Starting phenix.real_space_refine
on Tue May 13 01:02:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yiu_33864/05_2025/7yiu_33864.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yiu_33864/05_2025/7yiu_33864.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7yiu_33864/05_2025/7yiu_33864.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yiu_33864/05_2025/7yiu_33864.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yiu_33864/05_2025/7yiu_33864.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yiu_33864/05_2025/7yiu_33864.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.006
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       1      5.49       5
     S      52      5.16       5
     C    5994      2.51       5
     N    1561      2.21       5
     O    1677      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 78 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 9285
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "B"
      Number of atoms: 3940
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 499, 3940
          Classifications: {'peptide': 499}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 17, 'TRANS': 481}
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "E"
      Number of atoms: 341
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 43, 341
          Classifications: {'peptide': 43}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 1, 'TRANS': 41}
          Unresolved non-hydrogen bonds: 26
          Unresolved non-hydrogen angles: 34
          Unresolved non-hydrogen dihedrals: 25
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 22
    Chain: "D"
      Number of atoms: 1236
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 153, 1236
          Classifications: {'peptide': 153}
          Link IDs: {'PTRANS': 8, 'TRANS': 144}
    Chain: "C"
      Number of atoms: 411
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 48, 411
          Classifications: {'peptide': 48}
          Link IDs: {'PTRANS': 1, 'TRANS': 46}
    Chain: "A"
      Number of atoms: 3285
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 423, 3285
          Classifications: {'peptide': 423}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 21, 'TRANS': 401}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'PLP': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "D"
      Number of atoms: 57
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 57
          Unusual residues: {'6CM': 1, 'R16': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 3
  Time building chain proxies: 6.12, per 1000 atoms: 0.66
  Number of scatterers: 9285
  At special positions: 0
  Unit cell: (91.8, 85.32, 123.12, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      52     16.00
     P       1     15.00
     O    1677      8.00
     N    1561      7.00
     C    5994      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.65
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2160

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 8 sheets defined
      46.9% alpha, 8.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.12
  Creating SS restraints...
    Processing helix  chain 'B' and resid 67 through 73
      removed outlier: 3.508A  pdb=" N   LEU B  73 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 73 through 90
      removed outlier: 3.751A  pdb=" N   GLY B  77 " --> pdb=" O   LEU B  73 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   LEU B  87 " --> pdb=" O   LEU B  83 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   ARG B  88 " --> pdb=" O   PHE B  84 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   ASP B  89 " --> pdb=" O   GLY B  85 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 91 through 93
      No H-bonds generated for 'chain 'B' and resid 91 through 93'
    Processing helix  chain 'B' and resid 105 through 109
      removed outlier: 4.026A  pdb=" N   LYS B 109 " --> pdb=" O   GLU B 106 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 120 through 126
    Processing helix  chain 'B' and resid 130 through 134
      removed outlier: 3.599A  pdb=" N   ASN B 133 " --> pdb=" O   ILE B 130 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   TRP B 134 " --> pdb=" O   ARG B 131 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 130 through 134'
    Processing helix  chain 'B' and resid 177 through 181
      removed outlier: 4.232A  pdb=" N   PHE B 181 " --> pdb=" O   TYR B 178 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 214 through 228
      removed outlier: 3.717A  pdb=" N   GLU B 220 " --> pdb=" O   HIS B 216 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   GLU B 221 " --> pdb=" O   GLU B 217 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   LEU B 222 " --> pdb=" O   GLU B 218 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   ALA B 224 " --> pdb=" O   GLU B 220 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   ARG B 225 " --> pdb=" O   GLU B 221 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 238 through 244
      removed outlier: 4.022A  pdb=" N   ASN B 242 " --> pdb=" O   GLY B 238 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 245 through 249
    Processing helix  chain 'B' and resid 263 through 274
      removed outlier: 3.630A  pdb=" N   ALA B 270 " --> pdb=" O   LEU B 266 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ARG B 271 " --> pdb=" O   VAL B 267 " (cutoff:3.500A)
      removed outlier: 4.031A  pdb=" N   GLY B 274 " --> pdb=" O   ALA B 270 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 286 through 298
      removed outlier: 3.643A  pdb=" N   ALA B 295 " --> pdb=" O   LEU B 291 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   ILE B 296 " --> pdb=" O   LEU B 292 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   VAL B 297 " --> pdb=" O   LYS B 293 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 326 through 331
    Processing helix  chain 'B' and resid 358 through 364
    Processing helix  chain 'B' and resid 393 through 398
      removed outlier: 3.660A  pdb=" N   TYR B 397 " --> pdb=" O   GLU B 393 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 402 through 408
      removed outlier: 3.799A  pdb=" N   VAL B 406 " --> pdb=" O   SER B 402 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 412 through 427
      removed outlier: 3.524A  pdb=" N   GLN B 418 " --> pdb=" O   PRO B 414 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ILE B 426 " --> pdb=" O   SER B 422 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   MET B 427 " --> pdb=" O   MET B 423 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 433 through 455
      removed outlier: 3.633A  pdb=" N   CYS B 438 " --> pdb=" O   LEU B 434 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   VAL B 439 " --> pdb=" O   GLY B 435 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   GLN B 440 " --> pdb=" O   LYS B 436 " (cutoff:3.500A)
      removed outlier: 4.088A  pdb=" N   ALA B 443 " --> pdb=" O   VAL B 439 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   GLU B 444 " --> pdb=" O   GLN B 440 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ASN B 445 " --> pdb=" O   GLN B 441 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   LYS B 454 " --> pdb=" O   ARG B 450 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   GLU B 455 " --> pdb=" O   ARG B 451 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 475 through 490
      removed outlier: 3.840A  pdb=" N   ILE B 479 " --> pdb=" O   MET B 475 " (cutoff:3.500A)
      removed outlier: 4.326A  pdb=" N   GLY B 480 " --> pdb=" O   PRO B 476 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ALA B 481 " --> pdb=" O   ALA B 477 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   GLY B 483 " --> pdb=" O   ILE B 479 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   ARG B 484 " --> pdb=" O   GLY B 480 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   LEU B 487 " --> pdb=" O   GLY B 483 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 517 through 535
    Processing helix  chain 'E' and resid 10 through 16
      removed outlier: 3.647A  pdb=" N   VAL E  14 " --> pdb=" O   LEU E  10 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 21 through 40
      removed outlier: 3.543A  pdb=" N   LEU E  27 " --> pdb=" O   TYR E  23 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ILE E  32 " --> pdb=" O   GLU E  28 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   LEU E  33 " --> pdb=" O   GLY E  29 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   TRP E  34 " --> pdb=" O   ILE E  30 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   ILE E  36 " --> pdb=" O   ILE E  32 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 15 through 19
      removed outlier: 3.619A  pdb=" N   SER D  19 " --> pdb=" O   VAL D  16 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 26 through 38
      removed outlier: 3.607A  pdb=" N   ILE D  30 " --> pdb=" O   TYR D  26 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   VAL D  36 " --> pdb=" O   LEU D  32 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   LEU D  37 " --> pdb=" O   LEU D  33 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 44 through 66
      removed outlier: 3.672A  pdb=" N   ASN D  53 " --> pdb=" O   TRP D  49 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 84 through 89
    Processing helix  chain 'D' and resid 90 through 93
    Processing helix  chain 'D' and resid 96 through 116
      removed outlier: 3.595A  pdb=" N   PHE D 101 " --> pdb=" O   ALA D  97 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   THR D 103 " --> pdb=" O   ARG D  99 " (cutoff:3.500A)
      Proline residue:  D 106  - end of helix
      removed outlier: 3.531A  pdb=" N   THR D 113 " --> pdb=" O   LEU D 109 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 123 through 136
      removed outlier: 3.569A  pdb=" N   ASN D 127 " --> pdb=" O   HIS D 123 " (cutoff:3.500A)
      removed outlier: 4.654A  pdb=" N   VAL D 129 " --> pdb=" O   VAL D 125 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   SER D 133 " --> pdb=" O   VAL D 129 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   VAL D 134 " --> pdb=" O   SER D 130 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 139 through 143
      removed outlier: 3.728A  pdb=" N   HIS D 143 " --> pdb=" O   PRO D 140 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 146 through 150
    Processing helix  chain 'C' and resid 10 through 14
    Processing helix  chain 'C' and resid 14 through 24
      removed outlier: 3.694A  pdb=" N   THR C  24 " --> pdb=" O   TYR C  20 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 30 through 46
      removed outlier: 3.636A  pdb=" N   VAL C  36 " --> pdb=" O   TRP C  32 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   PHE C  37 " --> pdb=" O   GLU C  33 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   MET C  40 " --> pdb=" O   VAL C  36 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 46 through 51
      removed outlier: 3.708A  pdb=" N   TYR C  50 " --> pdb=" O   GLY C  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 53 through 64
      removed outlier: 3.811A  pdb=" N   GLU A  58 " --> pdb=" O   VAL A  54 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   GLU A  59 " --> pdb=" O   LYS A  55 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ILE A  61 " --> pdb=" O   LYS A  57 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   GLU A  62 " --> pdb=" O   GLU A  58 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   TRP A  64 " --> pdb=" O   LEU A  60 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 114 through 124
      removed outlier: 3.847A  pdb=" N   ALA A 123 " --> pdb=" O   ALA A 119 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   SER A 124 " --> pdb=" O   ALA A 120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 124 through 129
    Processing helix  chain 'A' and resid 144 through 156
      removed outlier: 3.583A  pdb=" N   ASP A 150 " --> pdb=" O   LEU A 146 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   ARG A 151 " --> pdb=" O   ASP A 147 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   LYS A 154 " --> pdb=" O   ASP A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 173
      removed outlier: 3.722A  pdb=" N   ALA A 172 " --> pdb=" O   PHE A 168 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 174 through 178
    Processing helix  chain 'A' and resid 192 through 202
    Processing helix  chain 'A' and resid 213 through 227
      removed outlier: 3.642A  pdb=" N   LEU A 217 " --> pdb=" O   ASP A 213 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   GLU A 223 " --> pdb=" O   ARG A 219 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   GLU A 225 " --> pdb=" O   LEU A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 236
      removed outlier: 3.664A  pdb=" N   ARG A 236 " --> pdb=" O   PRO A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 268
      removed outlier: 3.524A  pdb=" N   LEU A 260 " --> pdb=" O   PRO A 256 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   LYS A 262 " --> pdb=" O   PRO A 258 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   LEU A 263 " --> pdb=" O   GLU A 259 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   LYS A 264 " --> pdb=" O   LEU A 260 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   TYR A 265 " --> pdb=" O   VAL A 261 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   LYS A 266 " --> pdb=" O   LYS A 262 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 288 through 294
    Processing helix  chain 'A' and resid 296 through 300
      removed outlier: 3.894A  pdb=" N   ILE A 300 " --> pdb=" O   ILE A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 321 through 326
    Processing helix  chain 'A' and resid 332 through 337
    Processing helix  chain 'A' and resid 342 through 359
      removed outlier: 3.673A  pdb=" N   ALA A 348 " --> pdb=" O   LEU A 344 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ALA A 349 " --> pdb=" O   LEU A 345 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   GLU A 351 " --> pdb=" O   ALA A 347 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   ALA A 352 " --> pdb=" O   ALA A 348 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ASN A 359 " --> pdb=" O   ILE A 355 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 360 through 363
      removed outlier: 3.708A  pdb=" N   PHE A 363 " --> pdb=" O   PRO A 360 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 360 through 363'
    Processing helix  chain 'A' and resid 364 through 369
      removed outlier: 3.564A  pdb=" N   GLU A 368 " --> pdb=" O   ALA A 364 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   LYS A 369 " --> pdb=" O   VAL A 365 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 364 through 369'
    Processing helix  chain 'A' and resid 404 through 421
      removed outlier: 3.747A  pdb=" N   ASN A 421 " --> pdb=" O   ASP A 417 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 453 through 467
      removed outlier: 3.530A  pdb=" N   THR A 463 " --> pdb=" O   ARG A 459 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   LYS A 465 " --> pdb=" O   ALA A 461 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   VAL A 467 " --> pdb=" O   THR A 463 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 48
    Processing sheet with id=AA2, first strand: chain 'B' and resid 146 through 152
      removed outlier: 6.205A  pdb=" N   VAL B 146 " --> pdb=" O   GLY B 169 " (cutoff:3.500A)
      removed outlier: 4.697A  pdb=" N   GLY B 169 " --> pdb=" O   VAL B 146 " (cutoff:3.500A)
      removed outlier: 5.444A  pdb=" N   ASN B 165 " --> pdb=" O   GLU B 150 " (cutoff:3.500A)
      removed outlier: 8.449A  pdb=" N   GLN B 152 " --> pdb=" O   THR B 163 " (cutoff:3.500A)
      removed outlier: 6.550A  pdb=" N   THR B 163 " --> pdb=" O   GLN B 152 " (cutoff:3.500A)
      removed outlier: 7.817A  pdb=" N   GLY B 492 " --> pdb=" O   GLY B 169 " (cutoff:3.500A)
      removed outlier: 6.539A  pdb=" N   ILE B 171 " --> pdb=" O   GLY B 492 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 231 through 234
      removed outlier: 6.703A  pdb=" N   LEU B 341 " --> pdb=" O   VAL B 372 " (cutoff:3.500A)
      removed outlier: 7.756A  pdb=" N   MET B 374 " --> pdb=" O   LEU B 341 " (cutoff:3.500A)
      removed outlier: 6.399A  pdb=" N   LEU B 343 " --> pdb=" O   MET B 374 " (cutoff:3.500A)
      removed outlier: 8.552A  pdb=" N   THR B 376 " --> pdb=" O   LEU B 343 " (cutoff:3.500A)
      removed outlier: 6.937A  pdb=" N   ILE B 310 " --> pdb=" O   TYR B 340 " (cutoff:3.500A)
      removed outlier: 7.843A  pdb=" N   TYR B 342 " --> pdb=" O   ILE B 310 " (cutoff:3.500A)
      removed outlier: 6.384A  pdb=" N   ILE B 312 " --> pdb=" O   TYR B 342 " (cutoff:3.500A)
      removed outlier: 7.607A  pdb=" N   ASP B 344 " --> pdb=" O   ILE B 312 " (cutoff:3.500A)
      removed outlier: 7.392A  pdb=" N   VAL B 314 " --> pdb=" O   ASP B 344 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   ASP B 259 " --> pdb=" O   LEU B 313 " (cutoff:3.500A)
      removed outlier: 8.526A  pdb=" N   GLU B 315 " --> pdb=" O   ASP B 259 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 470 through 472
      removed outlier: 3.838A  pdb=" N   VAL B 494 " --> pdb=" O   ARG B 509 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 92 through 94
      removed outlier: 7.763A  pdb=" N   ALA A 425 " --> pdb=" O   GLU A  99 " (cutoff:3.500A)
      removed outlier: 7.037A  pdb=" N   ILE A 101 " --> pdb=" O   ALA A 425 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 160 through 164
      removed outlier: 3.611A  pdb=" N   GLY A 316 " --> pdb=" O   TYR A 164 " (cutoff:3.500A)
      removed outlier: 7.150A  pdb=" N   ILE A 271 " --> pdb=" O   LEU A 302 " (cutoff:3.500A)
      removed outlier: 8.671A  pdb=" N   SER A 304 " --> pdb=" O   ILE A 271 " (cutoff:3.500A)
      removed outlier: 6.906A  pdb=" N   LEU A 273 " --> pdb=" O   SER A 304 " (cutoff:3.500A)
      removed outlier: 9.133A  pdb=" N   ASN A 306 " --> pdb=" O   LEU A 273 " (cutoff:3.500A)
      removed outlier: 6.822A  pdb=" N   ARG A 240 " --> pdb=" O   ARG A 270 " (cutoff:3.500A)
      removed outlier: 7.879A  pdb=" N   PHE A 272 " --> pdb=" O   ARG A 240 " (cutoff:3.500A)
      removed outlier: 6.719A  pdb=" N   ILE A 242 " --> pdb=" O   PHE A 272 " (cutoff:3.500A)
      removed outlier: 7.607A  pdb=" N   GLU A 274 " --> pdb=" O   ILE A 242 " (cutoff:3.500A)
      removed outlier: 7.201A  pdb=" N   VAL A 244 " --> pdb=" O   GLU A 274 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ASP A 188 " --> pdb=" O   VAL A 243 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 383 through 386
      removed outlier: 3.520A  pdb=" N   VAL A 386 " --> pdb=" O   HIS A 395 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 427 through 428
      removed outlier: 4.487A  pdb=" N   THR A 427 " --> pdb=" O   ARG A 445 " (cutoff:3.500A)

    289 hydrogen bonds defined for protein.
    816 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.57

  Time building geometry restraints manager: 3.02 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2778
        1.33 -     1.45: 1310
        1.45 -     1.57: 5308
        1.57 -     1.69: 1
        1.69 -     1.81: 87
  Bond restraints: 9484
  Sorted by residual:
  bond pdb=" C2  PLP B 601 "
       pdb=" C3  PLP B 601 "
    ideal  model  delta    sigma   weight residual
    1.390  1.485 -0.095 2.00e-02 2.50e+03 2.26e+01
  bond pdb=" C4  PLP B 601 "
       pdb=" C5  PLP B 601 "
    ideal  model  delta    sigma   weight residual
    1.390  1.482 -0.092 2.00e-02 2.50e+03 2.12e+01
  bond pdb=" C3  PLP B 601 "
       pdb=" C4  PLP B 601 "
    ideal  model  delta    sigma   weight residual
    1.390  1.480 -0.090 2.00e-02 2.50e+03 2.02e+01
  bond pdb=" C   PHE B 498 "
       pdb=" O   PHE B 498 "
    ideal  model  delta    sigma   weight residual
    1.244  1.212  0.032 9.10e-03 1.21e+04 1.21e+01
  bond pdb=" CA  ASN B 120 "
       pdb=" CB  ASN B 120 "
    ideal  model  delta    sigma   weight residual
    1.532  1.565 -0.032 1.53e-02 4.27e+03 4.51e+00
  ... (remaining 9479 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.10: 12067
        2.10 -     4.20: 651
        4.20 -     6.30: 83
        6.30 -     8.40: 14
        8.40 -    10.50: 4
  Bond angle restraints: 12819
  Sorted by residual:
  angle pdb=" N   LYS B 168 "
        pdb=" CA  LYS B 168 "
        pdb=" C   LYS B 168 "
      ideal   model   delta    sigma   weight residual
     111.02  119.68   -8.66 1.22e+00 6.72e-01 5.04e+01
  angle pdb=" N   GLY B 497 "
        pdb=" CA  GLY B 497 "
        pdb=" C   GLY B 497 "
      ideal   model   delta    sigma   weight residual
     112.60  121.63   -9.03 1.43e+00 4.89e-01 3.98e+01
  angle pdb=" N   PRO A  78 "
        pdb=" CA  PRO A  78 "
        pdb=" CB  PRO A  78 "
      ideal   model   delta    sigma   weight residual
     103.33  110.19   -6.86 1.10e+00 8.26e-01 3.89e+01
  angle pdb=" C   GLN B 300 "
        pdb=" N   PRO B 301 "
        pdb=" CA  PRO B 301 "
      ideal   model   delta    sigma   weight residual
     119.84  127.47   -7.63 1.25e+00 6.40e-01 3.73e+01
  angle pdb=" N   MET B 456 "
        pdb=" CA  MET B 456 "
        pdb=" C   MET B 456 "
      ideal   model   delta    sigma   weight residual
     113.41  106.08    7.33 1.22e+00 6.72e-01 3.61e+01
  ... (remaining 12814 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.64: 4763
       17.64 -    35.28: 549
       35.28 -    52.91: 274
       52.91 -    70.55: 84
       70.55 -    88.19: 10
  Dihedral angle restraints: 5680
    sinusoidal: 2304
      harmonic: 3376
  Sorted by residual:
  dihedral pdb=" C   ASN B 120 "
           pdb=" N   ASN B 120 "
           pdb=" CA  ASN B 120 "
           pdb=" CB  ASN B 120 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -137.95   15.35     0      2.50e+00 1.60e-01 3.77e+01
  dihedral pdb=" N   ASN B 120 "
           pdb=" C   ASN B 120 "
           pdb=" CA  ASN B 120 "
           pdb=" CB  ASN B 120 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  136.47  -13.67     0      2.50e+00 1.60e-01 2.99e+01
  dihedral pdb=" N   LEU A 111 "
           pdb=" C   LEU A 111 "
           pdb=" CA  LEU A 111 "
           pdb=" CB  LEU A 111 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  133.25  -10.45     0      2.50e+00 1.60e-01 1.75e+01
  ... (remaining 5677 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.098: 1248
       0.098 -    0.196: 163
       0.196 -    0.294: 14
       0.294 -    0.392: 3
       0.392 -    0.490: 2
  Chirality restraints: 1430
  Sorted by residual:
  chirality pdb=" CA  ASN B 120 "
            pdb=" N   ASN B 120 "
            pdb=" C   ASN B 120 "
            pdb=" CB  ASN B 120 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.02    0.49 2.00e-01 2.50e+01 6.00e+00
  chirality pdb=" CA  LEU A 111 "
            pdb=" N   LEU A 111 "
            pdb=" C   LEU A 111 "
            pdb=" CB  LEU A 111 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.05    0.46 2.00e-01 2.50e+01 5.27e+00
  chirality pdb=" CA  LYS B 168 "
            pdb=" N   LYS B 168 "
            pdb=" C   LYS B 168 "
            pdb=" CB  LYS B 168 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.13    0.38 2.00e-01 2.50e+01 3.56e+00
  ... (remaining 1427 not shown)

  Planarity restraints: 1622
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C19 6CM D 801 "   -0.084 2.00e-02 2.50e+03   2.81e-01 9.90e+02
        pdb=" C2  6CM D 801 "    0.331 2.00e-02 2.50e+03
        pdb=" C20 6CM D 801 "    0.171 2.00e-02 2.50e+03
        pdb=" N2  6CM D 801 "   -0.495 2.00e-02 2.50e+03
        pdb=" O19 6CM D 801 "    0.077 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 501 "   -0.059 5.00e-02 4.00e+02   9.02e-02 1.30e+01
        pdb=" N   PRO B 502 "    0.156 5.00e-02 4.00e+02
        pdb=" CA  PRO B 502 "   -0.049 5.00e-02 4.00e+02
        pdb=" CD  PRO B 502 "   -0.048 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR B 501 "    0.010 2.00e-02 2.50e+03   2.08e-02 4.34e+00
        pdb=" C   THR B 501 "   -0.036 2.00e-02 2.50e+03
        pdb=" O   THR B 501 "    0.014 2.00e-02 2.50e+03
        pdb=" N   PRO B 502 "    0.012 2.00e-02 2.50e+03
  ... (remaining 1619 not shown)

  Histogram of nonbonded interaction distances:
        1.93 -     2.53: 32
        2.53 -     3.12: 6263
        3.12 -     3.71: 13016
        3.71 -     4.31: 20001
        4.31 -     4.90: 33819
  Nonbonded interactions: 73131
  Sorted by model distance:
  nonbonded pdb=" O   THR B  66 "
            pdb=" NH1 ARG D  20 "
     model   vdw
     1.932 3.120
  nonbonded pdb=" NH2 ARG A 151 "
            pdb=" OD1 ASN A 354 "
     model   vdw
     1.966 3.120
  nonbonded pdb=" OH  TYR A 128 "
            pdb=" OD1 ASP A 143 "
     model   vdw
     1.991 3.040
  nonbonded pdb=" O   LEU B 473 "
            pdb=" O   SER B 506 "
     model   vdw
     2.002 3.040
  nonbonded pdb=" O   ALA B 201 "
            pdb=" OG  SER B 412 "
     model   vdw
     2.011 3.040
  ... (remaining 73126 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.80 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.000
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.400
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     24.960
  Find NCS groups from input model:        0.100
  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:             0.010
  Load rotamer database and sin/cos tables:11.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.310
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8461
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   0.355   9485  Z= 0.541
  Angle     :  1.076  10.505  12819  Z= 0.718
  Chirality :  0.070   0.490   1430
  Planarity :  0.009   0.281   1622
  Dihedral  : 19.632  88.187   3520
  Min Nonbonded Distance : 1.932

Molprobity Statistics.
  All-atom Clashscore : 14.64
  Ramachandran Plot:
    Outliers :  1.21 %
    Allowed  :  6.49 %
    Favored  : 92.30 %
  Rotamer:
    Outliers : 16.13 %
    Allowed  : 10.14 %
    Favored  : 73.73 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.83 (0.20), residues: 1156
  helix: -4.19 (0.14), residues: 506
  sheet: -1.58 (0.44), residues: 123
  loop : -2.41 (0.24), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP C  32 
 HIS   0.006   0.001   HIS B 263 
 PHE   0.025   0.002   PHE A 138 
 TYR   0.021   0.002   TYR A 166 
 ARG   0.005   0.001   ARG A 233 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.34533 (  289)
  hydrogen bonds       : angle      10.26452 (  816)
  covalent geometry    : bond        0.00687 ( 9484)
  covalent geometry    : angle       1.07560 (12819)
  Misc. bond           : bond        0.35539 (    1)

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

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

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  286 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 159
    poor density    : 127
  time to evaluate  : 1.093 
Fit side-chains
REVERT: B   57 ARG cc_start: 0.7612 (mtm110) cc_final: 0.7011 (ptp-170)
REVERT: B   68 MET cc_start: 0.9137 (OUTLIER) cc_final: 0.8862 (tpt)
REVERT: B   92 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.8212 (ptt180)
REVERT: B  111 PHE cc_start: 0.9408 (OUTLIER) cc_final: 0.9016 (m-80)
REVERT: B  150 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7689 (tt0)
REVERT: B  165 ASN cc_start: 0.7754 (p0) cc_final: 0.7172 (p0)
REVERT: B  190 GLU cc_start: 0.8005 (tt0) cc_final: 0.7755 (tp30)
REVERT: B  197 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7436 (tm-30)
REVERT: B  271 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.8267 (mtt-85)
REVERT: B  305 ARG cc_start: 0.8291 (mmt-90) cc_final: 0.8053 (mmt-90)
REVERT: B  423 MET cc_start: 0.9117 (ttp) cc_final: 0.8830 (ttp)
REVERT: B  463 ASN cc_start: 0.8754 (OUTLIER) cc_final: 0.8517 (t0)
REVERT: B  475 MET cc_start: 0.9261 (OUTLIER) cc_final: 0.7463 (mtt)
REVERT: B  521 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8935 (mp)
REVERT: B  543 ARG cc_start: 0.6520 (OUTLIER) cc_final: 0.6294 (ttm170)
REVERT: E   10 LEU cc_start: 0.6703 (OUTLIER) cc_final: 0.6475 (tm)
REVERT: E   13 MET cc_start: 0.7927 (OUTLIER) cc_final: 0.7475 (mtp)
REVERT: E   15 GLN cc_start: 0.7545 (OUTLIER) cc_final: 0.7294 (tt0)
REVERT: E   37 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.6944 (tpt-90)
REVERT: E   42 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7752 (mttm)
REVERT: D  152 LYS cc_start: 0.8898 (tptm) cc_final: 0.8529 (tmtm)
REVERT: C   12 GLN cc_start: 0.7805 (tt0) cc_final: 0.7553 (tt0)
REVERT: C   53 TYR cc_start: 0.7671 (t80) cc_final: 0.7449 (t80)
REVERT: A   77 HIS cc_start: 0.6181 (OUTLIER) cc_final: 0.5604 (m90)
REVERT: A  236 ARG cc_start: 0.8061 (mtm-85) cc_final: 0.7727 (mtt180)
REVERT: A  249 MET cc_start: 0.8678 (ttm) cc_final: 0.8459 (ttt)
REVERT: A  268 LYS cc_start: 0.9082 (OUTLIER) cc_final: 0.8861 (mmtp)
REVERT: A  287 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.8441 (mtt180)
REVERT: A  368 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8336 (pp20)
REVERT: A  375 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8637 (tttm)
REVERT: A  407 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7668 (mt0)
REVERT: A  419 CYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8107 (m)
REVERT: A  427 THR cc_start: 0.8972 (p) cc_final: 0.8658 (t)
REVERT: A  464 ILE cc_start: 0.9236 (OUTLIER) cc_final: 0.9009 (mt)
  outliers start: 159
  outliers final: 79
  residues processed: 251
  average time/residue: 1.2440
  time to fit residues: 332.0159
Evaluate side-chains
  211 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 102
    poor density    : 109
  time to evaluate  : 1.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   60 ASN
Chi-restraints excluded: chain B residue   68 MET
Chi-restraints excluded: chain B residue   72 VAL
Chi-restraints excluded: chain B residue   83 LEU
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain B residue   94 TRP
Chi-restraints excluded: chain B residue  107 GLU
Chi-restraints excluded: chain B residue  110 ASP
Chi-restraints excluded: chain B residue  111 PHE
Chi-restraints excluded: chain B residue  113 SER
Chi-restraints excluded: chain B residue  149 MET
Chi-restraints excluded: chain B residue  150 GLU
Chi-restraints excluded: chain B residue  161 LYS
Chi-restraints excluded: chain B residue  183 ARG
Chi-restraints excluded: chain B residue  189 GLN
Chi-restraints excluded: chain B residue  197 GLU
Chi-restraints excluded: chain B residue  198 GLU
Chi-restraints excluded: chain B residue  205 SER
Chi-restraints excluded: chain B residue  210 ILE
Chi-restraints excluded: chain B residue  243 SER
Chi-restraints excluded: chain B residue  250 VAL
Chi-restraints excluded: chain B residue  258 SER
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  271 ARG
Chi-restraints excluded: chain B residue  303 THR
Chi-restraints excluded: chain B residue  345 GLU
Chi-restraints excluded: chain B residue  373 MET
Chi-restraints excluded: chain B residue  378 THR
Chi-restraints excluded: chain B residue  402 SER
Chi-restraints excluded: chain B residue  406 VAL
Chi-restraints excluded: chain B residue  434 LEU
Chi-restraints excluded: chain B residue  439 VAL
Chi-restraints excluded: chain B residue  440 GLN
Chi-restraints excluded: chain B residue  454 LYS
Chi-restraints excluded: chain B residue  463 ASN
Chi-restraints excluded: chain B residue  473 LEU
Chi-restraints excluded: chain B residue  475 MET
Chi-restraints excluded: chain B residue  519 GLU
Chi-restraints excluded: chain B residue  521 LEU
Chi-restraints excluded: chain B residue  526 LYS
Chi-restraints excluded: chain B residue  543 ARG
Chi-restraints excluded: chain E residue   10 LEU
Chi-restraints excluded: chain E residue   13 MET
Chi-restraints excluded: chain E residue   14 VAL
Chi-restraints excluded: chain E residue   15 GLN
Chi-restraints excluded: chain E residue   17 LEU
Chi-restraints excluded: chain E residue   18 TYR
Chi-restraints excluded: chain E residue   26 ILE
Chi-restraints excluded: chain E residue   27 LEU
Chi-restraints excluded: chain E residue   37 ARG
Chi-restraints excluded: chain E residue   38 LEU
Chi-restraints excluded: chain E residue   42 LYS
Chi-restraints excluded: chain E residue   44 TYR
Chi-restraints excluded: chain E residue   46 LEU
Chi-restraints excluded: chain D residue    1 MET
Chi-restraints excluded: chain D residue    8 SER
Chi-restraints excluded: chain D residue   17 MET
Chi-restraints excluded: chain D residue   27 VAL
Chi-restraints excluded: chain D residue   33 LEU
Chi-restraints excluded: chain D residue   35 ILE
Chi-restraints excluded: chain D residue   40 ILE
Chi-restraints excluded: chain D residue   72 PHE
Chi-restraints excluded: chain D residue  114 SER
Chi-restraints excluded: chain D residue  122 ILE
Chi-restraints excluded: chain D residue  145 VAL
Chi-restraints excluded: chain C residue   11 LYS
Chi-restraints excluded: chain C residue   14 SER
Chi-restraints excluded: chain C residue   39 SER
Chi-restraints excluded: chain C residue   45 VAL
Chi-restraints excluded: chain C residue   51 THR
Chi-restraints excluded: chain A residue   51 ASP
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   76 ASP
Chi-restraints excluded: chain A residue   77 HIS
Chi-restraints excluded: chain A residue   83 ASN
Chi-restraints excluded: chain A residue  105 SER
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  151 ARG
Chi-restraints excluded: chain A residue  230 LYS
Chi-restraints excluded: chain A residue  245 GLU
Chi-restraints excluded: chain A residue  268 LYS
Chi-restraints excluded: chain A residue  287 ARG
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  340 SER
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  367 LYS
Chi-restraints excluded: chain A residue  368 GLU
Chi-restraints excluded: chain A residue  369 LYS
Chi-restraints excluded: chain A residue  370 CYS
Chi-restraints excluded: chain A residue  373 ILE
Chi-restraints excluded: chain A residue  375 LYS
Chi-restraints excluded: chain A residue  402 THR
Chi-restraints excluded: chain A residue  405 ARG
Chi-restraints excluded: chain A residue  407 GLN
Chi-restraints excluded: chain A residue  419 CYS
Chi-restraints excluded: chain A residue  453 THR
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain A residue  464 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 96 optimal weight:    0.9990
   chunk 86 optimal weight:    0.5980
   chunk 47 optimal weight:    5.9990
   chunk 29 optimal weight:    0.9980
   chunk 58 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 89 optimal weight:    0.6980
   chunk 34 optimal weight:    0.7980
   chunk 54 optimal weight:    1.9990
   chunk 66 optimal weight:    0.5980
   chunk 103 optimal weight:    0.2980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
B  60 ASN
B 108 GLN
B 242 ASN
D   7 HIS
D  94 GLN
C  38 ASN
A 285 HIS
A 407 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.105980 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2874 r_free = 0.2874 target = 0.088123 restraints weight = 12265.578|
|-----------------------------------------------------------------------------|
r_work (start): 0.2868 rms_B_bonded: 1.55
r_work: 0.2770 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.2653 rms_B_bonded: 3.45 restraints_weight: 0.2500
r_work (final): 0.2653
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2649
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2649 r_free = 0.2649    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.80   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2649 r_free = 0.2649    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.73   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2649
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8607
moved from start:          0.1762

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9485  Z= 0.131
  Angle     :  0.612  10.059  12819  Z= 0.328
  Chirality :  0.045   0.186   1430
  Planarity :  0.005   0.061   1622
  Dihedral  : 13.836  75.797   1556
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.71 %
    Favored  : 94.29 %
  Rotamer:
    Outliers :  7.40 %
    Allowed  : 17.44 %
    Favored  : 75.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.48 (0.22), residues: 1156
  helix: -2.65 (0.19), residues: 522
  sheet: -1.13 (0.45), residues: 122
  loop : -2.08 (0.26), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C  10 
 HIS   0.003   0.001   HIS A 292 
 PHE   0.016   0.001   PHE B 121 
 TYR   0.013   0.001   TYR C  50 
 ARG   0.004   0.000   ARG B  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05256 (  289)
  hydrogen bonds       : angle       5.37237 (  816)
  covalent geometry    : bond        0.00277 ( 9484)
  covalent geometry    : angle       0.61171 (12819)
  Misc. bond           : bond        0.00021 (    1)

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

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

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 73
    poor density    : 118
  time to evaluate  : 1.029 
Fit side-chains
REVERT: B   50 GLN cc_start: 0.5664 (OUTLIER) cc_final: 0.5010 (pm20)
REVERT: B   57 ARG cc_start: 0.7559 (mtm110) cc_final: 0.6718 (ptp-170)
REVERT: B  149 MET cc_start: 0.8666 (mtp) cc_final: 0.8457 (mtp)
REVERT: B  150 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8272 (tt0)
REVERT: B  165 ASN cc_start: 0.7738 (p0) cc_final: 0.7300 (p0)
REVERT: B  183 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.7977 (ptt90)
REVERT: B  190 GLU cc_start: 0.8732 (tt0) cc_final: 0.8121 (tp30)
REVERT: B  197 GLU cc_start: 0.8243 (tm-30) cc_final: 0.7910 (tm-30)
REVERT: B  198 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8328 (pp20)
REVERT: B  434 LEU cc_start: 0.7869 (mm) cc_final: 0.7021 (tt)
REVERT: B  440 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.8309 (pp30)
REVERT: E   13 MET cc_start: 0.8176 (OUTLIER) cc_final: 0.7684 (mtp)
REVERT: E   18 TYR cc_start: 0.4315 (OUTLIER) cc_final: 0.4091 (t80)
REVERT: D   58 MET cc_start: 0.8058 (ttp) cc_final: 0.7593 (tpt)
REVERT: D  122 ILE cc_start: 0.8637 (OUTLIER) cc_final: 0.8419 (tp)
REVERT: D  152 LYS cc_start: 0.8947 (tptm) cc_final: 0.8555 (tmtm)
REVERT: A   77 HIS cc_start: 0.6391 (OUTLIER) cc_final: 0.5769 (m90)
REVERT: A  203 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7569 (mmt-90)
REVERT: A  360 PRO cc_start: 0.8940 (Cg_endo) cc_final: 0.8616 (Cg_exo)
REVERT: A  368 GLU cc_start: 0.8978 (OUTLIER) cc_final: 0.8586 (pp20)
REVERT: A  427 THR cc_start: 0.9023 (p) cc_final: 0.8706 (t)
REVERT: A  464 ILE cc_start: 0.9077 (OUTLIER) cc_final: 0.8749 (mt)
  outliers start: 73
  outliers final: 39
  residues processed: 172
  average time/residue: 1.2530
  time to fit residues: 229.6655
Evaluate side-chains
  160 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 109
  time to evaluate  : 1.056 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   50 GLN
Chi-restraints excluded: chain B residue   60 ASN
Chi-restraints excluded: chain B residue   94 TRP
Chi-restraints excluded: chain B residue  107 GLU
Chi-restraints excluded: chain B residue  150 GLU
Chi-restraints excluded: chain B residue  183 ARG
Chi-restraints excluded: chain B residue  189 GLN
Chi-restraints excluded: chain B residue  198 GLU
Chi-restraints excluded: chain B residue  243 SER
Chi-restraints excluded: chain B residue  345 GLU
Chi-restraints excluded: chain B residue  373 MET
Chi-restraints excluded: chain B residue  378 THR
Chi-restraints excluded: chain B residue  406 VAL
Chi-restraints excluded: chain B residue  439 VAL
Chi-restraints excluded: chain B residue  440 GLN
Chi-restraints excluded: chain B residue  473 LEU
Chi-restraints excluded: chain E residue    9 VAL
Chi-restraints excluded: chain E residue   13 MET
Chi-restraints excluded: chain E residue   14 VAL
Chi-restraints excluded: chain E residue   18 TYR
Chi-restraints excluded: chain E residue   38 LEU
Chi-restraints excluded: chain E residue   43 THR
Chi-restraints excluded: chain E residue   44 TYR
Chi-restraints excluded: chain E residue   46 LEU
Chi-restraints excluded: chain D residue    1 MET
Chi-restraints excluded: chain D residue   72 PHE
Chi-restraints excluded: chain D residue  122 ILE
Chi-restraints excluded: chain D residue  145 VAL
Chi-restraints excluded: chain C residue   42 VAL
Chi-restraints excluded: chain C residue   45 VAL
Chi-restraints excluded: chain C residue   51 THR
Chi-restraints excluded: chain A residue   51 ASP
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   77 HIS
Chi-restraints excluded: chain A residue   83 ASN
Chi-restraints excluded: chain A residue  105 SER
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  203 ARG
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  367 LYS
Chi-restraints excluded: chain A residue  368 GLU
Chi-restraints excluded: chain A residue  373 ILE
Chi-restraints excluded: chain A residue  402 THR
Chi-restraints excluded: chain A residue  453 THR
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain A residue  464 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 22 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9980
   chunk 97 optimal weight:    3.9990
   chunk 106 optimal weight:    0.5980
   chunk 0 optimal weight:   10.0000
   chunk 10 optimal weight:    1.9990
   chunk 49 optimal weight:    0.0870
   chunk 66 optimal weight:    0.0070
   chunk 58 optimal weight:    0.9990
   chunk 78 optimal weight:    3.9990
   chunk 110 optimal weight:    3.9990
   overall best weight:    0.4776

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

Flipped N/Q/H residues before XYZ refinement:
D  94 GLN
D 141 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.108335 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.090501 restraints weight = 12401.298|
|-----------------------------------------------------------------------------|
r_work (start): 0.2887 rms_B_bonded: 1.56
r_work: 0.2790 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.2674 rms_B_bonded: 3.45 restraints_weight: 0.2500
r_work (final): 0.2674
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2671
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2671 r_free = 0.2671    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.73   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2671 r_free = 0.2671    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.71   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2671
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8564
moved from start:          0.2159

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   9485  Z= 0.102
  Angle     :  0.518   7.900  12819  Z= 0.276
  Chirality :  0.043   0.185   1430
  Planarity :  0.004   0.035   1622
  Dihedral  : 10.383  59.864   1416
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  5.17 %
    Allowed  : 20.39 %
    Favored  : 74.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.36 (0.24), residues: 1156
  helix: -1.27 (0.22), residues: 521
  sheet: -0.88 (0.47), residues: 124
  loop : -1.96 (0.26), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 134 
 HIS   0.002   0.000   HIS B  47 
 PHE   0.014   0.001   PHE B 121 
 TYR   0.008   0.001   TYR A 166 
 ARG   0.002   0.000   ARG A 181 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03920 (  289)
  hydrogen bonds       : angle       4.58700 (  816)
  covalent geometry    : bond        0.00220 ( 9484)
  covalent geometry    : angle       0.51848 (12819)
  Misc. bond           : bond        0.00026 (    1)

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

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

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 128
  time to evaluate  : 1.152 
Fit side-chains
REVERT: B   57 ARG cc_start: 0.7558 (mtm110) cc_final: 0.6685 (ptp-170)
REVERT: B  190 GLU cc_start: 0.8715 (tt0) cc_final: 0.8076 (tp30)
REVERT: B  197 GLU cc_start: 0.8268 (tm-30) cc_final: 0.7892 (tm-30)
REVERT: B  198 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8293 (pp20)
REVERT: B  218 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8442 (tt0)
REVERT: B  291 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8588 (mt)
REVERT: B  434 LEU cc_start: 0.8113 (mm) cc_final: 0.7149 (tt)
REVERT: B  440 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.8240 (pp30)
REVERT: B  543 ARG cc_start: 0.6248 (OUTLIER) cc_final: 0.5994 (tmm160)
REVERT: E   18 TYR cc_start: 0.4308 (OUTLIER) cc_final: 0.4053 (t80)
REVERT: D   58 MET cc_start: 0.8082 (ttp) cc_final: 0.7548 (tpt)
REVERT: D  122 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8438 (tp)
REVERT: D  152 LYS cc_start: 0.8944 (tptm) cc_final: 0.8538 (tmtm)
REVERT: C   23 VAL cc_start: 0.8664 (t) cc_final: 0.8385 (p)
REVERT: A   62 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7914 (tm-30)
REVERT: A  360 PRO cc_start: 0.8859 (Cg_endo) cc_final: 0.8625 (Cg_exo)
REVERT: A  368 GLU cc_start: 0.8962 (OUTLIER) cc_final: 0.8629 (pp20)
REVERT: A  423 SER cc_start: 0.8305 (m) cc_final: 0.8039 (t)
REVERT: A  427 THR cc_start: 0.8980 (p) cc_final: 0.8686 (t)
REVERT: A  464 ILE cc_start: 0.9040 (OUTLIER) cc_final: 0.8618 (mt)
  outliers start: 51
  outliers final: 22
  residues processed: 164
  average time/residue: 1.2715
  time to fit residues: 221.9989
Evaluate side-chains
  148 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 116
  time to evaluate  : 1.014 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   60 ASN
Chi-restraints excluded: chain B residue   94 TRP
Chi-restraints excluded: chain B residue  107 GLU
Chi-restraints excluded: chain B residue  141 VAL
Chi-restraints excluded: chain B residue  198 GLU
Chi-restraints excluded: chain B residue  218 GLU
Chi-restraints excluded: chain B residue  291 LEU
Chi-restraints excluded: chain B residue  440 GLN
Chi-restraints excluded: chain B residue  473 LEU
Chi-restraints excluded: chain B residue  533 ASP
Chi-restraints excluded: chain B residue  543 ARG
Chi-restraints excluded: chain E residue   18 TYR
Chi-restraints excluded: chain E residue   38 LEU
Chi-restraints excluded: chain E residue   43 THR
Chi-restraints excluded: chain E residue   44 TYR
Chi-restraints excluded: chain E residue   46 LEU
Chi-restraints excluded: chain D residue   33 LEU
Chi-restraints excluded: chain D residue  122 ILE
Chi-restraints excluded: chain D residue  145 VAL
Chi-restraints excluded: chain C residue   43 SER
Chi-restraints excluded: chain A residue   51 ASP
Chi-restraints excluded: chain A residue   62 GLU
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  367 LYS
Chi-restraints excluded: chain A residue  368 GLU
Chi-restraints excluded: chain A residue  402 THR
Chi-restraints excluded: chain A residue  449 THR
Chi-restraints excluded: chain A residue  464 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 113 optimal weight:    5.9990
   chunk 51 optimal weight:    3.9990
   chunk 59 optimal weight:    2.9990
   chunk 78 optimal weight:    4.9990
   chunk 83 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 64 optimal weight:    2.9990
   chunk 111 optimal weight:    3.9990
   chunk 104 optimal weight:    4.9990
   chunk 36 optimal weight:    5.9990
   chunk 86 optimal weight:    0.8980
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
B  50 GLN
D  11 ASN
D 141 GLN
A  77 HIS
A 296 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.101629 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2798 r_free = 0.2798 target = 0.083656 restraints weight = 12299.968|
|-----------------------------------------------------------------------------|
r_work (start): 0.2798 rms_B_bonded: 1.55
r_work: 0.2695 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.2575 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.2575
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2571
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2571 r_free = 0.2571    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.71   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2571 r_free = 0.2571    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2571
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8669
moved from start:          0.2121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053   9485  Z= 0.220
  Angle     :  0.657   8.842  12819  Z= 0.342
  Chirality :  0.048   0.199   1430
  Planarity :  0.005   0.048   1622
  Dihedral  :  9.084  59.357   1369
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 4.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.31 %
    Favored  : 93.69 %
  Rotamer:
    Outliers :  5.27 %
    Allowed  : 21.20 %
    Favored  : 73.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.22 (0.24), residues: 1156
  helix: -1.07 (0.22), residues: 531
  sheet: -1.10 (0.46), residues: 126
  loop : -1.92 (0.26), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP B  94 
 HIS   0.004   0.001   HIS B 542 
 PHE   0.021   0.002   PHE A 138 
 TYR   0.018   0.002   TYR B 342 
 ARG   0.005   0.001   ARG A 181 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05644 (  289)
  hydrogen bonds       : angle       4.72889 (  816)
  covalent geometry    : bond        0.00540 ( 9484)
  covalent geometry    : angle       0.65699 (12819)
  Misc. bond           : bond        0.00043 (    1)

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

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

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 111
  time to evaluate  : 1.091 
Fit side-chains
REVERT: B   57 ARG cc_start: 0.7647 (mtm110) cc_final: 0.6747 (ptp-170)
REVERT: B   93 TYR cc_start: 0.6322 (m-80) cc_final: 0.5777 (m-10)
REVERT: B  106 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7710 (tt0)
REVERT: B  190 GLU cc_start: 0.8749 (tt0) cc_final: 0.8130 (tp30)
REVERT: B  197 GLU cc_start: 0.8293 (tm-30) cc_final: 0.7964 (tm-30)
REVERT: B  198 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8392 (pp20)
REVERT: B  440 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.8291 (pp30)
REVERT: E   13 MET cc_start: 0.8183 (OUTLIER) cc_final: 0.7783 (mtt)
REVERT: E   18 TYR cc_start: 0.4357 (OUTLIER) cc_final: 0.4142 (t80)
REVERT: D   58 MET cc_start: 0.8165 (ttp) cc_final: 0.7607 (tpt)
REVERT: D  122 ILE cc_start: 0.8697 (OUTLIER) cc_final: 0.8475 (tp)
REVERT: D  152 LYS cc_start: 0.9054 (tptm) cc_final: 0.8695 (tmtm)
REVERT: A   62 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7768 (tm-30)
REVERT: A  277 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8957 (mp)
REVERT: A  360 PRO cc_start: 0.8919 (Cg_endo) cc_final: 0.8642 (Cg_exo)
REVERT: A  367 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8372 (ptpp)
REVERT: A  368 GLU cc_start: 0.8997 (OUTLIER) cc_final: 0.8707 (pp20)
REVERT: A  405 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.7216 (ttt90)
REVERT: A  464 ILE cc_start: 0.9154 (OUTLIER) cc_final: 0.8712 (mt)
  outliers start: 52
  outliers final: 25
  residues processed: 149
  average time/residue: 1.3586
  time to fit residues: 215.2723
Evaluate side-chains
  145 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 108
  time to evaluate  : 1.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   50 GLN
Chi-restraints excluded: chain B residue  106 GLU
Chi-restraints excluded: chain B residue  107 GLU
Chi-restraints excluded: chain B residue  141 VAL
Chi-restraints excluded: chain B residue  189 GLN
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  198 GLU
Chi-restraints excluded: chain B residue  345 GLU
Chi-restraints excluded: chain B residue  422 SER
Chi-restraints excluded: chain B residue  440 GLN
Chi-restraints excluded: chain B residue  473 LEU
Chi-restraints excluded: chain B residue  517 THR
Chi-restraints excluded: chain E residue   13 MET
Chi-restraints excluded: chain E residue   18 TYR
Chi-restraints excluded: chain E residue   38 LEU
Chi-restraints excluded: chain E residue   43 THR
Chi-restraints excluded: chain E residue   44 TYR
Chi-restraints excluded: chain E residue   46 LEU
Chi-restraints excluded: chain D residue   72 PHE
Chi-restraints excluded: chain D residue  118 LYS
Chi-restraints excluded: chain D residue  122 ILE
Chi-restraints excluded: chain D residue  145 VAL
Chi-restraints excluded: chain C residue   42 VAL
Chi-restraints excluded: chain C residue   51 THR
Chi-restraints excluded: chain A residue   51 ASP
Chi-restraints excluded: chain A residue   62 GLU
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  367 LYS
Chi-restraints excluded: chain A residue  368 GLU
Chi-restraints excluded: chain A residue  405 ARG
Chi-restraints excluded: chain A residue  449 THR
Chi-restraints excluded: chain A residue  464 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 33 optimal weight:    4.9990
   chunk 64 optimal weight:    3.9990
   chunk 98 optimal weight:    5.9990
   chunk 81 optimal weight:    0.5980
   chunk 69 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9990
   chunk 38 optimal weight:    0.2980
   chunk 24 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 56 optimal weight:    4.9990
   chunk 93 optimal weight:    0.6980
   overall best weight:    0.7184

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

Flipped N/Q/H residues before XYZ refinement:
B 165 ASN
A  77 HIS
A 296 ASN
A 407 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.105204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2854 r_free = 0.2854 target = 0.087215 restraints weight = 12302.871|
|-----------------------------------------------------------------------------|
r_work (start): 0.2846 rms_B_bonded: 1.56
r_work: 0.2743 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.2624 rms_B_bonded: 3.48 restraints_weight: 0.2500
r_work (final): 0.2624
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2631
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2631 r_free = 0.2631    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2631 r_free = 0.2631    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.75   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2631
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8613
moved from start:          0.2345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   9485  Z= 0.109
  Angle     :  0.533   7.792  12819  Z= 0.280
  Chirality :  0.043   0.181   1430
  Planarity :  0.004   0.043   1622
  Dihedral  :  8.495  59.751   1364
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 3.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.28 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 22.21 %
    Favored  : 73.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.75 (0.24), residues: 1156
  helix: -0.51 (0.23), residues: 530
  sheet: -0.95 (0.47), residues: 124
  loop : -1.88 (0.26), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 134 
 HIS   0.001   0.000   HIS A 374 
 PHE   0.012   0.001   PHE B 121 
 TYR   0.010   0.001   TYR B 235 
 ARG   0.002   0.000   ARG D  99 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03896 (  289)
  hydrogen bonds       : angle       4.44609 (  816)
  covalent geometry    : bond        0.00246 ( 9484)
  covalent geometry    : angle       0.53281 (12819)
  Misc. bond           : bond        0.00017 (    1)

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

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

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 112
  time to evaluate  : 1.044 
Fit side-chains
REVERT: B   93 TYR cc_start: 0.6496 (m-80) cc_final: 0.5905 (m-10)
REVERT: B  106 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7717 (tt0)
REVERT: B  126 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8443 (mp)
REVERT: B  185 THR cc_start: 0.8313 (p) cc_final: 0.8034 (t)
REVERT: B  190 GLU cc_start: 0.8748 (tt0) cc_final: 0.8156 (tp30)
REVERT: B  197 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7907 (tm-30)
REVERT: B  198 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8388 (pp20)
REVERT: B  291 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8749 (mt)
REVERT: B  440 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.8272 (pp30)
REVERT: E   13 MET cc_start: 0.8105 (mtp) cc_final: 0.7733 (OUTLIER)
REVERT: E   18 TYR cc_start: 0.4504 (OUTLIER) cc_final: 0.4217 (t80)
REVERT: D   58 MET cc_start: 0.8118 (ttp) cc_final: 0.7545 (tpt)
REVERT: D  122 ILE cc_start: 0.8674 (OUTLIER) cc_final: 0.8452 (tp)
REVERT: D  152 LYS cc_start: 0.9046 (tptm) cc_final: 0.8673 (tmtm)
REVERT: A   62 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7789 (tm-30)
REVERT: A  360 PRO cc_start: 0.8887 (Cg_endo) cc_final: 0.8639 (Cg_exo)
REVERT: A  367 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8308 (ptpp)
REVERT: A  368 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.8659 (pp20)
REVERT: A  423 SER cc_start: 0.8336 (m) cc_final: 0.8020 (t)
REVERT: A  464 ILE cc_start: 0.9112 (OUTLIER) cc_final: 0.8700 (mt)
  outliers start: 42
  outliers final: 19
  residues processed: 144
  average time/residue: 1.2921
  time to fit residues: 198.2347
Evaluate side-chains
  134 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 104
  time to evaluate  : 1.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   94 TRP
Chi-restraints excluded: chain B residue  106 GLU
Chi-restraints excluded: chain B residue  107 GLU
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  141 VAL
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  197 GLU
Chi-restraints excluded: chain B residue  198 GLU
Chi-restraints excluded: chain B residue  291 LEU
Chi-restraints excluded: chain B residue  440 GLN
Chi-restraints excluded: chain B residue  473 LEU
Chi-restraints excluded: chain B residue  517 THR
Chi-restraints excluded: chain B residue  533 ASP
Chi-restraints excluded: chain E residue    9 VAL
Chi-restraints excluded: chain E residue   18 TYR
Chi-restraints excluded: chain E residue   38 LEU
Chi-restraints excluded: chain E residue   43 THR
Chi-restraints excluded: chain E residue   44 TYR
Chi-restraints excluded: chain D residue  118 LYS
Chi-restraints excluded: chain D residue  122 ILE
Chi-restraints excluded: chain A residue   51 ASP
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   62 GLU
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  367 LYS
Chi-restraints excluded: chain A residue  368 GLU
Chi-restraints excluded: chain A residue  449 THR
Chi-restraints excluded: chain A residue  464 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 52 optimal weight:    5.9990
   chunk 81 optimal weight:    4.9990
   chunk 94 optimal weight:    2.9990
   chunk 100 optimal weight:    4.9990
   chunk 28 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 67 optimal weight:    0.5980
   chunk 73 optimal weight:    0.9990
   chunk 110 optimal weight:    2.9990
   chunk 101 optimal weight:    5.9990
   chunk 103 optimal weight:    0.7980
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
A  77 HIS
A  83 ASN
A 296 ASN
A 407 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.103131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2814 r_free = 0.2814 target = 0.084712 restraints weight = 12227.449|
|-----------------------------------------------------------------------------|
r_work (start): 0.2809 rms_B_bonded: 1.64
r_work: 0.2702 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.2581 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.2581
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2582
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2582 r_free = 0.2582    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.75   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2582 r_free = 0.2582    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.72   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2582
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8662
moved from start:          0.2344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9485  Z= 0.157
  Angle     :  0.578   8.218  12819  Z= 0.301
  Chirality :  0.045   0.187   1430
  Planarity :  0.004   0.046   1622
  Dihedral  :  8.380  59.774   1360
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 3.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.06 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 23.02 %
    Favored  : 72.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.61 (0.24), residues: 1156
  helix: -0.36 (0.23), residues: 537
  sheet: -0.92 (0.47), residues: 123
  loop : -1.84 (0.26), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C  32 
 HIS   0.002   0.001   HIS B 542 
 PHE   0.017   0.002   PHE A 138 
 TYR   0.014   0.001   TYR B 342 
 ARG   0.003   0.000   ARG D  99 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04599 (  289)
  hydrogen bonds       : angle       4.46606 (  816)
  covalent geometry    : bond        0.00382 ( 9484)
  covalent geometry    : angle       0.57751 (12819)
  Misc. bond           : bond        0.00015 (    1)

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

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

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 103
  time to evaluate  : 1.043 
Fit side-chains
REVERT: B   93 TYR cc_start: 0.6542 (m-80) cc_final: 0.6062 (m-10)
REVERT: B  106 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7759 (tt0)
REVERT: B  165 ASN cc_start: 0.7725 (p0) cc_final: 0.7492 (p0)
REVERT: B  185 THR cc_start: 0.8361 (p) cc_final: 0.8089 (t)
REVERT: B  190 GLU cc_start: 0.8784 (tt0) cc_final: 0.8161 (tp30)
REVERT: B  197 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7968 (tm-30)
REVERT: B  198 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8398 (pp20)
REVERT: B  291 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8829 (mt)
REVERT: E   13 MET cc_start: 0.8162 (mtp) cc_final: 0.7779 (mtt)
REVERT: E   18 TYR cc_start: 0.4475 (OUTLIER) cc_final: 0.4217 (t80)
REVERT: D   58 MET cc_start: 0.8309 (ttp) cc_final: 0.7682 (tpt)
REVERT: D  152 LYS cc_start: 0.9070 (tptm) cc_final: 0.8643 (tmtm)
REVERT: A   58 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7572 (mt-10)
REVERT: A   62 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7822 (tm-30)
REVERT: A  277 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8928 (mp)
REVERT: A  360 PRO cc_start: 0.8898 (Cg_endo) cc_final: 0.8635 (Cg_exo)
REVERT: A  367 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8320 (ptpp)
REVERT: A  368 GLU cc_start: 0.8939 (OUTLIER) cc_final: 0.8678 (pp20)
REVERT: A  423 SER cc_start: 0.8345 (m) cc_final: 0.8024 (t)
REVERT: A  464 ILE cc_start: 0.9123 (OUTLIER) cc_final: 0.8702 (mt)
  outliers start: 42
  outliers final: 22
  residues processed: 137
  average time/residue: 1.3717
  time to fit residues: 199.9449
Evaluate side-chains
  135 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 102
  time to evaluate  : 1.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  106 GLU
Chi-restraints excluded: chain B residue  107 GLU
Chi-restraints excluded: chain B residue  141 VAL
Chi-restraints excluded: chain B residue  189 GLN
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  197 GLU
Chi-restraints excluded: chain B residue  198 GLU
Chi-restraints excluded: chain B residue  258 SER
Chi-restraints excluded: chain B residue  291 LEU
Chi-restraints excluded: chain B residue  345 GLU
Chi-restraints excluded: chain B residue  415 VAL
Chi-restraints excluded: chain B residue  473 LEU
Chi-restraints excluded: chain B residue  517 THR
Chi-restraints excluded: chain E residue    9 VAL
Chi-restraints excluded: chain E residue   18 TYR
Chi-restraints excluded: chain E residue   38 LEU
Chi-restraints excluded: chain E residue   43 THR
Chi-restraints excluded: chain D residue   33 LEU
Chi-restraints excluded: chain D residue  118 LYS
Chi-restraints excluded: chain D residue  134 VAL
Chi-restraints excluded: chain A residue   51 ASP
Chi-restraints excluded: chain A residue   58 GLU
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   62 GLU
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  367 LYS
Chi-restraints excluded: chain A residue  368 GLU
Chi-restraints excluded: chain A residue  419 CYS
Chi-restraints excluded: chain A residue  449 THR
Chi-restraints excluded: chain A residue  464 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 6 optimal weight:    3.9990
   chunk 61 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9980
   chunk 59 optimal weight:    0.9980
   chunk 23 optimal weight:    0.7980
   chunk 54 optimal weight:    0.7980
   chunk 65 optimal weight:    0.0570
   chunk 46 optimal weight:    6.9990
   chunk 37 optimal weight:    1.9990
   chunk 38 optimal weight:    0.0000
   chunk 85 optimal weight:    2.9990
   overall best weight:    0.5302

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

Flipped N/Q/H residues before XYZ refinement:
A  77 HIS
A  83 ASN
A 296 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.106483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2873 r_free = 0.2873 target = 0.088524 restraints weight = 12281.491|
|-----------------------------------------------------------------------------|
r_work (start): 0.2870 rms_B_bonded: 1.56
r_work: 0.2769 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.2651 rms_B_bonded: 3.47 restraints_weight: 0.2500
r_work (final): 0.2651
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2655
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2655 r_free = 0.2655    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.72   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2655 r_free = 0.2655    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.67   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2655
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8586
moved from start:          0.2569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   9485  Z= 0.100
  Angle     :  0.502   7.485  12819  Z= 0.262
  Chirality :  0.043   0.186   1430
  Planarity :  0.004   0.042   1622
  Dihedral  :  7.646  59.905   1353
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 22.92 %
    Favored  : 72.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.17 (0.25), residues: 1156
  helix:  0.14 (0.23), residues: 538
  sheet: -0.86 (0.48), residues: 123
  loop : -1.76 (0.27), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 134 
 HIS   0.002   0.000   HIS B  47 
 PHE   0.012   0.001   PHE B 121 
 TYR   0.008   0.001   TYR E  23 
 ARG   0.002   0.000   ARG B 124 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03401 (  289)
  hydrogen bonds       : angle       4.25452 (  816)
  covalent geometry    : bond        0.00225 ( 9484)
  covalent geometry    : angle       0.50176 (12819)
  Misc. bond           : bond        0.00006 (    1)

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

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

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 110
  time to evaluate  : 1.166 
Fit side-chains
REVERT: B   93 TYR cc_start: 0.6493 (m-80) cc_final: 0.5971 (m-10)
REVERT: B  106 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7760 (tt0)
REVERT: B  126 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8511 (mt)
REVERT: B  185 THR cc_start: 0.8323 (p) cc_final: 0.8063 (t)
REVERT: B  190 GLU cc_start: 0.8711 (tt0) cc_final: 0.8136 (tp30)
REVERT: B  197 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7910 (tm-30)
REVERT: B  198 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8372 (pp20)
REVERT: B  252 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8460 (tttm)
REVERT: B  291 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8709 (mt)
REVERT: E   13 MET cc_start: 0.8117 (mtp) cc_final: 0.7744 (mtt)
REVERT: E   18 TYR cc_start: 0.4475 (OUTLIER) cc_final: 0.4247 (t80)
REVERT: D   58 MET cc_start: 0.8107 (ttp) cc_final: 0.7523 (tpt)
REVERT: D  152 LYS cc_start: 0.9044 (tptm) cc_final: 0.8597 (tmtm)
REVERT: A   58 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7468 (mp0)
REVERT: A   62 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7823 (tm-30)
REVERT: A  277 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8897 (mp)
REVERT: A  360 PRO cc_start: 0.8877 (Cg_endo) cc_final: 0.8664 (Cg_exo)
REVERT: A  367 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8530 (ptmt)
REVERT: A  368 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8591 (pp20)
REVERT: A  423 SER cc_start: 0.8173 (m) cc_final: 0.7900 (t)
REVERT: A  454 GLU cc_start: 0.7368 (tt0) cc_final: 0.7165 (mt-10)
REVERT: A  464 ILE cc_start: 0.9053 (OUTLIER) cc_final: 0.8616 (mt)
  outliers start: 41
  outliers final: 17
  residues processed: 139
  average time/residue: 1.3575
  time to fit residues: 200.5286
Evaluate side-chains
  134 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 104
  time to evaluate  : 1.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  106 GLU
Chi-restraints excluded: chain B residue  107 GLU
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  141 VAL
Chi-restraints excluded: chain B residue  189 GLN
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  197 GLU
Chi-restraints excluded: chain B residue  198 GLU
Chi-restraints excluded: chain B residue  252 LYS
Chi-restraints excluded: chain B residue  291 LEU
Chi-restraints excluded: chain B residue  473 LEU
Chi-restraints excluded: chain B residue  517 THR
Chi-restraints excluded: chain B residue  533 ASP
Chi-restraints excluded: chain E residue    9 VAL
Chi-restraints excluded: chain E residue   18 TYR
Chi-restraints excluded: chain E residue   38 LEU
Chi-restraints excluded: chain D residue  118 LYS
Chi-restraints excluded: chain D residue  134 VAL
Chi-restraints excluded: chain A residue   51 ASP
Chi-restraints excluded: chain A residue   58 GLU
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   62 GLU
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  367 LYS
Chi-restraints excluded: chain A residue  368 GLU
Chi-restraints excluded: chain A residue  449 THR
Chi-restraints excluded: chain A residue  464 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 89 optimal weight:    0.6980
   chunk 65 optimal weight:    5.9990
   chunk 1 optimal weight:    3.9990
   chunk 63 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9980
   chunk 108 optimal weight:    0.9980
   chunk 48 optimal weight:    5.9990
   chunk 86 optimal weight:    1.9990
   chunk 93 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
B 165 ASN
A  77 HIS
A  83 ASN
A 296 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.103690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2822 r_free = 0.2822 target = 0.085219 restraints weight = 12405.338|
|-----------------------------------------------------------------------------|
r_work (start): 0.2817 rms_B_bonded: 1.65
r_work: 0.2708 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.2586 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.2586
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2585
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2585 r_free = 0.2585    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.67   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2585 r_free = 0.2585    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.71   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2585
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8655
moved from start:          0.2470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9485  Z= 0.146
  Angle     :  0.569  10.378  12819  Z= 0.293
  Chirality :  0.045   0.189   1430
  Planarity :  0.004   0.047   1622
  Dihedral  :  7.726  59.898   1353
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 3.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.14 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 22.41 %
    Favored  : 73.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.12 (0.25), residues: 1156
  helix:  0.20 (0.23), residues: 538
  sheet: -0.88 (0.48), residues: 123
  loop : -1.75 (0.27), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 134 
 HIS   0.002   0.001   HIS B  47 
 PHE   0.017   0.002   PHE A 138 
 TYR   0.014   0.001   TYR B 342 
 ARG   0.003   0.000   ARG D  99 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04364 (  289)
  hydrogen bonds       : angle       4.34112 (  816)
  covalent geometry    : bond        0.00352 ( 9484)
  covalent geometry    : angle       0.56876 (12819)
  Misc. bond           : bond        0.00013 (    1)

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

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

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 100
  time to evaluate  : 1.145 
Fit side-chains
REVERT: B   93 TYR cc_start: 0.6572 (m-80) cc_final: 0.6088 (m-10)
REVERT: B  106 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7780 (tt0)
REVERT: B  185 THR cc_start: 0.8349 (p) cc_final: 0.8083 (t)
REVERT: B  190 GLU cc_start: 0.8739 (tt0) cc_final: 0.8198 (tp30)
REVERT: B  197 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7967 (tm-30)
REVERT: B  198 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.7949 (pp20)
REVERT: B  291 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8772 (mt)
REVERT: E   13 MET cc_start: 0.8167 (OUTLIER) cc_final: 0.7792 (mtt)
REVERT: E   18 TYR cc_start: 0.4480 (OUTLIER) cc_final: 0.4250 (t80)
REVERT: D  152 LYS cc_start: 0.9065 (tptm) cc_final: 0.8633 (tmtm)
REVERT: A   58 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7421 (mp0)
REVERT: A   62 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.7831 (tm-30)
REVERT: A  277 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8933 (mp)
REVERT: A  360 PRO cc_start: 0.8875 (Cg_endo) cc_final: 0.8641 (Cg_exo)
REVERT: A  367 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8563 (ptmt)
REVERT: A  368 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.8633 (pp20)
REVERT: A  423 SER cc_start: 0.8221 (m) cc_final: 0.7927 (t)
REVERT: A  454 GLU cc_start: 0.7430 (tt0) cc_final: 0.7216 (mt-10)
REVERT: A  464 ILE cc_start: 0.9121 (OUTLIER) cc_final: 0.8708 (mt)
  outliers start: 41
  outliers final: 22
  residues processed: 131
  average time/residue: 1.3085
  time to fit residues: 182.6679
Evaluate side-chains
  134 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 100
  time to evaluate  : 0.992 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  106 GLU
Chi-restraints excluded: chain B residue  107 GLU
Chi-restraints excluded: chain B residue  141 VAL
Chi-restraints excluded: chain B residue  165 ASN
Chi-restraints excluded: chain B residue  189 GLN
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  197 GLU
Chi-restraints excluded: chain B residue  198 GLU
Chi-restraints excluded: chain B residue  258 SER
Chi-restraints excluded: chain B residue  291 LEU
Chi-restraints excluded: chain B residue  345 GLU
Chi-restraints excluded: chain B residue  473 LEU
Chi-restraints excluded: chain B residue  517 THR
Chi-restraints excluded: chain E residue    9 VAL
Chi-restraints excluded: chain E residue   13 MET
Chi-restraints excluded: chain E residue   18 TYR
Chi-restraints excluded: chain E residue   38 LEU
Chi-restraints excluded: chain D residue  118 LYS
Chi-restraints excluded: chain D residue  134 VAL
Chi-restraints excluded: chain C residue   51 THR
Chi-restraints excluded: chain A residue   51 ASP
Chi-restraints excluded: chain A residue   58 GLU
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   62 GLU
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  367 LYS
Chi-restraints excluded: chain A residue  368 GLU
Chi-restraints excluded: chain A residue  419 CYS
Chi-restraints excluded: chain A residue  449 THR
Chi-restraints excluded: chain A residue  464 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 18 optimal weight:    0.9990
   chunk 21 optimal weight:    2.9990
   chunk 44 optimal weight:    2.9990
   chunk 32 optimal weight:    3.9990
   chunk 11 optimal weight:    3.9990
   chunk 47 optimal weight:    5.9990
   chunk 13 optimal weight:    0.7980
   chunk 48 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9990
   chunk 99 optimal weight:    3.9990
   chunk 79 optimal weight:    0.9980
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
B 165 ASN
A  77 HIS
A  83 ASN
A 407 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.104234 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2837 r_free = 0.2837 target = 0.086263 restraints weight = 12122.918|
|-----------------------------------------------------------------------------|
r_work (start): 0.2830 rms_B_bonded: 1.56
r_work: 0.2726 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.2607 rms_B_bonded: 3.45 restraints_weight: 0.2500
r_work (final): 0.2607
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2615
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2615 r_free = 0.2615    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.71   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2615 r_free = 0.2615    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.71   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2615
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8624
moved from start:          0.2513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9485  Z= 0.133
  Angle     :  0.559  11.579  12819  Z= 0.289
  Chirality :  0.045   0.192   1430
  Planarity :  0.004   0.048   1622
  Dihedral  :  7.662  59.489   1353
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 3.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 22.72 %
    Favored  : 73.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.02 (0.25), residues: 1156
  helix:  0.31 (0.23), residues: 539
  sheet: -0.86 (0.48), residues: 123
  loop : -1.72 (0.27), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 134 
 HIS   0.002   0.001   HIS B  47 
 PHE   0.014   0.001   PHE A 138 
 TYR   0.012   0.001   TYR B 342 
 ARG   0.003   0.000   ARG D  99 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04145 (  289)
  hydrogen bonds       : angle       4.35260 (  816)
  covalent geometry    : bond        0.00322 ( 9484)
  covalent geometry    : angle       0.55938 (12819)
  Misc. bond           : bond        0.00010 (    1)

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

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

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 101
  time to evaluate  : 1.144 
Fit side-chains
REVERT: B   93 TYR cc_start: 0.6553 (m-80) cc_final: 0.6071 (m-10)
REVERT: B  106 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7749 (tt0)
REVERT: B  185 THR cc_start: 0.8325 (p) cc_final: 0.8063 (t)
REVERT: B  190 GLU cc_start: 0.8669 (tt0) cc_final: 0.8098 (tp30)
REVERT: B  197 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7964 (tm-30)
REVERT: B  198 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.7937 (pp20)
REVERT: B  252 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8460 (tttm)
REVERT: B  291 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8759 (mt)
REVERT: E   13 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7781 (mtt)
REVERT: E   18 TYR cc_start: 0.4479 (OUTLIER) cc_final: 0.4279 (t80)
REVERT: D   60 MET cc_start: 0.9048 (ttt) cc_final: 0.8727 (ttt)
REVERT: D  152 LYS cc_start: 0.9050 (tptm) cc_final: 0.8616 (tmtm)
REVERT: A   58 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7397 (mp0)
REVERT: A   62 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7781 (tm-30)
REVERT: A  249 MET cc_start: 0.9080 (OUTLIER) cc_final: 0.8753 (ttt)
REVERT: A  277 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8905 (mp)
REVERT: A  360 PRO cc_start: 0.8872 (Cg_endo) cc_final: 0.8642 (Cg_exo)
REVERT: A  367 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8574 (ptmt)
REVERT: A  368 GLU cc_start: 0.8885 (OUTLIER) cc_final: 0.8618 (pp20)
REVERT: A  423 SER cc_start: 0.8202 (m) cc_final: 0.7941 (t)
REVERT: A  454 GLU cc_start: 0.7386 (tt0) cc_final: 0.7173 (mt-10)
REVERT: A  464 ILE cc_start: 0.9110 (OUTLIER) cc_final: 0.8697 (mt)
  outliers start: 39
  outliers final: 22
  residues processed: 129
  average time/residue: 1.3150
  time to fit residues: 180.6765
Evaluate side-chains
  136 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 100
  time to evaluate  : 1.029 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  106 GLU
Chi-restraints excluded: chain B residue  107 GLU
Chi-restraints excluded: chain B residue  141 VAL
Chi-restraints excluded: chain B residue  189 GLN
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  197 GLU
Chi-restraints excluded: chain B residue  198 GLU
Chi-restraints excluded: chain B residue  252 LYS
Chi-restraints excluded: chain B residue  258 SER
Chi-restraints excluded: chain B residue  291 LEU
Chi-restraints excluded: chain B residue  345 GLU
Chi-restraints excluded: chain B residue  415 VAL
Chi-restraints excluded: chain B residue  473 LEU
Chi-restraints excluded: chain B residue  517 THR
Chi-restraints excluded: chain E residue    9 VAL
Chi-restraints excluded: chain E residue   13 MET
Chi-restraints excluded: chain E residue   18 TYR
Chi-restraints excluded: chain E residue   38 LEU
Chi-restraints excluded: chain D residue  118 LYS
Chi-restraints excluded: chain D residue  134 VAL
Chi-restraints excluded: chain C residue   51 THR
Chi-restraints excluded: chain A residue   51 ASP
Chi-restraints excluded: chain A residue   58 GLU
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   62 GLU
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  249 MET
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  367 LYS
Chi-restraints excluded: chain A residue  368 GLU
Chi-restraints excluded: chain A residue  419 CYS
Chi-restraints excluded: chain A residue  449 THR
Chi-restraints excluded: chain A residue  464 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 92 optimal weight:    2.9990
   chunk 99 optimal weight:    3.9990
   chunk 5 optimal weight:    8.9990
   chunk 64 optimal weight:    2.9990
   chunk 0 optimal weight:   20.0000
   chunk 38 optimal weight:    2.9990
   chunk 98 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 8 optimal weight:    4.9990
   chunk 82 optimal weight:    3.9990
   chunk 45 optimal weight:    0.8980
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
B 165 ASN
A  83 ASN
A 407 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.101288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2783 r_free = 0.2783 target = 0.082847 restraints weight = 12452.421|
|-----------------------------------------------------------------------------|
r_work (start): 0.2776 rms_B_bonded: 1.64
r_work: 0.2666 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.2545 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.2545
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2544
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2544 r_free = 0.2544    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.71   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2544 r_free = 0.2544    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.73   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2544
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8687
moved from start:          0.2409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.050   9485  Z= 0.228
  Angle     :  0.664  11.625  12819  Z= 0.340
  Chirality :  0.049   0.197   1430
  Planarity :  0.005   0.054   1622
  Dihedral  :  8.082  59.951   1353
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 4.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.31 %
    Favored  : 93.69 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 23.33 %
    Favored  : 72.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.30 (0.24), residues: 1156
  helix:  0.02 (0.23), residues: 537
  sheet: -0.94 (0.47), residues: 123
  loop : -1.80 (0.27), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP B 307 
 HIS   0.004   0.001   HIS D  65 
 PHE   0.024   0.002   PHE A 138 
 TYR   0.018   0.002   TYR B 342 
 ARG   0.005   0.001   ARG A 151 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05437 (  289)
  hydrogen bonds       : angle       4.57646 (  816)
  covalent geometry    : bond        0.00571 ( 9484)
  covalent geometry    : angle       0.66436 (12819)
  Misc. bond           : bond        0.00016 (    1)

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

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

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 98
  time to evaluate  : 1.142 
Fit side-chains
REVERT: B   93 TYR cc_start: 0.6468 (m-80) cc_final: 0.6049 (m-10)
REVERT: B  106 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7787 (tt0)
REVERT: B  190 GLU cc_start: 0.8723 (tt0) cc_final: 0.8120 (tp30)
REVERT: B  197 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.8020 (tm-30)
REVERT: B  198 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8459 (pt0)
REVERT: B  291 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8878 (mt)
REVERT: E   13 MET cc_start: 0.8221 (OUTLIER) cc_final: 0.7819 (mtt)
REVERT: E   42 LYS cc_start: 0.8278 (ptmm) cc_final: 0.8051 (mmmt)
REVERT: D   60 MET cc_start: 0.9060 (ttt) cc_final: 0.8787 (ttt)
REVERT: C   29 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.7995 (mp)
REVERT: A   62 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7816 (tm-30)
REVERT: A  277 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8896 (mp)
REVERT: A  360 PRO cc_start: 0.8913 (Cg_endo) cc_final: 0.8615 (Cg_exo)
REVERT: A  367 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.8300 (ptpp)
REVERT: A  368 GLU cc_start: 0.8943 (OUTLIER) cc_final: 0.8665 (pp20)
REVERT: A  407 GLN cc_start: 0.7965 (mt0) cc_final: 0.7497 (mt0)
REVERT: A  423 SER cc_start: 0.8282 (m) cc_final: 0.7955 (t)
REVERT: A  464 ILE cc_start: 0.9122 (OUTLIER) cc_final: 0.8681 (mt)
  outliers start: 37
  outliers final: 22
  residues processed: 127
  average time/residue: 1.4036
  time to fit residues: 189.5913
Evaluate side-chains
  130 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 97
  time to evaluate  : 1.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  106 GLU
Chi-restraints excluded: chain B residue  107 GLU
Chi-restraints excluded: chain B residue  141 VAL
Chi-restraints excluded: chain B residue  189 GLN
Chi-restraints excluded: chain B residue  195 VAL
Chi-restraints excluded: chain B residue  197 GLU
Chi-restraints excluded: chain B residue  198 GLU
Chi-restraints excluded: chain B residue  258 SER
Chi-restraints excluded: chain B residue  291 LEU
Chi-restraints excluded: chain B residue  345 GLU
Chi-restraints excluded: chain B residue  415 VAL
Chi-restraints excluded: chain B residue  473 LEU
Chi-restraints excluded: chain B residue  517 THR
Chi-restraints excluded: chain E residue    9 VAL
Chi-restraints excluded: chain E residue   13 MET
Chi-restraints excluded: chain E residue   38 LEU
Chi-restraints excluded: chain D residue  118 LYS
Chi-restraints excluded: chain D residue  134 VAL
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue   51 THR
Chi-restraints excluded: chain A residue   51 ASP
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   62 GLU
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  367 LYS
Chi-restraints excluded: chain A residue  368 GLU
Chi-restraints excluded: chain A residue  419 CYS
Chi-restraints excluded: chain A residue  449 THR
Chi-restraints excluded: chain A residue  464 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 61 optimal weight:    2.9990
   chunk 43 optimal weight:    0.7980
   chunk 112 optimal weight:    0.9980
   chunk 106 optimal weight:    0.1980
   chunk 56 optimal weight:    3.9990
   chunk 108 optimal weight:    3.9990
   chunk 78 optimal weight:    3.9990
   chunk 26 optimal weight:    0.7980
   chunk 107 optimal weight:    0.7980
   chunk 72 optimal weight:    0.6980
   chunk 22 optimal weight:    0.7980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B 165 ASN
A  83 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.106217 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2869 r_free = 0.2869 target = 0.088387 restraints weight = 12105.342|
|-----------------------------------------------------------------------------|
r_work (start): 0.2855 rms_B_bonded: 1.55
r_work: 0.2753 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.2634 rms_B_bonded: 3.45 restraints_weight: 0.2500
r_work (final): 0.2634
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2633
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2633 r_free = 0.2633    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.73   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2633 r_free = 0.2633    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.73   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2633
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8602
moved from start:          0.2609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044   9485  Z= 0.106
  Angle     :  0.525  11.313  12819  Z= 0.273
  Chirality :  0.043   0.182   1430
  Planarity :  0.004   0.045   1622
  Dihedral  :  7.428  58.338   1351
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 3.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 23.53 %
    Favored  : 73.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.89 (0.25), residues: 1156
  helix:  0.41 (0.23), residues: 545
  sheet: -0.81 (0.48), residues: 123
  loop : -1.68 (0.27), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C  32 
 HIS   0.002   0.000   HIS B  47 
 PHE   0.011   0.001   PHE A 209 
 TYR   0.008   0.001   TYR E  23 
 ARG   0.002   0.000   ARG A 270 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03558 (  289)
  hydrogen bonds       : angle       4.31135 (  816)
  covalent geometry    : bond        0.00245 ( 9484)
  covalent geometry    : angle       0.52459 (12819)
  Misc. bond           : bond        0.00012 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6715.04 seconds
wall clock time: 116 minutes 9.72 seconds (6969.72 seconds total)