB3, first strand: chain 'B' and resid 313 through 315
    Processing sheet with id=AB4, first strand: chain 'B' and resid 319 through 322
    Processing sheet with id=AB5, first strand: chain 'C' and resid 181 through 183
      removed outlier: 3.670A  pdb=" N   VAL C 202 " --> pdb=" O   LEU C 255 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   LEU C 255 " --> pdb=" O   VAL C 202 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 181 through 183
    Processing sheet with id=AB7, first strand: chain 'C' and resid 210 through 211
      removed outlier: 4.395A  pdb=" N   MET C 217 " --> pdb=" O   ILE C 238 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   ARG C 221 " --> pdb=" O   HIS C 234 " (cutoff:3.500A)
      removed outlier: 5.122A  pdb=" N   THR C 223 " --> pdb=" O   PRO C 232 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'C' and resid 210 through 211
    Processing sheet with id=AB9, first strand: chain 'C' and resid 313 through 315
    Processing sheet with id=AC1, first strand: chain 'C' and resid 319 through 322
    Processing sheet with id=AC2, first strand: chain 'D' and resid 181 through 183
      removed outlier: 3.670A  pdb=" N   VAL D 202 " --> pdb=" O   LEU D 255 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   LEU D 255 " --> pdb=" O   VAL D 202 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'D' and resid 181 through 183
    Processing sheet with id=AC4, first strand: chain 'D' and resid 210 through 211
      removed outlier: 4.395A  pdb=" N   MET D 217 " --> pdb=" O   ILE D 238 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   ARG D 221 " --> pdb=" O   HIS D 234 " (cutoff:3.500A)
      removed outlier: 5.121A  pdb=" N   THR D 223 " --> pdb=" O   PRO D 232 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'D' and resid 210 through 211
    Processing sheet with id=AC6, first strand: chain 'D' and resid 313 through 315
    Processing sheet with id=AC7, first strand: chain 'D' and resid 319 through 322
    Processing sheet with id=AC8, first strand: chain 'E' and resid 678 through 680
      removed outlier: 7.167A  pdb=" N   ILE E 704 " --> pdb=" O   CYS E 679 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'E' and resid 697 through 700
      removed outlier: 3.598A  pdb=" N   ASN E 699 " --> pdb=" O   GLY E 685 " (cutoff:3.500A)
      removed outlier: 5.947A  pdb=" N   GLY E 685 " --> pdb=" O   ASN E 699 " (cutoff:3.500A)
      removed outlier: 7.232A  pdb=" N   GLY E 684 " --> pdb=" O   GLY E 736 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   GLY E 736 " --> pdb=" O   GLY E 684 " (cutoff:3.500A)
      removed outlier: 7.018A  pdb=" N   TYR E 686 " --> pdb=" O   VAL E 734 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   GLN E 732 " --> pdb=" O   THR E 688 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'E' and resid 850 through 853
      removed outlier: 6.309A  pdb=" N   THR E 710 " --> pdb=" O   LEU E 886 " (cutoff:3.500A)
      removed outlier: 6.729A  pdb=" N   ILE E 900 " --> pdb=" O   GLU E 911 " (cutoff:3.500A)
      removed outlier: 4.727A  pdb=" N   GLU E 911 " --> pdb=" O   ILE E 900 " (cutoff:3.500A)
      removed outlier: 4.637A  pdb=" N   ALA E 902 " --> pdb=" O   GLN E 909 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'E' and resid 1365 through 1369
      removed outlier: 5.368A  pdb=" N   VAL E1365 " --> pdb=" O   ASN E1349 " (cutoff:3.500A)
      removed outlier: 6.667A  pdb=" N   SER E1351 " --> pdb=" O   PHE E1399 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   PHE E1399 " --> pdb=" O   SER E1351 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'E' and resid 1424 through 1425
      removed outlier: 3.528A  pdb=" N   VAL E1551 " --> pdb=" O   GLU E1559 " (cutoff:3.500A)
      removed outlier: 4.144A  pdb=" N   GLU E1559 " --> pdb=" O   VAL E1551 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   LYS E1553 " --> pdb=" O   ILE E1557 " (cutoff:3.500A)
      removed outlier: 5.481A  pdb=" N   ILE E1557 " --> pdb=" O   LYS E1553 " (cutoff:3.500A)
    Processing sheet with id=AD4, first strand: chain 'E' and resid 1434 through 1435

    1164 hydrogen bonds defined for protein.
    3384 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: 4.68

  Time building geometry restraints manager: 2.44 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 6588
        1.34 -     1.46: 4241
        1.46 -     1.58: 10580
        1.58 -     1.70: 8
        1.70 -     1.81: 194
  Bond restraints: 21611
  Sorted by residual:
  bond pdb=" C4  ATP E1604 "
       pdb=" C5  ATP E1604 "
    ideal  model  delta    sigma   weight residual
    1.388  1.465 -0.077 1.00e-02 1.00e+04 5.98e+01
  bond pdb=" C5  ATP E1604 "
       pdb=" C6  ATP E1604 "
    ideal  model  delta    sigma   weight residual
    1.409  1.471 -0.062 1.00e-02 1.00e+04 3.87e+01
  bond pdb=" C   ILE E1136 "
       pdb=" N   PRO E1137 "
    ideal  model  delta    sigma   weight residual
    1.336  1.403 -0.067 1.20e-02 6.94e+03 3.09e+01
  bond pdb=" C4  ATP E1604 "
       pdb=" N9  ATP E1604 "
    ideal  model  delta    sigma   weight residual
    1.374  1.325  0.049 1.00e-02 1.00e+04 2.42e+01
  bond pdb=" C5  ATP E1604 "
       pdb=" N7  ATP E1604 "
    ideal  model  delta    sigma   weight residual
    1.387  1.339  0.048 1.00e-02 1.00e+04 2.31e+01
  ... (remaining 21606 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.77: 29106
        3.77 -     7.54: 218
        7.54 -    11.30: 36
       11.30 -    15.07: 3
       15.07 -    18.84: 2
  Bond angle restraints: 29365
  Sorted by residual:
  angle pdb=" PA  ATP E1604 "
        pdb=" O3A ATP E1604 "
        pdb=" PB  ATP E1604 "
      ideal   model   delta    sigma   weight residual
     136.83  117.99   18.84 1.00e+00 1.00e+00 3.55e+02
  angle pdb=" PB  ATP E1604 "
        pdb=" O3B ATP E1604 "
        pdb=" PG  ATP E1604 "
      ideal   model   delta    sigma   weight residual
     139.87  125.45   14.42 1.00e+00 1.00e+00 2.08e+02
  angle pdb=" C5  ATP E1604 "
        pdb=" C4  ATP E1604 "
        pdb=" N3  ATP E1604 "
      ideal   model   delta    sigma   weight residual
     126.80  119.32    7.48 1.00e+00 1.00e+00 5.59e+01
  angle pdb=" N3  ATP E1604 "
        pdb=" C4  ATP E1604 "
        pdb=" N9  ATP E1604 "
      ideal   model   delta    sigma   weight residual
     127.04  134.77   -7.73 1.15e+00 7.59e-01 4.54e+01
  angle pdb=" C   ASN E 263 "
        pdb=" N   TYR E 264 "
        pdb=" CA  TYR E 264 "
      ideal   model   delta    sigma   weight residual
     121.54  131.73  -10.19 1.91e+00 2.74e-01 2.84e+01
  ... (remaining 29360 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.38: 11958
       26.38 -    52.75: 765
       52.75 -    79.13: 117
       79.13 -   105.50: 7
      105.50 -   131.88: 1
  Dihedral angle restraints: 12848
    sinusoidal: 5045
      harmonic: 7803
  Sorted by residual:
  dihedral pdb=" CB  CYS D 344 "
           pdb=" C   CYS D 344 "
           pdb=" SG  CYS D 344 "
           pdb=" CB  CYS D 344 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00   -0.00  -86.00     1      1.00e+01 1.00e-02 8.93e+01
  dihedral pdb=" CA  ILE E  61 "
           pdb=" C   ILE E  61 "
           pdb=" N   HIS E  62 "
           pdb=" CA  HIS E  62 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  141.72   38.28     0      5.00e+00 4.00e-02 5.86e+01
  dihedral pdb=" CB  CYS B 110 "
           pdb=" SG  CYS B 110 "
           pdb=" SG  CYS B 142 "
           pdb=" CB  CYS B 142 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   29.23   63.77     1      1.00e+01 1.00e-02 5.36e+01
  ... (remaining 12845 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 2639
       0.062 -    0.124: 717
       0.124 -    0.186: 97
       0.186 -    0.249: 18
       0.249 -    0.311: 3
  Chirality restraints: 3474
  Sorted by residual:
  chirality pdb=" CB  ILE E 712 "
            pdb=" CA  ILE E 712 "
            pdb=" CG1 ILE E 712 "
            pdb=" CG2 ILE E 712 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.33    0.31 2.00e-01 2.50e+01 2.41e+00
  chirality pdb=" CB  ILE E 704 "
            pdb=" CA  ILE E 704 "
            pdb=" CG1 ILE E 704 "
            pdb=" CG2 ILE E 704 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.39    0.26 2.00e-01 2.50e+01 1.65e+00
  chirality pdb=" CB  VAL E1396 "
            pdb=" CA  VAL E1396 "
            pdb=" CG1 VAL E1396 "
            pdb=" CG2 VAL E1396 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.38   -0.25 2.00e-01 2.50e+01 1.56e+00
  ... (remaining 3471 not shown)

  Planarity restraints: 3650
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR E 264 "   -0.020 2.00e-02 2.50e+03   3.94e-02 1.56e+01
        pdb=" C   TYR E 264 "    0.068 2.00e-02 2.50e+03
        pdb=" O   TYR E 264 "   -0.025 2.00e-02 2.50e+03
        pdb=" N   GLN E 265 "   -0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU E 261 "   -0.018 2.00e-02 2.50e+03   3.54e-02 1.25e+01
        pdb=" C   LEU E 261 "    0.061 2.00e-02 2.50e+03
        pdb=" O   LEU E 261 "   -0.023 2.00e-02 2.50e+03
        pdb=" N   THR E 262 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL E 422 "    0.014 2.00e-02 2.50e+03   2.75e-02 7.58e+00
        pdb=" C   VAL E 422 "   -0.048 2.00e-02 2.50e+03
        pdb=" O   VAL E 422 "    0.018 2.00e-02 2.50e+03
        pdb=" N   ALA E 423 "    0.016 2.00e-02 2.50e+03
  ... (remaining 3647 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.64: 337
        2.64 -     3.20: 19062
        3.20 -     3.77: 35649
        3.77 -     4.33: 45499
        4.33 -     4.90: 73763
  Nonbonded interactions: 174310
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN E 775 "
            pdb="MG    MG E1602 "
     model   vdw
     2.073 2.170
  nonbonded pdb="MG    MG E1602 "
            pdb=" O3A ATP E1604 "
     model   vdw
     2.085 2.170
  nonbonded pdb=" OG  SER E 721 "
            pdb="MG    MG E1602 "
     model   vdw
     2.088 2.170
  nonbonded pdb=" O1B ADP E1601 "
            pdb="MG    MG E1603 "
     model   vdw
     2.118 2.170
  nonbonded pdb=" NE2 GLN E 775 "
            pdb="MG    MG E1602 "
     model   vdw
     2.169 2.250
  ... (remaining 174305 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 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.090
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.070
  Set scattering table:                    0.050
  Process input model:                     20.790
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8359
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      :  0.008   0.855  21616  Z= 0.403
  Angle     :  1.067  66.611  29375  Z= 0.588
  Chirality :  0.056   0.311   3474
  Planarity :  0.007   0.069   3650
  Dihedral  : 16.842 131.879   7763
  Min Nonbonded Distance : 2.073

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  6.47 %
    Allowed  :  8.33 %
    Favored  : 85.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.30 (0.13), residues: 2663
  helix: -2.12 (0.10), residues: 1327
  sheet: -2.27 (0.26), residues: 274
  loop : -2.02 (0.17), residues: 1062

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E1421 
 TYR   0.023   0.002   TYR E 264 
 PHE   0.021   0.002   PHE E 578 
 TRP   0.015   0.002   TRP E 289 
 HIS   0.010   0.001   HIS E 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00535 (21611)
  covalent geometry    : angle       0.96026 (29365)
  SS BOND              : bond        0.38256 (    5)
  SS BOND              : angle      25.27643 (   10)
  hydrogen bonds       : bond        0.15788 ( 1148)
  hydrogen bonds       : angle       6.74386 ( 3384)

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

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

  5326 Ramachandran restraints generated.
    2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5326 Ramachandran restraints generated.
    2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  681 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 149
    poor density    : 532
  time to evaluate  : 0.834 
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: symmetry clash
   revert: symmetry clash
REVERT: A   39 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8690 (ttmt)
REVERT: A   51 GLU cc_start: 0.8210 (tp30) cc_final: 0.7682 (tp30)
REVERT: A   57 GLN cc_start: 0.8340 (tt0) cc_final: 0.7844 (tp40)
REVERT: A   66 LEU cc_start: 0.9173 (mt) cc_final: 0.8878 (mt)
REVERT: A   73 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8751 (tt)
REVERT: A  163 MET cc_start: 0.9473 (mmm) cc_final: 0.9263 (mmm)
REVERT: A  170 LYS cc_start: 0.9414 (tptp) cc_final: 0.9157 (tptt)
REVERT: A  237 ASP cc_start: 0.7724 (p0) cc_final: 0.7178 (p0)
REVERT: A  311 TRP cc_start: 0.9026 (t-100) cc_final: 0.8821 (t60)
REVERT: A  330 TYR cc_start: 0.8744 (m-80) cc_final: 0.8442 (m-80)
REVERT: B   57 GLN cc_start: 0.8386 (tt0) cc_final: 0.8183 (tp40)
REVERT: B   80 LEU cc_start: 0.9655 (mm) cc_final: 0.9439 (mp)
REVERT: B   84 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8859 (mt)
REVERT: B  160 ASN cc_start: 0.9147 (m110) cc_final: 0.8896 (m110)
REVERT: B  163 MET cc_start: 0.9506 (mmm) cc_final: 0.9102 (mmm)
REVERT: B  169 MET cc_start: 0.8820 (ttm) cc_final: 0.8612 (ttm)
REVERT: B  176 ARG cc_start: 0.7994 (mtm-85) cc_final: 0.7207 (mtp180)
REVERT: B  179 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8411 (mt-10)
REVERT: B  181 LEU cc_start: 0.9530 (mt) cc_final: 0.9306 (mt)
REVERT: B  202 VAL cc_start: 0.9675 (OUTLIER) cc_final: 0.9445 (p)
REVERT: B  220 VAL cc_start: 0.9575 (OUTLIER) cc_final: 0.9358 (p)
REVERT: B  231 VAL cc_start: 0.8899 (OUTLIER) cc_final: 0.8171 (m)
REVERT: B  240 MET cc_start: 0.9076 (tmm) cc_final: 0.8763 (tmm)
REVERT: B  302 THR cc_start: 0.9431 (OUTLIER) cc_final: 0.9025 (m)
REVERT: B  305 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8633 (mm)
REVERT: C   39 LYS cc_start: 0.9381 (OUTLIER) cc_final: 0.8798 (tmtt)
REVERT: C   41 ASN cc_start: 0.9013 (m110) cc_final: 0.8778 (m110)
REVERT: C   48 ASN cc_start: 0.8812 (m-40) cc_final: 0.7515 (m-40)
REVERT: C   56 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.9054 (mt)
REVERT: C   65 ASP cc_start: 0.8387 (t0) cc_final: 0.8073 (t0)
REVERT: C   91 TRP cc_start: 0.9275 (t60) cc_final: 0.9029 (t60)
REVERT: C  128 GLN cc_start: 0.9001 (tt0) cc_final: 0.8751 (tt0)
REVERT: C  160 ASN cc_start: 0.9074 (m110) cc_final: 0.8519 (m110)
REVERT: C  163 MET cc_start: 0.9272 (mmm) cc_final: 0.9053 (mmt)
REVERT: C  169 MET cc_start: 0.8994 (ttm) cc_final: 0.8697 (ttm)
REVERT: C  240 MET cc_start: 0.9158 (tmm) cc_final: 0.8645 (tmm)
REVERT: C  279 GLN cc_start: 0.8925 (tp40) cc_final: 0.8116 (tm-30)
REVERT: D   54 ARG cc_start: 0.8479 (ptp-110) cc_final: 0.8161 (ptm160)
REVERT: D   64 VAL cc_start: 0.9750 (OUTLIER) cc_final: 0.9526 (t)
REVERT: D   65 ASP cc_start: 0.9010 (t0) cc_final: 0.8611 (t70)
REVERT: D   77 MET cc_start: 0.8749 (OUTLIER) cc_final: 0.8435 (tpp)
REVERT: D  163 MET cc_start: 0.9107 (mmm) cc_final: 0.8698 (mmm)
REVERT: D  170 LYS cc_start: 0.9073 (tptp) cc_final: 0.8469 (tptt)
REVERT: D  262 ASP cc_start: 0.9209 (t0) cc_final: 0.8875 (t70)
REVERT: D  265 SER cc_start: 0.9077 (m) cc_final: 0.8767 (p)
REVERT: D  330 TYR cc_start: 0.8015 (m-80) cc_final: 0.7716 (m-80)
REVERT: E   30 ASP cc_start: 0.8793 (m-30) cc_final: 0.8541 (m-30)
REVERT: E  116 MET cc_start: 0.9425 (mmm) cc_final: 0.9111 (mmm)
REVERT: E  153 ILE cc_start: 0.9492 (mm) cc_final: 0.9185 (mm)
REVERT: E  508 LYS cc_start: 0.9468 (tttt) cc_final: 0.9217 (ttmm)
REVERT: E  547 MET cc_start: 0.9016 (tmm) cc_final: 0.8793 (tmm)
REVERT: E  584 PHE cc_start: 0.9022 (m-80) cc_final: 0.8735 (m-80)
REVERT: E  591 LEU cc_start: 0.9332 (tp) cc_final: 0.8978 (tp)
REVERT: E 1020 GLN cc_start: 0.9156 (mm-40) cc_final: 0.8817 (tt0)
REVERT: E 1034 LEU cc_start: 0.9343 (tp) cc_final: 0.9128 (tt)
REVERT: E 1188 ASP cc_start: 0.8658 (t70) cc_final: 0.8429 (t0)
REVERT: E 1191 GLN cc_start: 0.8992 (tm-30) cc_final: 0.8701 (tp-100)
REVERT: E 1229 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7874 (mp0)
REVERT: E 1290 MET cc_start: 0.8958 (tpp) cc_final: 0.8340 (mmp)
REVERT: E 1305 MET cc_start: 0.9341 (tpt) cc_final: 0.9100 (tpp)
REVERT: E 1496 PHE cc_start: 0.8602 (m-10) cc_final: 0.8307 (m-80)
  outliers start: 149
  outliers final: 35
  residues processed: 625
  average time/residue: 0.1497
  time to fit residues: 144.3084
Evaluate side-chains
  397 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 349
  time to evaluate  : 0.557 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LYS
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue  116 SER
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  224 THR
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  336 THR
Chi-restraints excluded: chain A residue  344 CYS
Chi-restraints excluded: chain B residue   64 VAL
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  179 GLU
Chi-restraints excluded: chain B residue  202 VAL
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  224 THR
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  244 VAL
Chi-restraints excluded: chain B residue  302 THR
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  332 LYS
Chi-restraints excluded: chain B residue  336 THR
Chi-restraints excluded: chain C residue   39 LYS
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue   64 VAL
Chi-restraints excluded: chain C residue   71 THR
Chi-restraints excluded: chain C residue  111 VAL
Chi-restraints excluded: chain C residue  116 SER
Chi-restraints excluded: chain C residue  138 VAL
Chi-restraints excluded: chain C residue  155 VAL
Chi-restraints excluded: chain C residue  223 THR
Chi-restraints excluded: chain C residue  224 THR
Chi-restraints excluded: chain C residue  344 CYS
Chi-restraints excluded: chain D residue   64 VAL
Chi-restraints excluded: chain D residue   77 MET
Chi-restraints excluded: chain D residue  116 SER
Chi-restraints excluded: chain D residue  138 VAL
Chi-restraints excluded: chain D residue  202 VAL
Chi-restraints excluded: chain D residue  220 VAL
Chi-restraints excluded: chain D residue  251 LEU
Chi-restraints excluded: chain D residue  316 VAL
Chi-restraints excluded: chain D residue  344 CYS
Chi-restraints excluded: chain E residue  770 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 268
   random chunks:
   chunk 197 optimal weight:    3.9990
   chunk 215 optimal weight:    9.9990
   chunk 20 optimal weight:    0.9980
   chunk 132 optimal weight:    1.9990
   chunk 261 optimal weight:   10.0000
   chunk 248 optimal weight:    9.9990
   chunk 207 optimal weight:    5.9990
   chunk 155 optimal weight:    0.8980
   chunk 244 optimal weight:    2.9990
   chunk 183 optimal weight:    0.9990
   chunk 111 optimal weight:    4.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 160 ASN
** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 277 HIS
B 279 GLN
** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 160 ASN
C 175 HIS
C 277 HIS
C 278 HIS
** D 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 277 HIS
E 106 HIS
E 167 GLN
E 407 ASN
E 438 ASN
E 499 GLN
E 715 GLN
E 923 GLN
E 933 ASN
** E1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E1308 GLN
E1348 GLN
E1364 HIS
E1439 ASN
E1486 GLN
E1488 GLN

Total number of N/Q/H flips: 22

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.064711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.053953 restraints weight = 91028.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.055626 restraints weight = 45272.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.056755 restraints weight = 28120.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.057510 restraints weight = 20096.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.058047 restraints weight = 15850.934|
|-----------------------------------------------------------------------------|
r_work (final): 0.3021
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8411
moved from start:          0.2333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.153  21616  Z= 0.171
  Angle     :  0.756  52.562  29375  Z= 0.387
  Chirality :  0.044   0.238   3474
  Planarity :  0.005   0.060   3650
  Dihedral  :  7.893 112.142   2979
  Min Nonbonded Distance : 1.949

Molprobity Statistics.
  All-atom Clashscore : 11.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 17.27 %
    Favored  : 79.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.59 (0.15), residues: 2663
  helix: -0.36 (0.13), residues: 1362
  sheet: -1.42 (0.31), residues: 242
  loop : -1.78 (0.17), residues: 1059

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 266 
 TYR   0.013   0.001   TYR E 379 
 PHE   0.026   0.002   PHE E1503 
 TRP   0.009   0.001   TRP C 311 
 HIS   0.006   0.001   HIS E 327 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 (21611)
  covalent geometry    : angle       0.66881 (29365)
  SS BOND              : bond        0.00909 (    5)
  SS BOND              : angle      19.15851 (   10)
  hydrogen bonds       : bond        0.04534 ( 1148)
  hydrogen bonds       : angle       4.75324 ( 3384)

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

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

  5326 Ramachandran restraints generated.
    2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5326 Ramachandran restraints generated.
    2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  446 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 77
    poor density    : 369
  time to evaluate  : 0.896 
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: A   59 VAL cc_start: 0.9302 (m) cc_final: 0.9000 (t)
REVERT: A   66 LEU cc_start: 0.9074 (mt) cc_final: 0.8771 (mt)
REVERT: A   83 TRP cc_start: 0.9577 (m-10) cc_final: 0.9147 (m-90)
REVERT: A  141 GLU cc_start: 0.8690 (tp30) cc_final: 0.8256 (tp30)
REVERT: A  163 MET cc_start: 0.9559 (mmm) cc_final: 0.9257 (mmm)
REVERT: A  170 LYS cc_start: 0.9498 (tptp) cc_final: 0.9085 (tptt)
REVERT: A  268 TYR cc_start: 0.8988 (t80) cc_final: 0.8723 (t80)
REVERT: A  330 TYR cc_start: 0.8758 (m-80) cc_final: 0.8528 (m-80)
REVERT: B   57 GLN cc_start: 0.8620 (tt0) cc_final: 0.8237 (tp40)
REVERT: B  160 ASN cc_start: 0.9201 (m-40) cc_final: 0.8926 (m-40)
REVERT: B  179 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8496 (mt-10)
REVERT: B  185 LYS cc_start: 0.9203 (ttmm) cc_final: 0.8600 (tptp)
REVERT: B  231 VAL cc_start: 0.9061 (OUTLIER) cc_final: 0.8859 (m)
REVERT: B  240 MET cc_start: 0.9294 (tmm) cc_final: 0.8725 (tmm)
REVERT: B  296 ILE cc_start: 0.9170 (mp) cc_final: 0.8937 (tt)
REVERT: B  330 TYR cc_start: 0.8608 (m-80) cc_final: 0.7869 (m-80)
REVERT: C   39 LYS cc_start: 0.9294 (mmmm) cc_final: 0.8759 (tmtt)
REVERT: C   47 LYS cc_start: 0.8241 (tppt) cc_final: 0.7893 (tppt)
REVERT: C   63 LEU cc_start: 0.9637 (tp) cc_final: 0.9321 (tt)
REVERT: C   65 ASP cc_start: 0.8387 (t0) cc_final: 0.8045 (t0)
REVERT: C   84 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.9011 (tt)
REVERT: C  160 ASN cc_start: 0.9205 (m-40) cc_final: 0.8760 (m110)
REVERT: C  169 MET cc_start: 0.8986 (ttm) cc_final: 0.8725 (ttm)
REVERT: C  170 LYS cc_start: 0.9444 (tptm) cc_final: 0.9203 (tttp)
REVERT: C  179 GLU cc_start: 0.8485 (mp0) cc_final: 0.8064 (mp0)
REVERT: C  185 LYS cc_start: 0.9385 (mmtm) cc_final: 0.9043 (mmtm)
REVERT: C  214 THR cc_start: 0.9420 (OUTLIER) cc_final: 0.8690 (t)
REVERT: C  240 MET cc_start: 0.8574 (tmm) cc_final: 0.8246 (tmm)
REVERT: C  247 ASN cc_start: 0.8712 (p0) cc_final: 0.8362 (p0)
REVERT: C  279 GLN cc_start: 0.8971 (tp40) cc_final: 0.8128 (tm-30)
REVERT: D   65 ASP cc_start: 0.8969 (t0) cc_final: 0.8653 (t70)
REVERT: D   77 MET cc_start: 0.8826 (OUTLIER) cc_final: 0.8300 (tpp)
REVERT: D  163 MET cc_start: 0.9188 (mmm) cc_final: 0.8824 (mmm)
REVERT: D  170 LYS cc_start: 0.9139 (tptp) cc_final: 0.8906 (tptt)
REVERT: D  179 GLU cc_start: 0.8142 (tp30) cc_final: 0.7887 (tp30)
REVERT: D  262 ASP cc_start: 0.9151 (t0) cc_final: 0.8899 (t70)
REVERT: D  293 THR cc_start: 0.9299 (p) cc_final: 0.8921 (p)
REVERT: D  335 ASN cc_start: 0.8591 (t0) cc_final: 0.8372 (t0)
REVERT: E   30 ASP cc_start: 0.8784 (m-30) cc_final: 0.8459 (m-30)
REVERT: E  116 MET cc_start: 0.9416 (mmm) cc_final: 0.9069 (mmm)
REVERT: E  153 ILE cc_start: 0.9506 (mm) cc_final: 0.9242 (mm)
REVERT: E  442 MET cc_start: 0.8733 (tpt) cc_final: 0.8485 (tpt)
REVERT: E  508 LYS cc_start: 0.9524 (tttt) cc_final: 0.9308 (ttmm)
REVERT: E  547 MET cc_start: 0.8754 (tmm) cc_final: 0.8444 (tmm)
REVERT: E  584 PHE cc_start: 0.8952 (m-80) cc_final: 0.8689 (m-80)
REVERT: E  790 PHE cc_start: 0.8636 (t80) cc_final: 0.8404 (t80)
REVERT: E 1188 ASP cc_start: 0.8573 (t70) cc_final: 0.8153 (t0)
REVERT: E 1191 GLN cc_start: 0.9014 (tm-30) cc_final: 0.8709 (tp-100)
REVERT: E 1290 MET cc_start: 0.8955 (tpp) cc_final: 0.8622 (mmp)
REVERT: E 1305 MET cc_start: 0.9393 (tpt) cc_final: 0.9180 (tpp)
REVERT: E 1395 MET cc_start: 0.8745 (mmm) cc_final: 0.8534 (mmm)
REVERT: E 1402 HIS cc_start: 0.8225 (m-70) cc_final: 0.7444 (t-170)
REVERT: E 1404 ILE cc_start: 0.9053 (mt) cc_final: 0.8604 (pt)
  outliers start: 77
  outliers final: 43
  residues processed: 428
  average time/residue: 0.1433
  time to fit residues: 98.1012
Evaluate side-chains
  358 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 310
  time to evaluate  : 0.941 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 ILE
Chi-restraints excluded: chain A residue  159 ILE
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  336 THR
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  179 GLU
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  244 VAL
Chi-restraints excluded: chain B residue  291 VAL
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  336 THR
Chi-restraints excluded: chain B residue  345 THR
Chi-restraints excluded: chain C residue   49 ILE
Chi-restraints excluded: chain C residue   71 THR
Chi-restraints excluded: chain C residue   80 LEU
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  111 VAL
Chi-restraints excluded: chain C residue  214 THR
Chi-restraints excluded: chain C residue  328 VAL
Chi-restraints excluded: chain C residue  332 LYS
Chi-restraints excluded: chain D residue   77 MET
Chi-restraints excluded: chain D residue   80 LEU
Chi-restraints excluded: chain D residue  220 VAL
Chi-restraints excluded: chain D residue  224 THR
Chi-restraints excluded: chain D residue  230 VAL
Chi-restraints excluded: chain D residue  302 THR
Chi-restraints excluded: chain D residue  305 LEU
Chi-restraints excluded: chain D residue  316 VAL
Chi-restraints excluded: chain D residue  344 CYS
Chi-restraints excluded: chain E residue   32 LEU
Chi-restraints excluded: chain E residue   94 ILE
Chi-restraints excluded: chain E residue  175 LEU
Chi-restraints excluded: chain E residue  190 VAL
Chi-restraints excluded: chain E residue  301 VAL
Chi-restraints excluded: chain E residue  306 PHE
Chi-restraints excluded: chain E residue  429 LEU
Chi-restraints excluded: chain E residue  439 LEU
Chi-restraints excluded: chain E residue  474 VAL
Chi-restraints excluded: chain E residue  770 VAL
Chi-restraints excluded: chain E residue  884 VAL
Chi-restraints excluded: chain E residue 1016 LEU
Chi-restraints excluded: chain E residue 1168 LEU
Chi-restraints excluded: chain E residue 1198 LEU
Chi-restraints excluded: chain E residue 1228 LEU
Chi-restraints excluded: chain E residue 1260 VAL
Chi-restraints excluded: chain E residue 1362 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 268
   random chunks:
   chunk 264 optimal weight:    0.9980
   chunk 132 optimal weight:    0.0980
   chunk 106 optimal weight:    3.9990
   chunk 148 optimal weight:    4.9990
   chunk 85 optimal weight:    6.9990
   chunk 59 optimal weight:    9.9990
   chunk 30 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 171 optimal weight:    7.9990
   chunk 38 optimal weight:    2.9990
   chunk 267 optimal weight:    6.9990
   overall best weight:    1.4184

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

Flipped N/Q/H residues before XYZ refinement:
** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 242 ASN
C 153 ASN
C 173 GLN
C 279 GLN
D  48 ASN
D 128 GLN
** D 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 475 GLN
** E1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.064568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2898 r_free = 0.2898 target = 0.053715 restraints weight = 92250.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.055373 restraints weight = 46182.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.056501 restraints weight = 28818.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.057239 restraints weight = 20622.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.057791 restraints weight = 16318.416|
|-----------------------------------------------------------------------------|
r_work (final): 0.3004
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8421
moved from start:          0.2897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.147  21616  Z= 0.154
  Angle     :  0.723  52.352  29375  Z= 0.363
  Chirality :  0.043   0.195   3474
  Planarity :  0.004   0.065   3650
  Dihedral  :  6.887  88.785   2931
  Min Nonbonded Distance : 1.999

Molprobity Statistics.
  All-atom Clashscore : 11.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 19.14 %
    Favored  : 77.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.80 (0.16), residues: 2663
  helix:  0.35 (0.14), residues: 1361
  sheet: -0.74 (0.31), residues: 254
  loop : -1.60 (0.18), residues: 1048

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG E1579 
 TYR   0.014   0.001   TYR E1287 
 PHE   0.032   0.001   PHE E1496 
 TRP   0.013   0.001   TRP B  83 
 HIS   0.006   0.001   HIS E  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 (21611)
  covalent geometry    : angle       0.63153 (29365)
  SS BOND              : bond        0.01809 (    5)
  SS BOND              : angle      19.05548 (   10)
  hydrogen bonds       : bond        0.04136 ( 1148)
  hydrogen bonds       : angle       4.43326 ( 3384)

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

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

  5326 Ramachandran restraints generated.
    2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5326 Ramachandran restraints generated.
    2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  430 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 83
    poor density    : 347
  time to evaluate  : 0.882 
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: A   83 TRP cc_start: 0.9578 (m-10) cc_final: 0.8973 (m-90)
REVERT: A  163 MET cc_start: 0.9561 (mmm) cc_final: 0.9252 (mmm)
REVERT: A  268 TYR cc_start: 0.9084 (t80) cc_final: 0.8797 (t80)
REVERT: A  292 GLU cc_start: 0.8410 (tm-30) cc_final: 0.8154 (tm-30)
REVERT: A  332 LYS cc_start: 0.9398 (pttt) cc_final: 0.9112 (ptpp)
REVERT: B   57 GLN cc_start: 0.8724 (tt0) cc_final: 0.8357 (tp40)
REVERT: B  160 ASN cc_start: 0.9113 (m-40) cc_final: 0.8829 (m110)
REVERT: B  169 MET cc_start: 0.9021 (ttm) cc_final: 0.8780 (ttm)
REVERT: B  179 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8440 (mt-10)
REVERT: B  185 LYS cc_start: 0.9289 (ttmm) cc_final: 0.8879 (tptt)
REVERT: B  231 VAL cc_start: 0.9070 (OUTLIER) cc_final: 0.8857 (m)
REVERT: B  240 MET cc_start: 0.9257 (tmm) cc_final: 0.8504 (tmm)
REVERT: C   39 LYS cc_start: 0.9295 (mmmm) cc_final: 0.8762 (tmtt)
REVERT: C   47 LYS cc_start: 0.8283 (tppt) cc_final: 0.7949 (tppt)
REVERT: C   63 LEU cc_start: 0.9621 (tp) cc_final: 0.9382 (tt)
REVERT: C   65 ASP cc_start: 0.8334 (t0) cc_final: 0.7976 (t0)
REVERT: C   84 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8958 (tt)
REVERT: C  169 MET cc_start: 0.9037 (ttm) cc_final: 0.8707 (ttm)
REVERT: C  170 LYS cc_start: 0.9472 (tptm) cc_final: 0.9228 (tttp)
REVERT: C  179 GLU cc_start: 0.8621 (mp0) cc_final: 0.8023 (mp0)
REVERT: C  185 LYS cc_start: 0.9371 (mmtm) cc_final: 0.8990 (mmtm)
REVERT: C  214 THR cc_start: 0.9367 (OUTLIER) cc_final: 0.8803 (t)
REVERT: C  240 MET cc_start: 0.8245 (tmm) cc_final: 0.7884 (tmm)
REVERT: C  332 LYS cc_start: 0.9288 (OUTLIER) cc_final: 0.9035 (pttp)
REVERT: C  349 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.9203 (mm)
REVERT: D   55 PHE cc_start: 0.8921 (OUTLIER) cc_final: 0.8649 (t80)
REVERT: D   65 ASP cc_start: 0.8991 (t0) cc_final: 0.8646 (t70)
REVERT: D   88 MET cc_start: 0.8466 (tmm) cc_final: 0.7911 (tmm)
REVERT: D  163 MET cc_start: 0.9142 (mmm) cc_final: 0.8741 (mmm)
REVERT: D  170 LYS cc_start: 0.9223 (tptp) cc_final: 0.8663 (tptt)
REVERT: D  179 GLU cc_start: 0.8302 (tp30) cc_final: 0.7789 (tp30)
REVERT: D  262 ASP cc_start: 0.9081 (t0) cc_final: 0.8768 (t70)
REVERT: D  335 ASN cc_start: 0.8570 (t0) cc_final: 0.8224 (t0)
REVERT: E   30 ASP cc_start: 0.8835 (m-30) cc_final: 0.8556 (m-30)
REVERT: E   83 LEU cc_start: 0.9535 (mt) cc_final: 0.9304 (mt)
REVERT: E  108 TYR cc_start: 0.8524 (OUTLIER) cc_final: 0.8011 (m-10)
REVERT: E  153 ILE cc_start: 0.9507 (mm) cc_final: 0.9195 (mm)
REVERT: E  226 LEU cc_start: 0.8642 (tt) cc_final: 0.8362 (tp)
REVERT: E  311 ASP cc_start: 0.8919 (OUTLIER) cc_final: 0.8535 (p0)
REVERT: E  442 MET cc_start: 0.8787 (tpt) cc_final: 0.8582 (tpt)
REVERT: E  508 LYS cc_start: 0.9500 (tttt) cc_final: 0.9237 (ttmm)
REVERT: E  584 PHE cc_start: 0.8931 (m-80) cc_final: 0.8628 (m-80)
REVERT: E  790 PHE cc_start: 0.8640 (t80) cc_final: 0.8353 (t80)
REVERT: E 1080 LEU cc_start: 0.9290 (tp) cc_final: 0.9054 (mt)
REVERT: E 1143 LEU cc_start: 0.9643 (tp) cc_final: 0.9230 (pp)
REVERT: E 1188 ASP cc_start: 0.8637 (t70) cc_final: 0.8314 (t0)
REVERT: E 1191 GLN cc_start: 0.9010 (tm-30) cc_final: 0.8709 (tp-100)
REVERT: E 1290 MET cc_start: 0.8939 (tpp) cc_final: 0.8600 (mmp)
REVERT: E 1402 HIS cc_start: 0.8166 (m-70) cc_final: 0.7856 (t-170)
REVERT: E 1505 MET cc_start: 0.8668 (mpp) cc_final: 0.8019 (mpp)
  outliers start: 83
  outliers final: 51
  residues processed: 406
  average time/residue: 0.1427
  time to fit residues: 93.3965
Evaluate side-chains
  366 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 307
  time to evaluate  : 0.776 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue  169 MET
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  328 VAL
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  197 CYS
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  244 VAL
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  336 THR
Chi-restraints excluded: chain C residue   42 CYS
Chi-restraints excluded: chain C residue   49 ILE
Chi-restraints excluded: chain C residue   80 LEU
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  146 ILE
Chi-restraints excluded: chain C residue  153 ASN
Chi-restraints excluded: chain C residue  214 THR
Chi-restraints excluded: chain C residue  328 VAL
Chi-restraints excluded: chain C residue  332 LYS
Chi-restraints excluded: chain C residue  349 LEU
Chi-restraints excluded: chain D residue   55 PHE
Chi-restraints excluded: chain D residue   80 LEU
Chi-restraints excluded: chain D residue  138 VAL
Chi-restraints excluded: chain D residue  142 CYS
Chi-restraints excluded: chain D residue  220 VAL
Chi-restraints excluded: chain D residue  230 VAL
Chi-restraints excluded: chain D residue  273 SER
Chi-restraints excluded: chain D residue  302 THR
Chi-restraints excluded: chain D residue  316 VAL
Chi-restraints excluded: chain D residue  336 THR
Chi-restraints excluded: chain D residue  344 CYS
Chi-restraints excluded: chain D residue  349 LEU
Chi-restraints excluded: chain E residue   32 LEU
Chi-restraints excluded: chain E residue   35 VAL
Chi-restraints excluded: chain E residue  108 TYR
Chi-restraints excluded: chain E residue  109 MET
Chi-restraints excluded: chain E residue  175 LEU
Chi-restraints excluded: chain E residue  190 VAL
Chi-restraints excluded: chain E residue  248 LEU
Chi-restraints excluded: chain E residue  311 ASP
Chi-restraints excluded: chain E residue  353 LEU
Chi-restraints excluded: chain E residue  365 LEU
Chi-restraints excluded: chain E residue  429 LEU
Chi-restraints excluded: chain E residue  439 LEU
Chi-restraints excluded: chain E residue  474 VAL
Chi-restraints excluded: chain E residue  770 VAL
Chi-restraints excluded: chain E residue  884 VAL
Chi-restraints excluded: chain E residue 1168 LEU
Chi-restraints excluded: chain E residue 1228 LEU
Chi-restraints excluded: chain E residue 1239 LEU
Chi-restraints excluded: chain E residue 1258 CYS
Chi-restraints excluded: chain E residue 1260 VAL
Chi-restraints excluded: chain E residue 1362 LEU
Chi-restraints excluded: chain E residue 1532 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 268
   random chunks:
   chunk 238 optimal weight:    8.9990
   chunk 67 optimal weight:    4.9990
   chunk 259 optimal weight:    2.9990
   chunk 201 optimal weight:    7.9990
   chunk 266 optimal weight:    3.9990
   chunk 171 optimal weight:    1.9990
   chunk 74 optimal weight:    4.9990
   chunk 168 optimal weight:    6.9990
   chunk 183 optimal weight:    6.9990
   chunk 51 optimal weight:    6.9990
   chunk 54 optimal weight:    2.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 128 GLN
** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 276 HIS
A 278 HIS
** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  70 HIS
** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 313 GLN
** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 153 ASN
D 259 HIS
E 106 HIS
** E 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 889 HIS
** E1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E1346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.061683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2841 r_free = 0.2841 target = 0.050877 restraints weight = 94346.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.052512 restraints weight = 47308.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2918 r_free = 0.2918 target = 0.053617 restraints weight = 29447.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.054372 restraints weight = 21069.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.054846 restraints weight = 16589.119|
|-----------------------------------------------------------------------------|
r_work (final): 0.2947
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8512
moved from start:          0.3465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.152  21616  Z= 0.277
  Angle     :  0.801  52.034  29375  Z= 0.406
  Chirality :  0.045   0.173   3474
  Planarity :  0.004   0.061   3650
  Dihedral  :  6.871  97.864   2922
  Min Nonbonded Distance : 1.882

Molprobity Statistics.
  All-atom Clashscore : 14.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 20.44 %
    Favored  : 74.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.48 (0.16), residues: 2663
  helix:  0.53 (0.14), residues: 1375
  sheet: -0.63 (0.32), residues: 233
  loop : -1.32 (0.19), residues: 1055

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG E1579 
 TYR   0.015   0.002   TYR C 268 
 PHE   0.024   0.002   PHE E1496 
 TRP   0.024   0.002   TRP A 311 
 HIS   0.005   0.001   HIS E  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00594 (21611)
  covalent geometry    : angle       0.71983 (29365)
  SS BOND              : bond        0.01933 (    5)
  SS BOND              : angle      19.04051 (   10)
  hydrogen bonds       : bond        0.04440 ( 1148)
  hydrogen bonds       : angle       4.56464 ( 3384)

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

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

  5326 Ramachandran restraints generated.
    2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5326 Ramachandran restraints generated.
    2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  416 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 116
    poor density    : 300
  time to evaluate  : 0.840 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 TRP cc_start: 0.9644 (m-10) cc_final: 0.9417 (m-10)
REVERT: B  160 ASN cc_start: 0.9098 (m-40) cc_final: 0.8821 (m-40)
REVERT: B  169 MET cc_start: 0.9079 (ttm) cc_final: 0.8771 (ttm)
REVERT: B  185 LYS cc_start: 0.9344 (ttmm) cc_final: 0.8960 (tptp)
REVERT: B  231 VAL cc_start: 0.9094 (OUTLIER) cc_final: 0.8876 (m)
REVERT: B  240 MET cc_start: 0.9184 (tmm) cc_final: 0.8262 (tmm)
REVERT: B  296 ILE cc_start: 0.9349 (mp) cc_final: 0.8821 (tt)
REVERT: C   39 LYS cc_start: 0.9342 (mmmm) cc_final: 0.8840 (tmtt)
REVERT: C   65 ASP cc_start: 0.8672 (t0) cc_final: 0.8125 (t0)
REVERT: C   84 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.9058 (tt)
REVERT: C  160 ASN cc_start: 0.9216 (m-40) cc_final: 0.8836 (m-40)
REVERT: C  169 MET cc_start: 0.9060 (ttm) cc_final: 0.8773 (ttm)
REVERT: C  170 LYS cc_start: 0.9545 (tptm) cc_final: 0.9289 (tttm)
REVERT: C  179 GLU cc_start: 0.8626 (mp0) cc_final: 0.8080 (mp0)
REVERT: C  204 ASP cc_start: 0.8415 (t0) cc_final: 0.8120 (t0)
REVERT: C  214 THR cc_start: 0.9417 (OUTLIER) cc_final: 0.8450 (t)
REVERT: C  247 ASN cc_start: 0.8757 (p0) cc_final: 0.8145 (p0)
REVERT: C  332 LYS cc_start: 0.9216 (OUTLIER) cc_final: 0.8977 (pttp)
REVERT: D   55 PHE cc_start: 0.9039 (OUTLIER) cc_final: 0.8684 (t80)
REVERT: D   56 LEU cc_start: 0.9352 (tp) cc_final: 0.9016 (tt)
REVERT: D   65 ASP cc_start: 0.9012 (t0) cc_final: 0.8797 (t70)
REVERT: D   88 MET cc_start: 0.8655 (tmm) cc_final: 0.7910 (tmm)
REVERT: D  163 MET cc_start: 0.9194 (mmm) cc_final: 0.8776 (mmm)
REVERT: D  179 GLU cc_start: 0.8297 (tp30) cc_final: 0.7893 (tp30)
REVERT: D  262 ASP cc_start: 0.9034 (t0) cc_final: 0.8697 (t70)
REVERT: E   30 ASP cc_start: 0.8903 (m-30) cc_final: 0.8669 (m-30)
REVERT: E   73 ASN cc_start: 0.9230 (OUTLIER) cc_final: 0.8814 (p0)
REVERT: E  108 TYR cc_start: 0.8567 (OUTLIER) cc_final: 0.7806 (m-80)
REVERT: E  179 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8831 (tt)
REVERT: E  226 LEU cc_start: 0.8875 (tt) cc_final: 0.8593 (tp)
REVERT: E  309 LEU cc_start: 0.9628 (OUTLIER) cc_final: 0.9427 (tp)
REVERT: E  442 MET cc_start: 0.8822 (tpt) cc_final: 0.8573 (tpt)
REVERT: E  503 MET cc_start: 0.9266 (tpt) cc_final: 0.9003 (tpt)
REVERT: E  584 PHE cc_start: 0.8974 (m-80) cc_final: 0.8746 (m-80)
REVERT: E  611 LEU cc_start: 0.9646 (OUTLIER) cc_final: 0.9338 (mm)
REVERT: E  790 PHE cc_start: 0.8656 (t80) cc_final: 0.8425 (t80)
REVERT: E 1080 LEU cc_start: 0.9417 (tp) cc_final: 0.9177 (mt)
REVERT: E 1110 MET cc_start: 0.8636 (mtp) cc_final: 0.8341 (mmm)
REVERT: E 1129 CYS cc_start: 0.8438 (OUTLIER) cc_final: 0.8130 (p)
REVERT: E 1191 GLN cc_start: 0.9089 (tm-30) cc_final: 0.8819 (tp-100)
REVERT: E 1239 LEU cc_start: 0.9752 (OUTLIER) cc_final: 0.9535 (tp)
REVERT: E 1402 HIS cc_start: 0.8138 (m-70) cc_final: 0.7936 (t-170)
REVERT: E 1539 ARG cc_start: 0.7665 (mtt90) cc_final: 0.7425 (mtt90)
  outliers start: 116
  outliers final: 71
  residues processed: 393
  average time/residue: 0.1338
  time to fit residues: 85.1245
Evaluate side-chains
  360 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 83
    poor density    : 277
  time to evaluate  : 0.768 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   59 VAL
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue   88 MET
Chi-restraints excluded: chain A residue  169 MET
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  284 ILE
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  328 VAL
Chi-restraints excluded: chain A residue  336 THR
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  138 VAL
Chi-restraints excluded: chain B residue  197 CYS
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  244 VAL
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  335 ASN
Chi-restraints excluded: chain B residue  345 THR
Chi-restraints excluded: chain C residue   42 CYS
Chi-restraints excluded: chain C residue   80 LEU
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  115 HIS
Chi-restraints excluded: chain C residue  131 ILE
Chi-restraints excluded: chain C residue  139 THR
Chi-restraints excluded: chain C residue  146 ILE
Chi-restraints excluded: chain C residue  214 THR
Chi-restraints excluded: chain C residue  328 VAL
Chi-restraints excluded: chain C residue  332 LYS
Chi-restraints excluded: chain D residue   55 PHE
Chi-restraints excluded: chain D residue   80 LEU
Chi-restraints excluded: chain D residue   84 LEU
Chi-restraints excluded: chain D residue  138 VAL
Chi-restraints excluded: chain D residue  142 CYS
Chi-restraints excluded: chain D residue  220 VAL
Chi-restraints excluded: chain D residue  224 THR
Chi-restraints excluded: chain D residue  230 VAL
Chi-restraints excluded: chain D residue  236 VAL
Chi-restraints excluded: chain D residue  273 SER
Chi-restraints excluded: chain D residue  302 THR
Chi-restraints excluded: chain D residue  305 LEU
Chi-restraints excluded: chain D residue  316 VAL
Chi-restraints excluded: chain D residue  344 CYS
Chi-restraints excluded: chain D residue  349 LEU
Chi-restraints excluded: chain E residue   12 HIS
Chi-restraints excluded: chain E residue   32 LEU
Chi-restraints excluded: chain E residue   35 VAL
Chi-restraints excluded: chain E residue   73 ASN
Chi-restraints excluded: chain E residue  108 TYR
Chi-restraints excluded: chain E residue  109 MET
Chi-restraints excluded: chain E residue  172 LEU
Chi-restraints excluded: chain E residue  179 LEU
Chi-restraints excluded: chain E residue  190 VAL
Chi-restraints excluded: chain E residue  248 LEU
Chi-restraints excluded: chain E residue  309 LEU
Chi-restraints excluded: chain E residue  353 LEU
Chi-restraints excluded: chain E residue  365 LEU
Chi-restraints excluded: chain E residue  429 LEU
Chi-restraints excluded: chain E residue  439 LEU
Chi-restraints excluded: chain E residue  474 VAL
Chi-restraints excluded: chain E residue  611 LEU
Chi-restraints excluded: chain E residue  702 ILE
Chi-restraints excluded: chain E residue  704 ILE
Chi-restraints excluded: chain E residue  770 VAL
Chi-restraints excluded: chain E residue  884 VAL
Chi-restraints excluded: chain E residue 1016 LEU
Chi-restraints excluded: chain E residue 1027 LEU
Chi-restraints excluded: chain E residue 1071 LEU
Chi-restraints excluded: chain E residue 1129 CYS
Chi-restraints excluded: chain E residue 1168 LEU
Chi-restraints excluded: chain E residue 1198 LEU
Chi-restraints excluded: chain E residue 1228 LEU
Chi-restraints excluded: chain E residue 1239 LEU
Chi-restraints excluded: chain E residue 1258 CYS
Chi-restraints excluded: chain E residue 1260 VAL
Chi-restraints excluded: chain E residue 1261 LEU
Chi-restraints excluded: chain E residue 1295 LEU
Chi-restraints excluded: chain E residue 1375 ILE
Chi-restraints excluded: chain E residue 1455 LEU
Chi-restraints excluded: chain E residue 1497 VAL
Chi-restraints excluded: chain E residue 1532 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 268
   random chunks:
   chunk 65 optimal weight:    3.9990
   chunk 183 optimal weight:    2.9990
   chunk 238 optimal weight:    3.9990
   chunk 134 optimal weight:    7.9990
   chunk 241 optimal weight:    5.9990
   chunk 190 optimal weight:    5.9990
   chunk 198 optimal weight:    5.9990
   chunk 250 optimal weight:   10.0000
   chunk 207 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9990
   chunk 57 optimal weight:    1.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 259 HIS
C 153 ASN
** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 153 ASN
** E  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E1197 GLN
** E1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E1346 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.063075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.052220 restraints weight = 92386.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.053870 restraints weight = 46250.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.054982 restraints weight = 28717.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.055746 restraints weight = 20498.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.056224 restraints weight = 16083.560|
|-----------------------------------------------------------------------------|
r_work (final): 0.3000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8483
moved from start:          0.3674

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.150  21616  Z= 0.193
  Angle     :  0.743  52.142  29375  Z= 0.372
  Chirality :  0.044   0.163   3474
  Planarity :  0.004   0.068   3650
  Dihedral  :  6.671 102.142   2921
  Min Nonbonded Distance : 1.947

Molprobity Statistics.
  All-atom Clashscore : 13.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 22.22 %
    Favored  : 72.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.25 (0.16), residues: 2663
  helix:  0.71 (0.14), residues: 1373
  sheet: -0.41 (0.32), residues: 238
  loop : -1.22 (0.19), residues: 1052

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E1579 
 TYR   0.018   0.001   TYR C 268 
 PHE   0.027   0.001   PHE E 133 
 TRP   0.016   0.001   TRP A 311 
 HIS   0.005   0.001   HIS E1024 

Details of bonding type rmsd
  covalent geometry    : bond        0.00424 (21611)
  covalent geometry    : angle       0.65509 (29365)
  SS BOND              : bond        0.01888 (    5)
  SS BOND              : angle      19.04133 (   10)
  hydrogen bonds       : bond        0.04156 ( 1148)
  hydrogen bonds       : angle       4.40811 ( 3384)

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

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

  5326 Ramachandran restraints generated.
    2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5326 Ramachandran restraints generated.
    2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  434 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 116
    poor density    : 318
  time to evaluate  : 0.996 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 LEU cc_start: 0.9365 (mt) cc_final: 0.8983 (pp)
REVERT: A  170 LYS cc_start: 0.9425 (tptt) cc_final: 0.9203 (tptt)
REVERT: A  292 GLU cc_start: 0.8453 (tm-30) cc_final: 0.8241 (tm-30)
REVERT: B   47 LYS cc_start: 0.9272 (tppt) cc_final: 0.9066 (tppt)
REVERT: B  160 ASN cc_start: 0.9125 (m-40) cc_final: 0.8831 (m110)
REVERT: B  169 MET cc_start: 0.9055 (ttm) cc_final: 0.8735 (ttm)
REVERT: B  185 LYS cc_start: 0.9344 (ttmm) cc_final: 0.8942 (tptt)
REVERT: B  231 VAL cc_start: 0.9102 (OUTLIER) cc_final: 0.8884 (m)
REVERT: B  240 MET cc_start: 0.9195 (tmm) cc_final: 0.8354 (tmm)
REVERT: B  296 ILE cc_start: 0.9361 (mp) cc_final: 0.8892 (tt)
REVERT: C   39 LYS cc_start: 0.9257 (mmmm) cc_final: 0.8765 (tmtt)
REVERT: C   65 ASP cc_start: 0.8420 (t0) cc_final: 0.7994 (t0)
REVERT: C   84 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9137 (tt)
REVERT: C  160 ASN cc_start: 0.9191 (m-40) cc_final: 0.8832 (m110)
REVERT: C  169 MET cc_start: 0.9066 (ttm) cc_final: 0.8771 (ttm)
REVERT: C  170 LYS cc_start: 0.9515 (tptm) cc_final: 0.9283 (tttm)
REVERT: C  179 GLU cc_start: 0.8593 (mp0) cc_final: 0.8312 (mp0)
REVERT: C  214 THR cc_start: 0.9402 (OUTLIER) cc_final: 0.8407 (t)
REVERT: C  240 MET cc_start: 0.7994 (tmm) cc_final: 0.7033 (tmm)
REVERT: C  247 ASN cc_start: 0.8711 (p0) cc_final: 0.8255 (p0)
REVERT: D   55 PHE cc_start: 0.9045 (OUTLIER) cc_final: 0.8682 (t80)
REVERT: D   56 LEU cc_start: 0.9353 (tp) cc_final: 0.9048 (tt)
REVERT: D   65 ASP cc_start: 0.8961 (t0) cc_final: 0.8706 (t70)
REVERT: D   88 MET cc_start: 0.8665 (tmm) cc_final: 0.7945 (tmm)
REVERT: D  137 MET cc_start: 0.8825 (tmm) cc_final: 0.8534 (tmm)
REVERT: D  163 MET cc_start: 0.9243 (mmm) cc_final: 0.8875 (mmm)
REVERT: D  170 LYS cc_start: 0.9144 (tptt) cc_final: 0.8532 (tptm)
REVERT: D  262 ASP cc_start: 0.9011 (t0) cc_final: 0.8788 (t70)
REVERT: D  292 GLU cc_start: 0.8346 (tm-30) cc_final: 0.8096 (tm-30)
REVERT: E   30 ASP cc_start: 0.8880 (m-30) cc_final: 0.8624 (m-30)
REVERT: E   73 ASN cc_start: 0.9182 (OUTLIER) cc_final: 0.8846 (p0)
REVERT: E  108 TYR cc_start: 0.8478 (OUTLIER) cc_final: 0.7856 (m-80)
REVERT: E  226 LEU cc_start: 0.8847 (tt) cc_final: 0.8641 (tp)
REVERT: E  251 ILE cc_start: 0.9446 (OUTLIER) cc_final: 0.9125 (tp)
REVERT: E  271 PHE cc_start: 0.8857 (OUTLIER) cc_final: 0.8212 (m-10)
REVERT: E  413 MET cc_start: 0.7857 (ptm) cc_final: 0.7475 (tmm)
REVERT: E  419 CYS cc_start: 0.9217 (m) cc_final: 0.8790 (t)
REVERT: E  442 MET cc_start: 0.8822 (tpt) cc_final: 0.8555 (tpt)
REVERT: E  486 GLN cc_start: 0.9698 (OUTLIER) cc_final: 0.9414 (mm110)
REVERT: E  503 MET cc_start: 0.9319 (tpt) cc_final: 0.9001 (tpt)
REVERT: E  584 PHE cc_start: 0.8954 (m-80) cc_final: 0.8719 (m-80)
REVERT: E  591 LEU cc_start: 0.9171 (tp) cc_final: 0.8874 (tp)
REVERT: E  611 LEU cc_start: 0.9643 (OUTLIER) cc_final: 0.9321 (mm)
REVERT: E 1129 CYS cc_start: 0.8426 (OUTLIER) cc_final: 0.8151 (p)
REVERT: E 1143 LEU cc_start: 0.9604 (tp) cc_final: 0.9258 (pp)
REVERT: E 1191 GLN cc_start: 0.9074 (tm-30) cc_final: 0.8802 (tp-100)
REVERT: E 1280 LEU cc_start: 0.9270 (mm) cc_final: 0.8795 (tp)
REVERT: E 1395 MET cc_start: 0.8930 (OUTLIER) cc_final: 0.8686 (tpt)
REVERT: E 1524 VAL cc_start: 0.9493 (OUTLIER) cc_final: 0.9181 (p)
REVERT: E 1539 ARG cc_start: 0.7646 (mtt90) cc_final: 0.7291 (mtt90)
  outliers start: 116
  outliers final: 74
  residues processed: 409
  average time/residue: 0.1367
  time to fit residues: 90.3936
Evaluate side-chains
  384 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 87
    poor density    : 297
  time to evaluate  : 0.837 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue  169 MET
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  328 VAL
Chi-restraints excluded: chain A residue  336 THR
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  142 CYS
Chi-restraints excluded: chain B residue  197 CYS
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  259 HIS
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain C residue   42 CYS
Chi-restraints excluded: chain C residue   49 ILE
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue   80 LEU
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  115 HIS
Chi-restraints excluded: chain C residue  139 THR
Chi-restraints excluded: chain C residue  146 ILE
Chi-restraints excluded: chain C residue  153 ASN
Chi-restraints excluded: chain C residue  214 THR
Chi-restraints excluded: chain C residue  328 VAL
Chi-restraints excluded: chain D residue   55 PHE
Chi-restraints excluded: chain D residue   80 LEU
Chi-restraints excluded: chain D residue   84 LEU
Chi-restraints excluded: chain D residue  115 HIS
Chi-restraints excluded: chain D residue  138 VAL
Chi-restraints excluded: chain D residue  220 VAL
Chi-restraints excluded: chain D residue  224 THR
Chi-restraints excluded: chain D residue  230 VAL
Chi-restraints excluded: chain D residue  236 VAL
Chi-restraints excluded: chain D residue  251 LEU
Chi-restraints excluded: chain D residue  302 THR
Chi-restraints excluded: chain D residue  305 LEU
Chi-restraints excluded: chain D residue  316 VAL
Chi-restraints excluded: chain D residue  344 CYS
Chi-restraints excluded: chain E residue   10 GLU
Chi-restraints excluded: chain E residue   12 HIS
Chi-restraints excluded: chain E residue   32 LEU
Chi-restraints excluded: chain E residue   35 VAL
Chi-restraints excluded: chain E residue   73 ASN
Chi-restraints excluded: chain E residue   86 LEU
Chi-restraints excluded: chain E residue  108 TYR
Chi-restraints excluded: chain E residue  109 MET
Chi-restraints excluded: chain E residue  133 PHE
Chi-restraints excluded: chain E residue  172 LEU
Chi-restraints excluded: chain E residue  175 LEU
Chi-restraints excluded: chain E residue  190 VAL
Chi-restraints excluded: chain E residue  248 LEU
Chi-restraints excluded: chain E residue  251 ILE
Chi-restraints excluded: chain E residue  271 PHE
Chi-restraints excluded: chain E residue  353 LEU
Chi-restraints excluded: chain E residue  429 LEU
Chi-restraints excluded: chain E residue  439 LEU
Chi-restraints excluded: chain E residue  474 VAL
Chi-restraints excluded: chain E residue  486 GLN
Chi-restraints excluded: chain E residue  611 LEU
Chi-restraints excluded: chain E residue  682 ILE
Chi-restraints excluded: chain E residue  702 ILE
Chi-restraints excluded: chain E residue  712 ILE
Chi-restraints excluded: chain E residue  770 VAL
Chi-restraints excluded: chain E residue  884 VAL
Chi-restraints excluded: chain E residue 1016 LEU
Chi-restraints excluded: chain E residue 1027 LEU
Chi-restraints excluded: chain E residue 1064 TYR
Chi-restraints excluded: chain E residue 1129 CYS
Chi-restraints excluded: chain E residue 1168 LEU
Chi-restraints excluded: chain E residue 1175 CYS
Chi-restraints excluded: chain E residue 1228 LEU
Chi-restraints excluded: chain E residue 1239 LEU
Chi-restraints excluded: chain E residue 1258 CYS
Chi-restraints excluded: chain E residue 1260 VAL
Chi-restraints excluded: chain E residue 1261 LEU
Chi-restraints excluded: chain E residue 1295 LEU
Chi-restraints excluded: chain E residue 1375 ILE
Chi-restraints excluded: chain E residue 1395 MET
Chi-restraints excluded: chain E residue 1455 LEU
Chi-restraints excluded: chain E residue 1497 VAL
Chi-restraints excluded: chain E residue 1524 VAL
Chi-restraints excluded: chain E residue 1532 THR
Chi-restraints excluded: chain E residue 1581 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 268
   random chunks:
   chunk 150 optimal weight:    3.9990
   chunk 106 optimal weight:    5.9990
   chunk 4 optimal weight:    0.8980
   chunk 27 optimal weight:    4.9990
   chunk 65 optimal weight:   10.0000
   chunk 21 optimal weight:    4.9990
   chunk 59 optimal weight:    9.9990
   chunk 209 optimal weight:   10.0000
   chunk 83 optimal weight:    3.9990
   chunk 124 optimal weight:    1.9990
   chunk 88 optimal weight:    7.9990
   overall best weight:    3.1788

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

Flipped N/Q/H residues before XYZ refinement:
** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 242 ASN
** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  46 HIS
** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 153 ASN
E  60 HIS
E  73 ASN
E 161 HIS
** E 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 896 HIS
** E1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.060989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2842 r_free = 0.2842 target = 0.050588 restraints weight = 93671.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.052147 restraints weight = 47131.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2917 r_free = 0.2917 target = 0.053211 restraints weight = 29721.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.053897 restraints weight = 21353.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.054442 restraints weight = 16982.770|
|-----------------------------------------------------------------------------|
r_work (final): 0.2957
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8512
moved from start:          0.3945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.152  21616  Z= 0.256
  Angle     :  0.786  52.053  29375  Z= 0.397
  Chirality :  0.045   0.190   3474
  Planarity :  0.004   0.061   3650
  Dihedral  :  6.757 108.615   2920
  Min Nonbonded Distance : 1.873

Molprobity Statistics.
  All-atom Clashscore : 15.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.60 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  5.43 %
    Allowed  : 22.53 %
    Favored  : 72.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.28 (0.16), residues: 2663
  helix:  0.67 (0.14), residues: 1373
  sheet: -0.47 (0.32), residues: 239
  loop : -1.19 (0.19), residues: 1051

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 314 
 TYR   0.015   0.002   TYR C 268 
 PHE   0.026   0.002   PHE E 133 
 TRP   0.021   0.002   TRP A  83 
 HIS   0.008   0.001   HIS B 259 

Details of bonding type rmsd
  covalent geometry    : bond        0.00553 (21611)
  covalent geometry    : angle       0.70345 (29365)
  SS BOND              : bond        0.01955 (    5)
  SS BOND              : angle      19.05957 (   10)
  hydrogen bonds       : bond        0.04343 ( 1148)
  hydrogen bonds       : angle       4.52559 ( 3384)

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

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

  5326 Ramachandran restraints generated.
    2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5326 Ramachandran restraints generated.
    2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  418 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 125
    poor density    : 293
  time to evaluate  : 0.849 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 ASN cc_start: 0.8704 (m-40) cc_final: 0.8404 (m-40)
REVERT: A   56 LEU cc_start: 0.9361 (mt) cc_final: 0.8959 (pp)
REVERT: B   90 TRP cc_start: 0.9095 (m100) cc_final: 0.8875 (m100)
REVERT: B  160 ASN cc_start: 0.9110 (m-40) cc_final: 0.8812 (m110)
REVERT: B  163 MET cc_start: 0.9428 (mmm) cc_final: 0.9189 (mmm)
REVERT: B  169 MET cc_start: 0.9050 (ttm) cc_final: 0.8748 (ttm)
REVERT: B  185 LYS cc_start: 0.9366 (ttmm) cc_final: 0.8988 (tptp)
REVERT: B  231 VAL cc_start: 0.9104 (OUTLIER) cc_final: 0.8870 (m)
REVERT: B  240 MET cc_start: 0.9187 (tmm) cc_final: 0.8307 (tmm)
REVERT: B  332 LYS cc_start: 0.9226 (mtmt) cc_final: 0.8926 (mmtm)
REVERT: C   39 LYS cc_start: 0.9346 (mmmm) cc_final: 0.8766 (tmtt)
REVERT: C   47 LYS cc_start: 0.8460 (tppt) cc_final: 0.7930 (tppt)
REVERT: C   65 ASP cc_start: 0.8600 (t0) cc_final: 0.8141 (t0)
REVERT: C   84 LEU cc_start: 0.9404 (OUTLIER) cc_final: 0.9127 (tt)
REVERT: C  144 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.9184 (tp)
REVERT: C  160 ASN cc_start: 0.9187 (m-40) cc_final: 0.8847 (m110)
REVERT: C  169 MET cc_start: 0.9091 (ttm) cc_final: 0.8796 (ttm)
REVERT: C  170 LYS cc_start: 0.9547 (tptm) cc_final: 0.9195 (tttm)
REVERT: C  179 GLU cc_start: 0.8643 (mp0) cc_final: 0.8315 (mp0)
REVERT: C  204 ASP cc_start: 0.8451 (t0) cc_final: 0.8168 (t0)
REVERT: C  214 THR cc_start: 0.9454 (OUTLIER) cc_final: 0.8552 (t)
REVERT: C  247 ASN cc_start: 0.8830 (p0) cc_final: 0.8264 (p0)
REVERT: D   55 PHE cc_start: 0.9029 (OUTLIER) cc_final: 0.8679 (t80)
REVERT: D   56 LEU cc_start: 0.9357 (tp) cc_final: 0.9060 (tt)
REVERT: D   65 ASP cc_start: 0.8995 (t0) cc_final: 0.8743 (t70)
REVERT: D   88 MET cc_start: 0.8707 (tmm) cc_final: 0.7939 (tmm)
REVERT: D  163 MET cc_start: 0.9190 (mmm) cc_final: 0.8804 (mmm)
REVERT: D  170 LYS cc_start: 0.9157 (tptt) cc_final: 0.8567 (tptm)
REVERT: D  222 LYS cc_start: 0.9492 (ttmt) cc_final: 0.9281 (ttmm)
REVERT: D  240 MET cc_start: 0.8717 (tmm) cc_final: 0.8306 (tmm)
REVERT: D  262 ASP cc_start: 0.9032 (t0) cc_final: 0.8771 (t70)
REVERT: D  288 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7659 (tt0)
REVERT: D  292 GLU cc_start: 0.8422 (tm-30) cc_final: 0.8212 (tm-30)
REVERT: E   30 ASP cc_start: 0.8930 (m-30) cc_final: 0.8682 (m-30)
REVERT: E   73 ASN cc_start: 0.9214 (OUTLIER) cc_final: 0.8846 (p0)
REVERT: E  108 TYR cc_start: 0.8565 (OUTLIER) cc_final: 0.7847 (m-80)
REVERT: E  251 ILE cc_start: 0.9374 (OUTLIER) cc_final: 0.9056 (tp)
REVERT: E  271 PHE cc_start: 0.8862 (OUTLIER) cc_final: 0.8262 (m-10)
REVERT: E  413 MET cc_start: 0.7991 (ptm) cc_final: 0.7520 (tmm)
REVERT: E  442 MET cc_start: 0.8766 (tpt) cc_final: 0.8481 (tpt)
REVERT: E  486 GLN cc_start: 0.9719 (OUTLIER) cc_final: 0.9469 (mm110)
REVERT: E  503 MET cc_start: 0.9339 (tpt) cc_final: 0.9010 (tpt)
REVERT: E  584 PHE cc_start: 0.8994 (m-80) cc_final: 0.8554 (m-80)
REVERT: E  591 LEU cc_start: 0.9321 (tp) cc_final: 0.9011 (tp)
REVERT: E  611 LEU cc_start: 0.9707 (OUTLIER) cc_final: 0.9321 (mm)
REVERT: E 1066 MET cc_start: 0.7932 (mmm) cc_final: 0.7720 (mmt)
REVERT: E 1080 LEU cc_start: 0.9308 (tp) cc_final: 0.9090 (mm)
REVERT: E 1129 CYS cc_start: 0.8430 (OUTLIER) cc_final: 0.8159 (p)
REVERT: E 1143 LEU cc_start: 0.9598 (tp) cc_final: 0.9264 (pp)
REVERT: E 1191 GLN cc_start: 0.9148 (tm-30) cc_final: 0.8873 (tp-100)
REVERT: E 1280 LEU cc_start: 0.9283 (mm) cc_final: 0.8810 (tp)
REVERT: E 1287 TYR cc_start: 0.8927 (m-80) cc_final: 0.8581 (m-80)
REVERT: E 1395 MET cc_start: 0.8926 (OUTLIER) cc_final: 0.8659 (tpt)
  outliers start: 125
  outliers final: 82
  residues processed: 393
  average time/residue: 0.1399
  time to fit residues: 88.6065
Evaluate side-chains
  371 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 95
    poor density    : 276
  time to evaluate  : 0.753 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   59 VAL
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  169 MET
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  284 ILE
Chi-restraints excluded: chain A residue  296 ILE
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  336 THR
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  349 LEU
Chi-restraints excluded: chain B residue   55 PHE
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  142 CYS
Chi-restraints excluded: chain B residue  197 CYS
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  251 LEU
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  335 ASN
Chi-restraints excluded: chain C residue   42 CYS
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue   80 LEU
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  139 THR
Chi-restraints excluded: chain C residue  144 LEU
Chi-restraints excluded: chain C residue  146 ILE
Chi-restraints excluded: chain C residue  214 THR
Chi-restraints excluded: chain C residue  328 VAL
Chi-restraints excluded: chain C residue  339 VAL
Chi-restraints excluded: chain D residue   55 PHE
Chi-restraints excluded: chain D residue   80 LEU
Chi-restraints excluded: chain D residue   84 LEU
Chi-restraints excluded: chain D residue  138 VAL
Chi-restraints excluded: chain D residue  181 LEU
Chi-restraints excluded: chain D residue  220 VAL
Chi-restraints excluded: chain D residue  224 THR
Chi-restraints excluded: chain D residue  230 VAL
Chi-restraints excluded: chain D residue  236 VAL
Chi-restraints excluded: chain D residue  251 LEU
Chi-restraints excluded: chain D residue  259 HIS
Chi-restraints excluded: chain D residue  273 SER
Chi-restraints excluded: chain D residue  302 THR
Chi-restraints excluded: chain D residue  305 LEU
Chi-restraints excluded: chain D residue  316 VAL
Chi-restraints excluded: chain D residue  336 THR
Chi-restraints excluded: chain D residue  344 CYS
Chi-restraints excluded: chain E residue   10 GLU
Chi-restraints excluded: chain E residue   12 HIS
Chi-restraints excluded: chain E residue   32 LEU
Chi-restraints excluded: chain E residue   35 VAL
Chi-restraints excluded: chain E residue   73 ASN
Chi-restraints excluded: chain E residue  108 TYR
Chi-restraints excluded: chain E residue  109 MET
Chi-restraints excluded: chain E residue  133 PHE
Chi-restraints excluded: chain E residue  172 LEU
Chi-restraints excluded: chain E residue  179 LEU
Chi-restraints excluded: chain E residue  190 VAL
Chi-restraints excluded: chain E residue  248 LEU
Chi-restraints excluded: chain E residue  251 ILE
Chi-restraints excluded: chain E residue  271 PHE
Chi-restraints excluded: chain E residue  353 LEU
Chi-restraints excluded: chain E residue  365 LEU
Chi-restraints excluded: chain E residue  429 LEU
Chi-restraints excluded: chain E residue  439 LEU
Chi-restraints excluded: chain E residue  474 VAL
Chi-restraints excluded: chain E residue  486 GLN
Chi-restraints excluded: chain E residue  611 LEU
Chi-restraints excluded: chain E residue  682 ILE
Chi-restraints excluded: chain E residue  702 ILE
Chi-restraints excluded: chain E residue  712 ILE
Chi-restraints excluded: chain E residue  770 VAL
Chi-restraints excluded: chain E residue  884 VAL
Chi-restraints excluded: chain E residue 1016 LEU
Chi-restraints excluded: chain E residue 1027 LEU
Chi-restraints excluded: chain E residue 1064 TYR
Chi-restraints excluded: chain E residue 1129 CYS
Chi-restraints excluded: chain E residue 1136 ILE
Chi-restraints excluded: chain E residue 1168 LEU
Chi-restraints excluded: chain E residue 1175 CYS
Chi-restraints excluded: chain E residue 1228 LEU
Chi-restraints excluded: chain E residue 1258 CYS
Chi-restraints excluded: chain E residue 1260 VAL
Chi-restraints excluded: chain E residue 1261 LEU
Chi-restraints excluded: chain E residue 1295 LEU
Chi-restraints excluded: chain E residue 1375 ILE
Chi-restraints excluded: chain E residue 1395 MET
Chi-restraints excluded: chain E residue 1455 LEU
Chi-restraints excluded: chain E residue 1497 VAL
Chi-restraints excluded: chain E residue 1532 THR
Chi-restraints excluded: chain E residue 1581 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 268
   random chunks:
   chunk 219 optimal weight:    0.6980
   chunk 108 optimal weight:    0.9990
   chunk 91 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9990
   chunk 141 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 256 optimal weight:    3.9990
   chunk 119 optimal weight:    4.9990
   chunk 154 optimal weight:    0.0770
   chunk 47 optimal weight:    5.9990
   chunk 123 optimal weight:    3.9990
   overall best weight:    0.9544

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

Flipped N/Q/H residues before XYZ refinement:
** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 153 ASN
C 335 ASN
** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 153 ASN
E  11 ASN
E  73 ASN
** E 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E1234 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.064527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.053669 restraints weight = 91457.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.055350 restraints weight = 45536.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.056498 restraints weight = 28071.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.057251 restraints weight = 19920.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.057736 restraints weight = 15628.008|
|-----------------------------------------------------------------------------|
r_work (final): 0.3022
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8447
moved from start:          0.4061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.148  21616  Z= 0.135
  Angle     :  0.742  52.317  29375  Z= 0.365
  Chirality :  0.044   0.212   3474
  Planarity :  0.004   0.067   3650
  Dihedral  :  6.516 107.885   2920
  Min Nonbonded Distance : 2.003

Molprobity Statistics.
  All-atom Clashscore : 12.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 24.13 %
    Favored  : 71.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.13 (0.16), residues: 2663
  helix:  0.73 (0.14), residues: 1387
  sheet: -0.03 (0.34), residues: 231
  loop : -1.15 (0.19), residues: 1045

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E1579 
 TYR   0.010   0.001   TYR E 379 
 PHE   0.026   0.001   PHE E 364 
 TRP   0.014   0.001   TRP A  83 
 HIS   0.005   0.001   HIS E  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 (21611)
  covalent geometry    : angle       0.65336 (29365)
  SS BOND              : bond        0.01792 (    5)
  SS BOND              : angle      19.06338 (   10)
  hydrogen bonds       : bond        0.04038 ( 1148)
  hydrogen bonds       : angle       4.33246 ( 3384)

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

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

  5326 Ramachandran restraints generated.
    2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5326 Ramachandran restraints generated.
    2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  432 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 94
    poor density    : 338
  time to evaluate  : 0.861 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 LEU cc_start: 0.9298 (mt) cc_final: 0.8831 (pp)
REVERT: A   77 MET cc_start: 0.8851 (tpp) cc_final: 0.8202 (ttt)
REVERT: B  148 ILE cc_start: 0.9676 (tt) cc_final: 0.9435 (tp)
REVERT: B  160 ASN cc_start: 0.9085 (m-40) cc_final: 0.8799 (m110)
REVERT: B  163 MET cc_start: 0.9477 (mmm) cc_final: 0.9239 (mmm)
REVERT: B  169 MET cc_start: 0.9094 (ttm) cc_final: 0.8666 (ttm)
REVERT: B  185 LYS cc_start: 0.9358 (ttmm) cc_final: 0.8852 (tptt)
REVERT: B  231 VAL cc_start: 0.9075 (OUTLIER) cc_final: 0.8841 (m)
REVERT: B  240 MET cc_start: 0.9155 (tmm) cc_final: 0.8350 (tmm)
REVERT: B  296 ILE cc_start: 0.9297 (mp) cc_final: 0.8880 (tt)
REVERT: B  349 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.9047 (mm)
REVERT: C   39 LYS cc_start: 0.9257 (mmmm) cc_final: 0.8718 (tmtt)
REVERT: C   47 LYS cc_start: 0.8329 (tppt) cc_final: 0.7907 (tppt)
REVERT: C   65 ASP cc_start: 0.8362 (t0) cc_final: 0.7968 (t0)
REVERT: C   84 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9140 (tt)
REVERT: C  144 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9113 (tp)
REVERT: C  160 ASN cc_start: 0.9139 (m-40) cc_final: 0.8813 (m110)
REVERT: C  169 MET cc_start: 0.9026 (ttm) cc_final: 0.8671 (ttm)
REVERT: C  170 LYS cc_start: 0.9460 (tptm) cc_final: 0.9215 (tttm)
REVERT: C  179 GLU cc_start: 0.8555 (mp0) cc_final: 0.8212 (mp0)
REVERT: C  214 THR cc_start: 0.9354 (OUTLIER) cc_final: 0.8788 (t)
REVERT: C  240 MET cc_start: 0.7659 (tmm) cc_final: 0.7323 (tmm)
REVERT: C  247 ASN cc_start: 0.8697 (p0) cc_final: 0.8456 (p0)
REVERT: D   56 LEU cc_start: 0.9373 (tp) cc_final: 0.9055 (tt)
REVERT: D   65 ASP cc_start: 0.8933 (t0) cc_final: 0.8670 (t70)
REVERT: D   88 MET cc_start: 0.8561 (tmm) cc_final: 0.7810 (tmm)
REVERT: D  163 MET cc_start: 0.9273 (mmm) cc_final: 0.8929 (mmm)
REVERT: D  170 LYS cc_start: 0.8963 (tptt) cc_final: 0.8458 (tptm)
REVERT: D  240 MET cc_start: 0.8662 (tmm) cc_final: 0.8346 (tmm)
REVERT: D  262 ASP cc_start: 0.8984 (t0) cc_final: 0.8735 (t70)
REVERT: D  288 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7659 (tt0)
REVERT: E   30 ASP cc_start: 0.8884 (m-30) cc_final: 0.8588 (m-30)
REVERT: E   80 PHE cc_start: 0.8591 (m-80) cc_final: 0.8165 (m-80)
REVERT: E  105 LEU cc_start: 0.9512 (mt) cc_final: 0.9305 (mt)
REVERT: E  108 TYR cc_start: 0.8438 (OUTLIER) cc_final: 0.7886 (m-80)
REVERT: E  153 ILE cc_start: 0.9650 (mm) cc_final: 0.9385 (mm)
REVERT: E  271 PHE cc_start: 0.8884 (OUTLIER) cc_final: 0.8235 (m-10)
REVERT: E  413 MET cc_start: 0.7709 (ptm) cc_final: 0.7440 (tmm)
REVERT: E  419 CYS cc_start: 0.9283 (m) cc_final: 0.9004 (t)
REVERT: E  486 GLN cc_start: 0.9666 (OUTLIER) cc_final: 0.9425 (mm110)
REVERT: E  503 MET cc_start: 0.9219 (tpt) cc_final: 0.8863 (tpt)
REVERT: E  584 PHE cc_start: 0.8920 (m-80) cc_final: 0.8564 (m-80)
REVERT: E  711 MET cc_start: 0.8320 (mtm) cc_final: 0.8117 (ptp)
REVERT: E 1066 MET cc_start: 0.8001 (mmm) cc_final: 0.7754 (mmt)
REVERT: E 1080 LEU cc_start: 0.9302 (tp) cc_final: 0.8999 (mt)
REVERT: E 1129 CYS cc_start: 0.8365 (OUTLIER) cc_final: 0.8145 (p)
REVERT: E 1143 LEU cc_start: 0.9612 (tp) cc_final: 0.9274 (pp)
REVERT: E 1190 GLN cc_start: 0.8383 (tp40) cc_final: 0.7275 (tm-30)
REVERT: E 1280 LEU cc_start: 0.9339 (mm) cc_final: 0.8852 (tp)
REVERT: E 1395 MET cc_start: 0.8875 (OUTLIER) cc_final: 0.8655 (tpt)
REVERT: E 1539 ARG cc_start: 0.7568 (mtt90) cc_final: 0.7302 (mtt90)
  outliers start: 94
  outliers final: 63
  residues processed: 411
  average time/residue: 0.1414
  time to fit residues: 93.9659
Evaluate side-chains
  372 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 73
    poor density    : 299
  time to evaluate  : 0.808 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  169 MET
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  296 ILE
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  328 VAL
Chi-restraints excluded: chain A residue  336 THR
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  349 LEU
Chi-restraints excluded: chain B residue   81 CYS
Chi-restraints excluded: chain B residue  142 CYS
Chi-restraints excluded: chain B residue  197 CYS
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  299 GLN
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  115 HIS
Chi-restraints excluded: chain C residue  139 THR
Chi-restraints excluded: chain C residue  144 LEU
Chi-restraints excluded: chain C residue  153 ASN
Chi-restraints excluded: chain C residue  214 THR
Chi-restraints excluded: chain C residue  328 VAL
Chi-restraints excluded: chain C residue  339 VAL
Chi-restraints excluded: chain D residue  138 VAL
Chi-restraints excluded: chain D residue  220 VAL
Chi-restraints excluded: chain D residue  230 VAL
Chi-restraints excluded: chain D residue  236 VAL
Chi-restraints excluded: chain D residue  302 THR
Chi-restraints excluded: chain D residue  305 LEU
Chi-restraints excluded: chain D residue  344 CYS
Chi-restraints excluded: chain E residue   32 LEU
Chi-restraints excluded: chain E residue   35 VAL
Chi-restraints excluded: chain E residue   86 LEU
Chi-restraints excluded: chain E residue  108 TYR
Chi-restraints excluded: chain E residue  109 MET
Chi-restraints excluded: chain E residue  172 LEU
Chi-restraints excluded: chain E residue  175 LEU
Chi-restraints excluded: chain E residue  179 LEU
Chi-restraints excluded: chain E residue  237 PHE
Chi-restraints excluded: chain E residue  248 LEU
Chi-restraints excluded: chain E residue  271 PHE
Chi-restraints excluded: chain E residue  353 LEU
Chi-restraints excluded: chain E residue  429 LEU
Chi-restraints excluded: chain E residue  439 LEU
Chi-restraints excluded: chain E residue  474 VAL
Chi-restraints excluded: chain E residue  486 GLN
Chi-restraints excluded: chain E residue  682 ILE
Chi-restraints excluded: chain E residue  704 ILE
Chi-restraints excluded: chain E residue  712 ILE
Chi-restraints excluded: chain E residue  770 VAL
Chi-restraints excluded: chain E residue  884 VAL
Chi-restraints excluded: chain E residue 1016 LEU
Chi-restraints excluded: chain E residue 1027 LEU
Chi-restraints excluded: chain E residue 1064 TYR
Chi-restraints excluded: chain E residue 1129 CYS
Chi-restraints excluded: chain E residue 1136 ILE
Chi-restraints excluded: chain E residue 1168 LEU
Chi-restraints excluded: chain E residue 1175 CYS
Chi-restraints excluded: chain E residue 1258 CYS
Chi-restraints excluded: chain E residue 1260 VAL
Chi-restraints excluded: chain E residue 1375 ILE
Chi-restraints excluded: chain E residue 1395 MET
Chi-restraints excluded: chain E residue 1497 VAL
Chi-restraints excluded: chain E residue 1532 THR
Chi-restraints excluded: chain E residue 1581 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 268
   random chunks:
   chunk 208 optimal weight:    1.9990
   chunk 155 optimal weight:    2.9990
   chunk 18 optimal weight:    4.9990
   chunk 13 optimal weight:    1.9990
   chunk 215 optimal weight:    3.9990
   chunk 222 optimal weight:    6.9990
   chunk 52 optimal weight:    4.9990
   chunk 4 optimal weight:    0.6980
   chunk 90 optimal weight:    0.9980
   chunk 7 optimal weight:   10.0000
   chunk 248 optimal weight:    0.9980
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
A 218 GLN
** A 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 153 ASN
** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 153 ASN
** E 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.063712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.052815 restraints weight = 91366.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.054471 restraints weight = 46176.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2966 r_free = 0.2966 target = 0.055582 restraints weight = 28703.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.056361 restraints weight = 20479.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.056902 restraints weight = 16080.139|
|-----------------------------------------------------------------------------|
r_work (final): 0.3000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8451
moved from start:          0.4197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.150  21616  Z= 0.150
  Angle     :  0.764  52.245  29375  Z= 0.375
  Chirality :  0.044   0.202   3474
  Planarity :  0.004   0.065   3650
  Dihedral  :  6.444 108.743   2918
  Min Nonbonded Distance : 1.963

Molprobity Statistics.
  All-atom Clashscore : 12.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 25.43 %
    Favored  : 70.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.06 (0.16), residues: 2663
  helix:  0.77 (0.14), residues: 1392
  sheet:  0.04 (0.34), residues: 238
  loop : -1.12 (0.19), residues: 1033

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  50 
 TYR   0.013   0.001   TYR E1287 
 PHE   0.028   0.001   PHE E 364 
 TRP   0.017   0.001   TRP B  83 
 HIS   0.006   0.001   HIS E1024 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 (21611)
  covalent geometry    : angle       0.67879 (29365)
  SS BOND              : bond        0.01810 (    5)
  SS BOND              : angle      19.03558 (   10)
  hydrogen bonds       : bond        0.03978 ( 1148)
  hydrogen bonds       : angle       4.31566 ( 3384)

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

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

  5326 Ramachandran restraints generated.
    2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5326 Ramachandran restraints generated.
    2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  407 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 90
    poor density    : 317
  time to evaluate  : 0.891 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 LEU cc_start: 0.9290 (mt) cc_final: 0.8869 (pp)
REVERT: A   83 TRP cc_start: 0.9684 (m-10) cc_final: 0.9085 (m-90)
REVERT: B  148 ILE cc_start: 0.9655 (tt) cc_final: 0.9430 (tp)
REVERT: B  160 ASN cc_start: 0.9102 (m-40) cc_final: 0.8799 (m110)
REVERT: B  163 MET cc_start: 0.9488 (mmm) cc_final: 0.9274 (mmm)
REVERT: B  185 LYS cc_start: 0.9363 (ttmm) cc_final: 0.8839 (tptt)
REVERT: B  231 VAL cc_start: 0.9071 (OUTLIER) cc_final: 0.8840 (m)
REVERT: B  240 MET cc_start: 0.9200 (tmm) cc_final: 0.8397 (tmm)
REVERT: B  250 PHE cc_start: 0.8414 (t80) cc_final: 0.8188 (t80)
REVERT: B  296 ILE cc_start: 0.9257 (mp) cc_final: 0.8840 (tt)
REVERT: B  349 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9051 (mm)
REVERT: C   39 LYS cc_start: 0.9243 (mmmm) cc_final: 0.8679 (tmtt)
REVERT: C   47 LYS cc_start: 0.8414 (tppt) cc_final: 0.7989 (tppt)
REVERT: C   65 ASP cc_start: 0.8380 (t0) cc_final: 0.7994 (t0)
REVERT: C   84 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9113 (tt)
REVERT: C  144 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.9122 (tp)
REVERT: C  160 ASN cc_start: 0.9141 (m-40) cc_final: 0.8784 (m110)
REVERT: C  169 MET cc_start: 0.9039 (ttm) cc_final: 0.8654 (ttm)
REVERT: C  170 LYS cc_start: 0.9474 (tptm) cc_final: 0.9238 (tttp)
REVERT: C  179 GLU cc_start: 0.8563 (mp0) cc_final: 0.7920 (mp0)
REVERT: C  214 THR cc_start: 0.9311 (OUTLIER) cc_final: 0.8672 (t)
REVERT: C  240 MET cc_start: 0.7718 (tmm) cc_final: 0.7307 (tmm)
REVERT: C  247 ASN cc_start: 0.8678 (p0) cc_final: 0.8363 (p0)
REVERT: D   56 LEU cc_start: 0.9368 (tp) cc_final: 0.9011 (tt)
REVERT: D   65 ASP cc_start: 0.8940 (t0) cc_final: 0.8683 (t70)
REVERT: D   88 MET cc_start: 0.8600 (tmm) cc_final: 0.7855 (tmm)
REVERT: D  163 MET cc_start: 0.9258 (mmm) cc_final: 0.8920 (mmm)
REVERT: D  170 LYS cc_start: 0.8973 (tptt) cc_final: 0.8458 (tptm)
REVERT: D  240 MET cc_start: 0.8648 (tmm) cc_final: 0.8296 (tmm)
REVERT: D  262 ASP cc_start: 0.8978 (t0) cc_final: 0.8670 (t70)
REVERT: D  288 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7728 (tt0)
REVERT: E   30 ASP cc_start: 0.8918 (m-30) cc_final: 0.8616 (m-30)
REVERT: E   62 HIS cc_start: 0.8394 (t-90) cc_final: 0.7987 (t-90)
REVERT: E   80 PHE cc_start: 0.8958 (m-80) cc_final: 0.8607 (m-80)
REVERT: E   81 MET cc_start: 0.9153 (ptp) cc_final: 0.8913 (pmm)
REVERT: E  105 LEU cc_start: 0.9482 (mt) cc_final: 0.9257 (mt)
REVERT: E  108 TYR cc_start: 0.8477 (OUTLIER) cc_final: 0.7903 (m-80)
REVERT: E  153 ILE cc_start: 0.9656 (mm) cc_final: 0.9365 (mm)
REVERT: E  271 PHE cc_start: 0.8891 (OUTLIER) cc_final: 0.8221 (m-10)
REVERT: E  413 MET cc_start: 0.7621 (ptm) cc_final: 0.7421 (tmm)
REVERT: E  419 CYS cc_start: 0.9303 (OUTLIER) cc_final: 0.9054 (t)
REVERT: E  486 GLN cc_start: 0.9676 (OUTLIER) cc_final: 0.9462 (mm110)
REVERT: E  503 MET cc_start: 0.9216 (tpt) cc_final: 0.8853 (tpt)
REVERT: E  584 PHE cc_start: 0.8885 (m-80) cc_final: 0.8596 (m-80)
REVERT: E  711 MET cc_start: 0.8408 (mtm) cc_final: 0.8200 (ptp)
REVERT: E 1066 MET cc_start: 0.8079 (mmm) cc_final: 0.7834 (mmt)
REVERT: E 1080 LEU cc_start: 0.9314 (tp) cc_final: 0.9010 (mt)
REVERT: E 1143 LEU cc_start: 0.9610 (tp) cc_final: 0.9267 (pp)
REVERT: E 1190 GLN cc_start: 0.8449 (tp40) cc_final: 0.7554 (tm-30)
REVERT: E 1226 LYS cc_start: 0.8768 (mmtp) cc_final: 0.8475 (mmtp)
REVERT: E 1280 LEU cc_start: 0.9323 (mm) cc_final: 0.8846 (tp)
REVERT: E 1395 MET cc_start: 0.8883 (OUTLIER) cc_final: 0.8645 (tpt)
REVERT: E 1505 MET cc_start: 0.8856 (mpp) cc_final: 0.8480 (mmm)
  outliers start: 90
  outliers final: 67
  residues processed: 388
  average time/residue: 0.1405
  time to fit residues: 88.2658
Evaluate side-chains
  384 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 77
    poor density    : 307
  time to evaluate  : 0.847 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  169 MET
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  296 ILE
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  336 THR
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain B residue   55 PHE
Chi-restraints excluded: chain B residue  142 CYS
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  299 GLN
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  115 HIS
Chi-restraints excluded: chain C residue  139 THR
Chi-restraints excluded: chain C residue  144 LEU
Chi-restraints excluded: chain C residue  153 ASN
Chi-restraints excluded: chain C residue  214 THR
Chi-restraints excluded: chain C residue  328 VAL
Chi-restraints excluded: chain C residue  339 VAL
Chi-restraints excluded: chain D residue  138 VAL
Chi-restraints excluded: chain D residue  220 VAL
Chi-restraints excluded: chain D residue  230 VAL
Chi-restraints excluded: chain D residue  236 VAL
Chi-restraints excluded: chain D residue  251 LEU
Chi-restraints excluded: chain D residue  259 HIS
Chi-restraints excluded: chain D residue  302 THR
Chi-restraints excluded: chain D residue  305 LEU
Chi-restraints excluded: chain D residue  316 VAL
Chi-restraints excluded: chain D residue  336 THR
Chi-restraints excluded: chain D residue  344 CYS
Chi-restraints excluded: chain E residue   32 LEU
Chi-restraints excluded: chain E residue   35 VAL
Chi-restraints excluded: chain E residue  108 TYR
Chi-restraints excluded: chain E residue  172 LEU
Chi-restraints excluded: chain E residue  179 LEU
Chi-restraints excluded: chain E residue  211 LEU
Chi-restraints excluded: chain E residue  237 PHE
Chi-restraints excluded: chain E residue  248 LEU
Chi-restraints excluded: chain E residue  271 PHE
Chi-restraints excluded: chain E residue  306 PHE
Chi-restraints excluded: chain E residue  353 LEU
Chi-restraints excluded: chain E residue  365 LEU
Chi-restraints excluded: chain E residue  419 CYS
Chi-restraints excluded: chain E residue  429 LEU
Chi-restraints excluded: chain E residue  439 LEU
Chi-restraints excluded: chain E residue  474 VAL
Chi-restraints excluded: chain E residue  486 GLN
Chi-restraints excluded: chain E residue  682 ILE
Chi-restraints excluded: chain E residue  704 ILE
Chi-restraints excluded: chain E residue  712 ILE
Chi-restraints excluded: chain E residue  770 VAL
Chi-restraints excluded: chain E residue  884 VAL
Chi-restraints excluded: chain E residue 1016 LEU
Chi-restraints excluded: chain E residue 1027 LEU
Chi-restraints excluded: chain E residue 1064 TYR
Chi-restraints excluded: chain E residue 1071 LEU
Chi-restraints excluded: chain E residue 1136 ILE
Chi-restraints excluded: chain E residue 1168 LEU
Chi-restraints excluded: chain E residue 1175 CYS
Chi-restraints excluded: chain E residue 1258 CYS
Chi-restraints excluded: chain E residue 1260 VAL
Chi-restraints excluded: chain E residue 1261 LEU
Chi-restraints excluded: chain E residue 1375 ILE
Chi-restraints excluded: chain E residue 1395 MET
Chi-restraints excluded: chain E residue 1497 VAL
Chi-restraints excluded: chain E residue 1532 THR
Chi-restraints excluded: chain E residue 1581 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 268
   random chunks:
   chunk 108 optimal weight:    0.6980
   chunk 77 optimal weight:    7.9990
   chunk 1 optimal weight:    8.9990
   chunk 152 optimal weight:    2.9990
   chunk 131 optimal weight:    0.9980
   chunk 258 optimal weight:    7.9990
   chunk 253 optimal weight:    5.9990
   chunk 208 optimal weight:   10.0000
   chunk 179 optimal weight:   10.0000
   chunk 157 optimal weight:    9.9990
   chunk 168 optimal weight:    6.9990
   overall best weight:    3.5386

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

Flipped N/Q/H residues before XYZ refinement:
** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 153 ASN
** E 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E1348 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.060539 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2820 r_free = 0.2820 target = 0.049888 restraints weight = 92566.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2864 r_free = 0.2864 target = 0.051457 restraints weight = 46927.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.052516 restraints weight = 29640.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.053218 restraints weight = 21425.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.053738 restraints weight = 17052.486|
|-----------------------------------------------------------------------------|
r_work (final): 0.2929
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8516
moved from start:          0.4378

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.150  21616  Z= 0.280
  Angle     :  0.832  52.130  29375  Z= 0.417
  Chirality :  0.046   0.208   3474
  Planarity :  0.004   0.062   3650
  Dihedral  :  6.723 118.047   2918
  Min Nonbonded Distance : 1.882

Molprobity Statistics.
  All-atom Clashscore : 15.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.48 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 25.48 %
    Favored  : 70.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.04 (0.16), residues: 2663
  helix:  0.80 (0.14), residues: 1343
  sheet: -0.06 (0.33), residues: 239
  loop : -1.01 (0.19), residues: 1081

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 314 
 TYR   0.017   0.002   TYR C 268 
 PHE   0.029   0.002   PHE E 133 
 TRP   0.018   0.002   TRP B  83 
 HIS   0.005   0.001   HIS E1203 

Details of bonding type rmsd
  covalent geometry    : bond        0.00605 (21611)
  covalent geometry    : angle       0.75421 (29365)
  SS BOND              : bond        0.01936 (    5)
  SS BOND              : angle      19.02737 (   10)
  hydrogen bonds       : bond        0.04383 ( 1148)
  hydrogen bonds       : angle       4.58199 ( 3384)

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

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

  5326 Ramachandran restraints generated.
    2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5326 Ramachandran restraints generated.
    2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  387 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 102
    poor density    : 285
  time to evaluate  : 0.710 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 LEU cc_start: 0.9388 (mt) cc_final: 0.8971 (pp)
REVERT: A  292 GLU cc_start: 0.8549 (tm-30) cc_final: 0.8339 (tm-30)
REVERT: B  148 ILE cc_start: 0.9731 (tt) cc_final: 0.9473 (tp)
REVERT: B  160 ASN cc_start: 0.9135 (m-40) cc_final: 0.8828 (m110)
REVERT: B  169 MET cc_start: 0.8965 (ttm) cc_final: 0.8716 (ttm)
REVERT: B  185 LYS cc_start: 0.9366 (ttmm) cc_final: 0.8871 (tptp)
REVERT: B  231 VAL cc_start: 0.9096 (OUTLIER) cc_final: 0.8862 (m)
REVERT: B  240 MET cc_start: 0.9144 (tmm) cc_final: 0.8499 (tmm)
REVERT: B  250 PHE cc_start: 0.8400 (t80) cc_final: 0.8124 (t80)
REVERT: B  296 ILE cc_start: 0.9326 (mp) cc_final: 0.8897 (tt)
REVERT: B  332 LYS cc_start: 0.9271 (mtmt) cc_final: 0.8955 (mmtm)
REVERT: B  349 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.9087 (mm)
REVERT: C   39 LYS cc_start: 0.9332 (mmmm) cc_final: 0.8727 (tmtt)
REVERT: C   47 LYS cc_start: 0.8565 (tppt) cc_final: 0.8009 (tppt)
REVERT: C   48 ASN cc_start: 0.8637 (m-40) cc_final: 0.7947 (m-40)
REVERT: C   65 ASP cc_start: 0.8730 (t0) cc_final: 0.8198 (t0)
REVERT: C   84 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.9101 (tt)
REVERT: C  144 LEU cc_start: 0.9460 (OUTLIER) cc_final: 0.9228 (tp)
REVERT: C  160 ASN cc_start: 0.9165 (m-40) cc_final: 0.8842 (m110)
REVERT: C  169 MET cc_start: 0.9099 (ttm) cc_final: 0.8820 (ttm)
REVERT: C  170 LYS cc_start: 0.9548 (tptm) cc_final: 0.9286 (tttm)
REVERT: C  179 GLU cc_start: 0.8659 (mp0) cc_final: 0.8257 (mp0)
REVERT: C  204 ASP cc_start: 0.8428 (t0) cc_final: 0.8167 (t0)
REVERT: C  214 THR cc_start: 0.9458 (OUTLIER) cc_final: 0.8951 (t)
REVERT: C  240 MET cc_start: 0.8175 (tmm) cc_final: 0.7228 (tmm)
REVERT: C  247 ASN cc_start: 0.8865 (p0) cc_final: 0.8579 (p0)
REVERT: D   56 LEU cc_start: 0.9442 (tp) cc_final: 0.9140 (tt)
REVERT: D   88 MET cc_start: 0.8747 (tmm) cc_final: 0.7962 (tmm)
REVERT: D  163 MET cc_start: 0.9219 (mmm) cc_final: 0.8850 (mmm)
REVERT: D  170 LYS cc_start: 0.9151 (tptt) cc_final: 0.8561 (tptm)
REVERT: D  240 MET cc_start: 0.8767 (tmm) cc_final: 0.8341 (tmm)
REVERT: D  288 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7654 (tt0)
REVERT: E   16 TYR cc_start: 0.7634 (OUTLIER) cc_final: 0.7429 (m-10)
REVERT: E   30 ASP cc_start: 0.8984 (m-30) cc_final: 0.8716 (m-30)
REVERT: E   62 HIS cc_start: 0.8601 (t-90) cc_final: 0.8204 (t-90)
REVERT: E  108 TYR cc_start: 0.8609 (OUTLIER) cc_final: 0.7904 (m-80)
REVERT: E  251 ILE cc_start: 0.9468 (OUTLIER) cc_final: 0.9139 (tp)
REVERT: E  271 PHE cc_start: 0.8999 (OUTLIER) cc_final: 0.8315 (m-10)
REVERT: E  413 MET cc_start: 0.7810 (ptm) cc_final: 0.7415 (tmm)
REVERT: E  445 GLN cc_start: 0.8957 (tt0) cc_final: 0.8671 (tp40)
REVERT: E  503 MET cc_start: 0.9282 (tpt) cc_final: 0.8883 (tpt)
REVERT: E  584 PHE cc_start: 0.9006 (m-80) cc_final: 0.8555 (m-80)
REVERT: E 1066 MET cc_start: 0.8305 (mmm) cc_final: 0.7896 (mmt)
REVERT: E 1226 LYS cc_start: 0.8839 (mmtp) cc_final: 0.8611 (mmtp)
REVERT: E 1280 LEU cc_start: 0.9286 (mm) cc_final: 0.8792 (tp)
REVERT: E 1287 TYR cc_start: 0.8951 (m-80) cc_final: 0.8672 (m-80)
REVERT: E 1395 MET cc_start: 0.8953 (OUTLIER) cc_final: 0.8645 (tpt)
REVERT: E 1505 MET cc_start: 0.9025 (mpp) cc_final: 0.8349 (mmm)
  outliers start: 102
  outliers final: 78
  residues processed: 364
  average time/residue: 0.1390
  time to fit residues: 82.0533
Evaluate side-chains
  369 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 88
    poor density    : 281
  time to evaluate  : 0.831 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  115 HIS
Chi-restraints excluded: chain A residue  169 MET
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  217 MET
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  336 THR
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  349 LEU
Chi-restraints excluded: chain B residue   55 PHE
Chi-restraints excluded: chain B residue  142 CYS
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  335 ASN
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain C residue   42 CYS
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  115 HIS
Chi-restraints excluded: chain C residue  139 THR
Chi-restraints excluded: chain C residue  144 LEU
Chi-restraints excluded: chain C residue  146 ILE
Chi-restraints excluded: chain C residue  166 SER
Chi-restraints excluded: chain C residue  214 THR
Chi-restraints excluded: chain C residue  328 VAL
Chi-restraints excluded: chain C residue  339 VAL
Chi-restraints excluded: chain D residue   93 ILE
Chi-restraints excluded: chain D residue  138 VAL
Chi-restraints excluded: chain D residue  220 VAL
Chi-restraints excluded: chain D residue  230 VAL
Chi-restraints excluded: chain D residue  236 VAL
Chi-restraints excluded: chain D residue  251 LEU
Chi-restraints excluded: chain D residue  259 HIS
Chi-restraints excluded: chain D residue  302 THR
Chi-restraints excluded: chain D residue  305 LEU
Chi-restraints excluded: chain D residue  316 VAL
Chi-restraints excluded: chain D residue  336 THR
Chi-restraints excluded: chain D residue  344 CYS
Chi-restraints excluded: chain E residue   12 HIS
Chi-restraints excluded: chain E residue   16 TYR
Chi-restraints excluded: chain E residue   32 LEU
Chi-restraints excluded: chain E residue   35 VAL
Chi-restraints excluded: chain E residue  108 TYR
Chi-restraints excluded: chain E residue  109 MET
Chi-restraints excluded: chain E residue  133 PHE
Chi-restraints excluded: chain E residue  172 LEU
Chi-restraints excluded: chain E residue  179 LEU
Chi-restraints excluded: chain E residue  190 VAL
Chi-restraints excluded: chain E residue  211 LEU
Chi-restraints excluded: chain E residue  248 LEU
Chi-restraints excluded: chain E residue  251 ILE
Chi-restraints excluded: chain E residue  271 PHE
Chi-restraints excluded: chain E residue  306 PHE
Chi-restraints excluded: chain E residue  353 LEU
Chi-restraints excluded: chain E residue  359 LEU
Chi-restraints excluded: chain E residue  365 LEU
Chi-restraints excluded: chain E residue  429 LEU
Chi-restraints excluded: chain E residue  439 LEU
Chi-restraints excluded: chain E residue  474 VAL
Chi-restraints excluded: chain E residue  682 ILE
Chi-restraints excluded: chain E residue  704 ILE
Chi-restraints excluded: chain E residue  712 ILE
Chi-restraints excluded: chain E residue  770 VAL
Chi-restraints excluded: chain E residue  884 VAL
Chi-restraints excluded: chain E residue 1016 LEU
Chi-restraints excluded: chain E residue 1027 LEU
Chi-restraints excluded: chain E residue 1064 TYR
Chi-restraints excluded: chain E residue 1071 LEU
Chi-restraints excluded: chain E residue 1136 ILE
Chi-restraints excluded: chain E residue 1168 LEU
Chi-restraints excluded: chain E residue 1175 CYS
Chi-restraints excluded: chain E residue 1258 CYS
Chi-restraints excluded: chain E residue 1260 VAL
Chi-restraints excluded: chain E residue 1261 LEU
Chi-restraints excluded: chain E residue 1362 LEU
Chi-restraints excluded: chain E residue 1375 ILE
Chi-restraints excluded: chain E residue 1395 MET
Chi-restraints excluded: chain E residue 1497 VAL
Chi-restraints excluded: chain E residue 1532 THR
Chi-restraints excluded: chain E residue 1581 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 268
   random chunks:
   chunk 100 optimal weight:    0.7980
   chunk 176 optimal weight:    4.9990
   chunk 67 optimal weight:    0.0170
   chunk 109 optimal weight:    0.6980
   chunk 24 optimal weight:    5.9990
   chunk 127 optimal weight:    0.0050
   chunk 65 optimal weight:    4.9990
   chunk 223 optimal weight:    0.9980
   chunk 205 optimal weight:   10.0000
   chunk 261 optimal weight:    4.9990
   chunk 183 optimal weight:    2.9990
   overall best weight:    0.5032

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

Flipped N/Q/H residues before XYZ refinement:
** A 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 242 ASN
C  48 ASN
C 153 ASN
** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 153 ASN
D 279 GLN
** E 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E1348 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.065450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.054432 restraints weight = 90962.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.056142 restraints weight = 45172.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.057321 restraints weight = 27949.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.058137 restraints weight = 19794.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.058664 restraints weight = 15395.651|
|-----------------------------------------------------------------------------|
r_work (final): 0.3040
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8412
moved from start:          0.4457

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.150  21616  Z= 0.128
  Angle     :  0.778  52.291  29375  Z= 0.376
  Chirality :  0.044   0.209   3474
  Planarity :  0.004   0.066   3650
  Dihedral  :  6.407 111.828   2918
  Min Nonbonded Distance : 2.018

Molprobity Statistics.
  All-atom Clashscore : 11.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 27.52 %
    Favored  : 69.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.10 (0.16), residues: 2663
  helix:  0.89 (0.14), residues: 1369
  sheet:  0.24 (0.34), residues: 231
  loop : -1.02 (0.19), residues: 1063

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 837 
 TYR   0.014   0.001   TYR E1254 
 PHE   0.026   0.001   PHE E 364 
 TRP   0.015   0.001   TRP B  83 
 HIS   0.005   0.001   HIS E1024 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 (21611)
  covalent geometry    : angle       0.69435 (29365)
  SS BOND              : bond        0.01774 (    5)
  SS BOND              : angle      19.03688 (   10)
  hydrogen bonds       : bond        0.03915 ( 1148)
  hydrogen bonds       : angle       4.31404 ( 3384)

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

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

  5326 Ramachandran restraints generated.
    2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5326 Ramachandran restraints generated.
    2663 Oldfield, 0 Emsley, 2663 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  428 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 361
  time to evaluate  : 0.906 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 LEU cc_start: 0.9280 (mt) cc_final: 0.8853 (pp)
REVERT: A   83 TRP cc_start: 0.9693 (m-10) cc_final: 0.9116 (m-90)
REVERT: A  292 GLU cc_start: 0.8372 (tm-30) cc_final: 0.8086 (tm-30)
REVERT: B  148 ILE cc_start: 0.9675 (tt) cc_final: 0.9421 (tp)
REVERT: B  160 ASN cc_start: 0.9129 (m-40) cc_final: 0.8838 (m110)
REVERT: B  169 MET cc_start: 0.8958 (ttm) cc_final: 0.8712 (ttm)
REVERT: B  185 LYS cc_start: 0.9313 (ttmm) cc_final: 0.8814 (tptt)
REVERT: B  231 VAL cc_start: 0.9079 (OUTLIER) cc_final: 0.8862 (m)
REVERT: B  240 MET cc_start: 0.9126 (tmm) cc_final: 0.8406 (tmm)
REVERT: B  250 PHE cc_start: 0.8370 (t80) cc_final: 0.8095 (t80)
REVERT: B  296 ILE cc_start: 0.9253 (mp) cc_final: 0.8852 (tt)
REVERT: B  349 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.9060 (mm)
REVERT: C   39 LYS cc_start: 0.9259 (mmmm) cc_final: 0.8646 (tmtt)
REVERT: C   65 ASP cc_start: 0.8459 (t0) cc_final: 0.8031 (t0)
REVERT: C  144 LEU cc_start: 0.9363 (mm) cc_final: 0.9131 (tp)
REVERT: C  160 ASN cc_start: 0.9051 (m-40) cc_final: 0.8705 (m110)
REVERT: C  169 MET cc_start: 0.8973 (ttm) cc_final: 0.8605 (ttm)
REVERT: C  170 LYS cc_start: 0.9423 (tptm) cc_final: 0.9154 (tttp)
REVERT: C  179 GLU cc_start: 0.8544 (mp0) cc_final: 0.7864 (mp0)
REVERT: C  199 MET cc_start: 0.8844 (mtm) cc_final: 0.8355 (mpp)
REVERT: C  214 THR cc_start: 0.9268 (OUTLIER) cc_final: 0.8650 (t)
REVERT: C  240 MET cc_start: 0.7564 (tmm) cc_final: 0.7293 (tmm)
REVERT: C  247 ASN cc_start: 0.8571 (p0) cc_final: 0.8331 (p0)
REVERT: D   56 LEU cc_start: 0.9421 (tp) cc_final: 0.9033 (tt)
REVERT: D   65 ASP cc_start: 0.8950 (t0) cc_final: 0.8749 (t70)
REVERT: D   77 MET cc_start: 0.8391 (tpp) cc_final: 0.7657 (tpp)
REVERT: D   88 MET cc_start: 0.8515 (tmm) cc_final: 0.7783 (tmm)
REVERT: D  163 MET cc_start: 0.9293 (mmm) cc_final: 0.8990 (mmm)
REVERT: D  262 ASP cc_start: 0.8970 (t0) cc_final: 0.8659 (t70)
REVERT: D  288 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7736 (tt0)
REVERT: E   30 ASP cc_start: 0.8925 (m-30) cc_final: 0.8612 (m-30)
REVERT: E   62 HIS cc_start: 0.8412 (t-90) cc_final: 0.8085 (t-90)
REVERT: E   81 MET cc_start: 0.8940 (pmm) cc_final: 0.8635 (pmm)
REVERT: E  105 LEU cc_start: 0.9497 (mt) cc_final: 0.9270 (mt)
REVERT: E  108 TYR cc_start: 0.8367 (OUTLIER) cc_final: 0.7953 (m-10)
REVERT: E  153 ILE cc_start: 0.9623 (mm) cc_final: 0.9312 (mm)
REVERT: E  251 ILE cc_start: 0.9206 (OUTLIER) cc_final: 0.8885 (tp)
REVERT: E  271 PHE cc_start: 0.8970 (OUTLIER) cc_final: 0.8223 (m-10)
REVERT: E  315 PHE cc_start: 0.8191 (m-80) cc_final: 0.7394 (m-80)
REVERT: E  413 MET cc_start: 0.7716 (ptm) cc_final: 0.7462 (tmm)
REVERT: E  419 CYS cc_start: 0.9287 (m) cc_final: 0.9065 (t)
REVERT: E  503 MET cc_start: 0.9213 (tpt) cc_final: 0.8856 (tpt)
REVERT: E  584 PHE cc_start: 0.8958 (m-80) cc_final: 0.8752 (m-80)
REVERT: E 1066 MET cc_start: 0.8176 (mmm) cc_final: 0.7714 (mmt)
REVERT: E 1143 LEU cc_start: 0.9549 (tt) cc_final: 0.9231 (pp)
REVERT: E 1154 LEU cc_start: 0.9314 (mm) cc_final: 0.8929 (tt)
REVERT: E 1188 ASP cc_start: 0.8751 (t70) cc_final: 0.8301 (t0)
REVERT: E 1226 LYS cc_start: 0.8746 (mmtp) cc_final: 0.8443 (mmtp)
REVERT: E 1280 LEU cc_start: 0.9396 (mm) cc_final: 0.8926 (tp)
REVERT: E 1290 MET cc_start: 0.8861 (tpp) cc_final: 0.8408 (mmp)
REVERT: E 1395 MET cc_start: 0.8873 (OUTLIER) cc_final: 0.8645 (tpt)
REVERT: E 1505 MET cc_start: 0.8933 (mpp) cc_final: 0.8407 (mmm)
  outliers start: 67
  outliers final: 52
  residues processed: 416
  average time/residue: 0.1406
  time to fit residues: 94.3519
Evaluate side-chains
  383 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 324
  time to evaluate  : 0.831 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue  115 HIS
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  296 ILE
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  336 THR
Chi-restraints excluded: chain A residue  341 THR
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain B residue  142 CYS
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue  115 HIS
Chi-restraints excluded: chain C residue  139 THR
Chi-restraints excluded: chain C residue  153 ASN
Chi-restraints excluded: chain C residue  214 THR
Chi-restraints excluded: chain C residue  328 VAL
Chi-restraints excluded: chain C residue  345 THR
Chi-restraints excluded: chain D residue  138 VAL
Chi-restraints excluded: chain D residue  220 VAL
Chi-restraints excluded: chain D residue  230 VAL
Chi-restraints excluded: chain D residue  236 VAL
Chi-restraints excluded: chain D residue  302 THR
Chi-restraints excluded: chain D residue  305 LEU
Chi-restraints excluded: chain D residue  316 VAL
Chi-restraints excluded: chain D residue  336 THR
Chi-restraints excluded: chain D residue  344 CYS
Chi-restraints excluded: chain E residue   32 LEU
Chi-restraints excluded: chain E residue  108 TYR
Chi-restraints excluded: chain E residue  172 LEU
Chi-restraints excluded: chain E residue  179 LEU
Chi-restraints excluded: chain E residue  190 VAL
Chi-restraints excluded: chain E residue  248 LEU
Chi-restraints excluded: chain E residue  251 ILE
Chi-restraints excluded: chain E residue  271 PHE
Chi-restraints excluded: chain E residue  353 LEU
Chi-restraints excluded: chain E residue  359 LEU
Chi-restraints excluded: chain E residue  365 LEU
Chi-restraints excluded: chain E residue  429 LEU
Chi-restraints excluded: chain E residue  439 LEU
Chi-restraints excluded: chain E residue  682 ILE
Chi-restraints excluded: chain E residue  704 ILE
Chi-restraints excluded: chain E residue  712 ILE
Chi-restraints excluded: chain E residue  770 VAL
Chi-restraints excluded: chain E residue  884 VAL
Chi-restraints excluded: chain E residue 1016 LEU
Chi-restraints excluded: chain E residue 1027 LEU
Chi-restraints excluded: chain E residue 1064 TYR
Chi-restraints excluded: chain E residue 1136 ILE
Chi-restraints excluded: chain E residue 1175 CYS
Chi-restraints excluded: chain E residue 1261 LEU
Chi-restraints excluded: chain E residue 1375 ILE
Chi-restraints excluded: chain E residue 1395 MET
Chi-restraints excluded: chain E residue 1497 VAL
Chi-restraints excluded: chain E residue 1581 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 268
   random chunks:
   chunk 186 optimal weight:    4.9990
   chunk 245 optimal weight:   10.0000
   chunk 61 optimal weight:    9.9990
   chunk 250 optimal weight:    0.9990
   chunk 196 optimal weight:    2.9990
   chunk 21 optimal weight:    0.6980
   chunk 247 optimal weight:   20.0000
   chunk 16 optimal weight:    0.8980
   chunk 189 optimal weight:    0.3980
   chunk 212 optimal weight:    9.9990
   chunk 133 optimal weight:    0.0000
   overall best weight:    0.5986

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

Flipped N/Q/H residues before XYZ refinement:
** A 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 153 ASN
C  52 GLN
C 153 ASN
** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 153 ASN
E 563 HIS
** E 797 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 = 0.3233 r_free = 0.3233 target = 0.065923 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.054989 restraints weight = 90479.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.056676 restraints weight = 44394.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.057820 restraints weight = 27562.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.058617 restraints weight = 19663.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.059162 restraints weight = 15360.636|
|-----------------------------------------------------------------------------|
r_work (final): 0.3067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8408
moved from start:          0.4581

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.150  21616  Z= 0.130
  Angle     :  0.784  52.255  29375  Z= 0.379
  Chirality :  0.044   0.196   3474
  Planarity :  0.004   0.065   3650
  Dihedral  :  6.306 110.347   2918
  Min Nonbonded Distance : 2.008

Molprobity Statistics.
  All-atom Clashscore : 11.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 28.08 %
    Favored  : 69.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.15 (0.16), residues: 2663
  helix:  0.94 (0.14), residues: 1369
  sheet:  0.30 (0.34), residues: 238
  loop : -1.01 (0.19), residues: 1056

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  50 
 TYR   0.019   0.001   TYR E1254 
 PHE   0.025   0.001   PHE E 133 
 TRP   0.016   0.001   TRP B  83 
 HIS   0.005   0.001   HIS E1024 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 (21611)
  covalent geometry    : angle       0.70100 (29365)
  SS BOND              : bond        0.01783 (    5)
  SS BOND              : angle      19.03437 (   10)
  hydrogen bonds       : bond        0.03877 ( 1148)
  hydrogen bonds       : angle       4.24964 ( 3384)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3390.08 seconds
wall clock time: 59 minutes 44.83 seconds (3584.83 seconds total)