Starting phenix.real_space_refine
on Mon Apr 28 14:24:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6irs_9721/04_2025/6irs_9721.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6irs_9721/04_2025/6irs_9721.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6irs_9721/04_2025/6irs_9721.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6irs_9721/04_2025/6irs_9721.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6irs_9721/04_2025/6irs_9721.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6irs_9721/04_2025/6irs_9721.cif"
  }
  resolution = 3.3
  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=   0.007
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       2      5.49       5
     S      27      5.16       5
     C    4807      2.51       5
     N    1172      2.21       5
     O    1329      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 7337
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 3650
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 469, 3650
          Classifications: {'peptide': 469}
          Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 446}
    Chain: "B"
      Number of atoms: 3479
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 457, 3479
          Classifications: {'peptide': 457}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'PTRANS': 24, 'TRANS': 432}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 52
          Unresolved non-hydrogen angles: 67
          Unresolved non-hydrogen dihedrals: 42
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 31
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 96
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 96
          Unusual residues: {'3PH': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 4.91, per 1000 atoms: 0.67
  Number of scatterers: 7337
  At special positions: 0
  Unit cell: (82.916, 84.007, 124.374, 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      27     16.00
     P       2     15.00
     O    1329      8.00
     N    1172      7.00
     C    4807      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 211 " - pdb=" SG  CYS B 164 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
    NAG-ASN
      " NAG C   1 " - " ASN A 507 "
      " NAG D   1 " - " ASN A 366 "
      " NAG E   1 " - " ASN A 382 "
      " NAG F   1 " - " ASN A 425 "
  Time building additional restraints: 1.90
  Conformation dependent library (CDL) restraints added in 996.6 milliseconds
  

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1704

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 3 sheets defined
      57.8% alpha, 5.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.73
  Creating SS restraints...
    Processing helix  chain 'A' and resid 167 through 175
    Processing helix  chain 'A' and resid 180 through 207
      removed outlier: 3.677A  pdb=" N   LEU A 186 " --> pdb=" O   THR A 182 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   TRP A 191 " --> pdb=" O   LEU A 187 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   LEU A 192 " --> pdb=" O   LEU A 188 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   MET A 197 " --> pdb=" O   GLY A 193 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   ILE A 204 " --> pdb=" O   GLY A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 218 through 223
      removed outlier: 3.863A  pdb=" N   THR A 222 " --> pdb=" O   TRP A 219 " (cutoff:3.500A)
      removed outlier: 4.216A  pdb=" N   GLY A 223 " --> pdb=" O   TRP A 220 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 236
    Processing helix  chain 'A' and resid 241 through 246
    Processing helix  chain 'A' and resid 248 through 253
    Processing helix  chain 'A' and resid 287 through 301
      removed outlier: 3.631A  pdb=" N   LYS A 300 " --> pdb=" O   GLN A 296 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   LYS A 301 " --> pdb=" O   SER A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 342
      removed outlier: 4.212A  pdb=" N   GLU A 336 " --> pdb=" O   LYS A 332 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   LEU A 339 " --> pdb=" O   LEU A 335 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 350 through 354
    Processing helix  chain 'A' and resid 356 through 372
      removed outlier: 3.676A  pdb=" N   PHE A 360 " --> pdb=" O   ASP A 356 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   ALA A 362 " --> pdb=" O   SER A 358 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   PHE A 371 " --> pdb=" O   ILE A 367 " (cutoff:3.500A)
      removed outlier: 4.240A  pdb=" N   SER A 372 " --> pdb=" O   THR A 368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 393
      removed outlier: 3.837A  pdb=" N   LEU A 390 " --> pdb=" O   LEU A 386 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   SER A 391 " --> pdb=" O   GLN A 387 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   LEU A 392 " --> pdb=" O   GLN A 388 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 412 through 428
      removed outlier: 3.530A  pdb=" N   THR A 427 " --> pdb=" O   TYR A 423 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 450 through 461
      removed outlier: 3.921A  pdb=" N   GLN A 455 " --> pdb=" O   LEU A 451 " (cutoff:3.500A)
      removed outlier: 4.476A  pdb=" N   LEU A 456 " --> pdb=" O   ARG A 452 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   MET A 457 " --> pdb=" O   LEU A 453 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 509 through 514
    Processing helix  chain 'A' and resid 519 through 534
      removed outlier: 3.619A  pdb=" N   ARG A 526 " --> pdb=" O   SER A 522 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   SER A 532 " --> pdb=" O   SER A 528 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 534 through 540
    Processing helix  chain 'B' and resid 53 through 64
      removed outlier: 3.908A  pdb=" N   ILE B  59 " --> pdb=" O   GLY B  55 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   GLY B  61 " --> pdb=" O   ALA B  57 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ILE B  63 " --> pdb=" O   ILE B  59 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 65 through 70
      removed outlier: 3.963A  pdb=" N   ILE B  68 " --> pdb=" O   GLY B  65 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   PHE B  69 " --> pdb=" O   SER B  66 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   VAL B  70 " --> pdb=" O   GLY B  67 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 65 through 70'
    Processing helix  chain 'B' and resid 71 through 80
      removed outlier: 3.760A  pdb=" N   GLU B  78 " --> pdb=" O   GLY B  74 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 81 through 110
      removed outlier: 3.553A  pdb=" N   PHE B  95 " --> pdb=" O   ALA B  91 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   SER B  96 " --> pdb=" O   CYS B  92 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   ILE B  97 " --> pdb=" O   GLY B  93 " (cutoff:3.500A)
      removed outlier: 4.179A  pdb=" N   THR B 108 " --> pdb=" O   ALA B 104 " (cutoff:3.500A)
      removed outlier: 4.029A  pdb=" N   ILE B 110 " --> pdb=" O   LEU B 106 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 115 through 124
      removed outlier: 3.823A  pdb=" N   VAL B 123 " --> pdb=" O   TYR B 119 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 126 through 137
      removed outlier: 3.542A  pdb=" N   GLU B 136 " --> pdb=" O   LYS B 132 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 139 through 155
      removed outlier: 3.860A  pdb=" N   GLN B 145 " --> pdb=" O   ARG B 141 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   VAL B 148 " --> pdb=" O   SER B 144 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 167 through 186
      removed outlier: 4.036A  pdb=" N   LEU B 173 " --> pdb=" O   GLU B 169 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   LEU B 177 " --> pdb=" O   LEU B 173 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   ALA B 184 " --> pdb=" O   LEU B 180 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ASN B 186 " --> pdb=" O   LEU B 182 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 189 through 221
      removed outlier: 3.848A  pdb=" N   ARG B 195 " --> pdb=" O   LYS B 191 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   ALA B 199 " --> pdb=" O   ARG B 195 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   PHE B 200 " --> pdb=" O   VAL B 196 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   ALA B 201 " --> pdb=" O   GLN B 197 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   ALA B 202 " --> pdb=" O   ASP B 198 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   ALA B 203 " --> pdb=" O   ALA B 199 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   LEU B 205 " --> pdb=" O   ALA B 201 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   LEU B 208 " --> pdb=" O   LYS B 204 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   ILE B 212 " --> pdb=" O   LEU B 208 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   VAL B 217 " --> pdb=" O   LEU B 213 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   ILE B 219 " --> pdb=" O   GLY B 215 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 240 through 254
      removed outlier: 3.866A  pdb=" N   VAL B 244 " --> pdb=" O   VAL B 240 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   SER B 249 " --> pdb=" O   LEU B 245 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   TYR B 254 " --> pdb=" O   GLY B 250 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 261 through 267
      removed outlier: 3.916A  pdb=" N   MET B 267 " --> pdb=" O   VAL B 263 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 273 through 300
      removed outlier: 3.698A  pdb=" N   ILE B 279 " --> pdb=" O   PRO B 275 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   SER B 281 " --> pdb=" O   ALA B 277 " (cutoff:3.500A)
      Proline residue:  B 283  - end of helix
      removed outlier: 4.205A  pdb=" N   ASN B 293 " --> pdb=" O   TYR B 289 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   THR B 298 " --> pdb=" O   LEU B 294 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   THR B 299 " --> pdb=" O   ALA B 295 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 301 through 308
      removed outlier: 3.817A  pdb=" N   LEU B 306 " --> pdb=" O   THR B 302 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   SER B 308 " --> pdb=" O   GLN B 304 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 310 through 320
      removed outlier: 3.796A  pdb=" N   ASP B 314 " --> pdb=" O   ALA B 310 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 326 through 338
      removed outlier: 3.855A  pdb=" N   SER B 338 " --> pdb=" O   SER B 334 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 340 through 345
      removed outlier: 3.657A  pdb=" N   THR B 345 " --> pdb=" O   GLY B 341 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 346 through 356
      removed outlier: 4.397A  pdb=" N   PHE B 350 " --> pdb=" O   SER B 346 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   PHE B 351 " --> pdb=" O   SER B 347 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   VAL B 352 " --> pdb=" O   ARG B 348 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   ARG B 355 " --> pdb=" O   PHE B 351 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 373 through 386
      removed outlier: 3.510A  pdb=" N   MET B 383 " --> pdb=" O   PHE B 379 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 387 through 390
      removed outlier: 3.585A  pdb=" N   SER B 390 " --> pdb=" O   TYR B 387 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 387 through 390'
    Processing helix  chain 'B' and resid 392 through 421
      removed outlier: 3.619A  pdb=" N   ASN B 398 " --> pdb=" O   PHE B 394 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   PHE B 402 " --> pdb=" O   ASN B 398 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   PHE B 403 " --> pdb=" O   PHE B 399 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   ALA B 409 " --> pdb=" O   TRP B 405 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   MET B 415 " --> pdb=" O   ALA B 411 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 433 through 453
      removed outlier: 3.841A  pdb=" N   VAL B 437 " --> pdb=" O   LEU B 433 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   PHE B 439 " --> pdb=" O   LEU B 435 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   LEU B 441 " --> pdb=" O   VAL B 437 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   ALA B 442 " --> pdb=" O   PHE B 438 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   PHE B 445 " --> pdb=" O   LEU B 441 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ILE B 447 " --> pdb=" O   CYS B 443 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   VAL B 449 " --> pdb=" O   PHE B 445 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   PHE B 451 " --> pdb=" O   ILE B 447 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   TRP B 452 " --> pdb=" O   ALA B 448 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 456 through 462
    Processing helix  chain 'B' and resid 469 through 474
    Processing helix  chain 'B' and resid 483 through 501
      removed outlier: 3.953A  pdb=" N   GLN B 487 " --> pdb=" O   LYS B 483 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   GLY B 488 " --> pdb=" O   TRP B 484 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   CYS B 496 " --> pdb=" O   THR B 492 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 377 through 379
      removed outlier: 6.389A  pdb=" N   PHE A 346 " --> pdb=" O   ILE A 378 " (cutoff:3.500A)
      removed outlier: 6.623A  pdb=" N   LEU A 307 " --> pdb=" O   GLN A 347 " (cutoff:3.500A)
      removed outlier: 6.753A  pdb=" N   TYR A 226 " --> pdb=" O   VAL A 261 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 266 through 268
      removed outlier: 6.986A  pdb=" N   GLN A 280 " --> pdb=" O   LYS A 267 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 541 through 545
      removed outlier: 4.514A  pdb=" N   SER A 553 " --> pdb=" O   PHE A 545 " (cutoff:3.500A)
      removed outlier: 6.957A  pdb=" N   LEU A 624 " --> pdb=" O   LEU A 597 " (cutoff:3.500A)

    311 hydrogen bonds defined for protein.
    915 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: 1.92

  Time building geometry restraints manager: 2.22 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1456
        1.33 -     1.45: 1777
        1.45 -     1.57: 4235
        1.57 -     1.69: 4
        1.69 -     1.81: 40
  Bond restraints: 7512
  Sorted by residual:
  bond pdb=" C31 3PH B 601 "
       pdb=" O31 3PH B 601 "
    ideal  model  delta    sigma   weight residual
    1.325  1.454 -0.129 2.00e-02 2.50e+03 4.18e+01
  bond pdb=" C31 3PH B 602 "
       pdb=" O31 3PH B 602 "
    ideal  model  delta    sigma   weight residual
    1.325  1.452 -0.127 2.00e-02 2.50e+03 4.04e+01
  bond pdb=" C21 3PH B 602 "
       pdb=" O21 3PH B 602 "
    ideal  model  delta    sigma   weight residual
    1.328  1.455 -0.127 2.00e-02 2.50e+03 4.02e+01
  bond pdb=" C21 3PH B 601 "
       pdb=" O21 3PH B 601 "
    ideal  model  delta    sigma   weight residual
    1.328  1.455 -0.127 2.00e-02 2.50e+03 4.00e+01
  bond pdb=" C1  NAG D   1 "
       pdb=" C2  NAG D   1 "
    ideal  model  delta    sigma   weight residual
    1.532  1.632 -0.100 2.00e-02 2.50e+03 2.50e+01
  ... (remaining 7507 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.50: 9580
        2.50 -     5.00: 514
        5.00 -     7.49: 87
        7.49 -     9.99: 21
        9.99 -    12.49: 8
  Bond angle restraints: 10210
  Sorted by residual:
  angle pdb=" C   SER A 176 "
        pdb=" N   PRO A 177 "
        pdb=" CA  PRO A 177 "
      ideal   model   delta    sigma   weight residual
     119.84  129.79   -9.95 1.25e+00 6.40e-01 6.34e+01
  angle pdb=" N   MET A 490 "
        pdb=" CA  MET A 490 "
        pdb=" C   MET A 490 "
      ideal   model   delta    sigma   weight residual
     109.15   97.87   11.28 1.44e+00 4.82e-01 6.14e+01
  angle pdb=" N   MET A 508 "
        pdb=" CA  MET A 508 "
        pdb=" C   MET A 508 "
      ideal   model   delta    sigma   weight residual
     111.28  118.86   -7.58 1.09e+00 8.42e-01 4.84e+01
  angle pdb=" N   HIS B 319 "
        pdb=" CA  HIS B 319 "
        pdb=" C   HIS B 319 "
      ideal   model   delta    sigma   weight residual
     111.28  117.70   -6.42 1.09e+00 8.42e-01 3.47e+01
  angle pdb=" C   PHE B 161 "
        pdb=" N   PRO B 162 "
        pdb=" CA  PRO B 162 "
      ideal   model   delta    sigma   weight residual
     119.84  127.10   -7.26 1.25e+00 6.40e-01 3.38e+01
  ... (remaining 10205 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.15: 4267
       21.15 -    42.29: 213
       42.29 -    63.44: 36
       63.44 -    84.59: 13
       84.59 -   105.74: 7
  Dihedral angle restraints: 4536
    sinusoidal: 1883
      harmonic: 2653
  Sorted by residual:
  dihedral pdb=" CB  CYS A 211 "
           pdb=" SG  CYS A 211 "
           pdb=" SG  CYS B 164 "
           pdb=" CB  CYS B 164 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00 -178.35  -88.65     1      1.00e+01 1.00e-02 9.37e+01
  dihedral pdb=" CA  PRO B 360 "
           pdb=" C   PRO B 360 "
           pdb=" N   SER B 361 "
           pdb=" CA  SER B 361 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.14  -24.86     0      5.00e+00 4.00e-02 2.47e+01
  dihedral pdb=" CA  HIS A 221 "
           pdb=" C   HIS A 221 "
           pdb=" N   THR A 222 "
           pdb=" CA  THR A 222 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -155.73  -24.27     0      5.00e+00 4.00e-02 2.36e+01
  ... (remaining 4533 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.081: 983
       0.081 -    0.162: 184
       0.162 -    0.242: 23
       0.242 -    0.323: 6
       0.323 -    0.404: 4
  Chirality restraints: 1200
  Sorted by residual:
  chirality pdb=" C1  NAG C   2 "
            pdb=" O4  NAG C   1 "
            pdb=" C2  NAG C   2 "
            pdb=" O5  NAG C   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.31   -0.09 2.00e-02 2.50e+03 2.17e+01
  chirality pdb=" C1  NAG D   2 "
            pdb=" O4  NAG D   1 "
            pdb=" C2  NAG D   2 "
            pdb=" O5  NAG D   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.32   -0.08 2.00e-02 2.50e+03 1.58e+01
  chirality pdb=" C1  NAG C   1 "
            pdb=" ND2 ASN A 507 "
            pdb=" C2  NAG C   1 "
            pdb=" O5  NAG C   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.00   -0.40 2.00e-01 2.50e+01 4.07e+00
  ... (remaining 1197 not shown)

  Planarity restraints: 1258
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG D   2 "    0.337 2.00e-02 2.50e+03   2.87e-01 1.03e+03
        pdb=" C7  NAG D   2 "   -0.085 2.00e-02 2.50e+03
        pdb=" C8  NAG D   2 "    0.177 2.00e-02 2.50e+03
        pdb=" N2  NAG D   2 "   -0.503 2.00e-02 2.50e+03
        pdb=" O7  NAG D   2 "    0.075 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG D   1 "   -0.321 2.00e-02 2.50e+03   2.77e-01 9.60e+02
        pdb=" C7  NAG D   1 "    0.072 2.00e-02 2.50e+03
        pdb=" C8  NAG D   1 "   -0.021 2.00e-02 2.50e+03
        pdb=" N2  NAG D   1 "    0.481 2.00e-02 2.50e+03
        pdb=" O7  NAG D   1 "   -0.210 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 507 "   -0.090 2.00e-02 2.50e+03   1.14e-01 1.62e+02
        pdb=" CG  ASN A 507 "    0.033 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 507 "   -0.007 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 507 "    0.196 2.00e-02 2.50e+03
        pdb=" C1  NAG C   1 "   -0.133 2.00e-02 2.50e+03
  ... (remaining 1255 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 399
        2.70 -     3.25: 7072
        3.25 -     3.80: 11547
        3.80 -     4.35: 14537
        4.35 -     4.90: 23858
  Nonbonded interactions: 57413
  Sorted by model distance:
  nonbonded pdb=" ND1 HIS B 367 "
            pdb=" CD  PRO B 368 "
     model   vdw
     2.150 3.520
  nonbonded pdb=" O   GLY B 107 "
            pdb=" OG  SER B 111 "
     model   vdw
     2.199 3.040
  nonbonded pdb=" C   TRP A 492 "
            pdb=" CG2 THR A 509 "
     model   vdw
     2.221 3.690
  nonbonded pdb=" CD1 ILE A 228 "
            pdb=" CZ  PHE A 234 "
     model   vdw
     2.250 3.760
  nonbonded pdb=" O   CYS B  92 "
            pdb=" OH  TYR B 254 "
     model   vdw
     2.277 3.040
  ... (remaining 57408 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.430
  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:             0.000
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     20.180
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7651
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      :  0.011   0.129   7521  Z= 0.514
  Angle     :  1.409  17.746  10236  Z= 0.753
  Chirality :  0.069   0.404   1200
  Planarity :  0.014   0.287   1254
  Dihedral  : 14.191 105.736   2829
  Min Nonbonded Distance : 2.150

Molprobity Statistics.
  All-atom Clashscore : 13.11
  Ramachandran Plot:
    Outliers :  0.87 %
    Allowed  :  8.79 %
    Favored  : 90.35 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  :  6.81 %
    Favored  : 89.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    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: -5.69 (0.19), residues: 922
  helix: -4.10 (0.12), residues: 475
  sheet: -1.86 (0.67), residues: 51
  loop : -3.48 (0.25), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.005   TRP A 558 
 HIS   0.012   0.003   HIS A 221 
 PHE   0.034   0.004   PHE A 552 
 TYR   0.050   0.004   TYR A 454 
 ARG   0.015   0.002   ARG A 227 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.06460 (    4)
  link_NAG-ASN         : angle      10.93273 (   12)
  link_BETA1-4         : bond        0.00209 (    4)
  link_BETA1-4         : angle       2.39261 (   12)
  hydrogen bonds       : bond        0.30586 (  311)
  hydrogen bonds       : angle      10.45425 (  915)
  SS BOND              : bond        0.00722 (    1)
  SS BOND              : angle       1.63140 (    2)
  covalent geometry    : bond        0.01116 ( 7512)
  covalent geometry    : angle       1.35716 (10210)

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 221
  time to evaluate  : 0.843 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  191 TRP cc_start: 0.7934 (m100) cc_final: 0.7555 (m-10)
REVERT: A  290 ASP cc_start: 0.8431 (m-30) cc_final: 0.8038 (t0)
REVERT: A  332 LYS cc_start: 0.8937 (tttt) cc_final: 0.8619 (tttm)
REVERT: A  458 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8452 (mp)
REVERT: A  480 LEU cc_start: 0.8759 (tp) cc_final: 0.8544 (tt)
REVERT: A  554 TYR cc_start: 0.8030 (p90) cc_final: 0.7266 (p90)
REVERT: B  137 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8171 (mt)
REVERT: B  145 GLN cc_start: 0.8348 (mt0) cc_final: 0.8015 (mt0)
REVERT: B  210 LEU cc_start: 0.8944 (tt) cc_final: 0.8678 (tt)
REVERT: B  305 MET cc_start: 0.7393 (mtp) cc_final: 0.6996 (mtp)
REVERT: B  452 TRP cc_start: 0.6384 (t60) cc_final: 0.6011 (t60)
  outliers start: 28
  outliers final: 7
  residues processed: 238
  average time/residue: 0.2192
  time to fit residues: 67.6350
Evaluate side-chains
  144 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 135
  time to evaluate  : 0.835 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  458 LEU
Chi-restraints excluded: chain A residue  485 MET
Chi-restraints excluded: chain A residue  489 VAL
Chi-restraints excluded: chain A residue  490 MET
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  160 LEU
Chi-restraints excluded: chain B residue  163 THR
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain B residue  370 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 76 optimal weight:    0.0000
   chunk 68 optimal weight:   10.0000
   chunk 38 optimal weight:    0.8980
   chunk 23 optimal weight:    1.9990
   chunk 46 optimal weight:    0.0070
   chunk 36 optimal weight:    0.6980
   chunk 71 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 53 optimal weight:    0.0970
   chunk 82 optimal weight:    3.9990
   overall best weight:    0.3400

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

Flipped N/Q/H residues before XYZ refinement:
A 217 GLN
A 323 GLN
A 620 HIS
** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 432 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.134781 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.103619 restraints weight = 11868.448|
|-----------------------------------------------------------------------------|
r_work (start): 0.3420 rms_B_bonded: 3.07
r_work: 0.3288 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.3288
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7862
moved from start:          0.2905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7521  Z= 0.155
  Angle     :  0.881  16.374  10236  Z= 0.413
  Chirality :  0.047   0.217   1200
  Planarity :  0.006   0.059   1254
  Dihedral  : 12.518  91.106   1254
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  7.70 %
    Favored  : 92.08 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 15.18 %
    Favored  : 81.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    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: -3.94 (0.23), residues: 922
  helix: -2.29 (0.18), residues: 502
  sheet: -1.11 (0.73), residues: 51
  loop : -3.20 (0.28), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 558 
 HIS   0.009   0.002   HIS B 367 
 PHE   0.023   0.002   PHE B 474 
 TYR   0.014   0.002   TYR B 259 
 ARG   0.005   0.001   ARG A 314 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00569 (    4)
  link_NAG-ASN         : angle       9.00751 (   12)
  link_BETA1-4         : bond        0.00418 (    4)
  link_BETA1-4         : angle       2.37321 (   12)
  hydrogen bonds       : bond        0.05820 (  311)
  hydrogen bonds       : angle       5.59733 (  915)
  SS BOND              : bond        0.00320 (    1)
  SS BOND              : angle       0.45422 (    2)
  covalent geometry    : bond        0.00324 ( 7512)
  covalent geometry    : angle       0.82192 (10210)

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 157
  time to evaluate  : 0.850 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  191 TRP cc_start: 0.7897 (m100) cc_final: 0.7517 (m-10)
REVERT: A  192 LEU cc_start: 0.8760 (mm) cc_final: 0.8520 (mm)
REVERT: A  278 LEU cc_start: 0.8264 (mt) cc_final: 0.8021 (mt)
REVERT: A  290 ASP cc_start: 0.8312 (m-30) cc_final: 0.7852 (t0)
REVERT: A  332 LYS cc_start: 0.8932 (tttt) cc_final: 0.8623 (tttm)
REVERT: A  454 TYR cc_start: 0.8533 (m-80) cc_final: 0.8170 (m-80)
REVERT: A  458 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8489 (mp)
REVERT: A  480 LEU cc_start: 0.8782 (tp) cc_final: 0.8530 (tp)
REVERT: A  485 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.8012 (ptt)
REVERT: A  511 LYS cc_start: 0.8432 (mmtt) cc_final: 0.8181 (mmtt)
REVERT: A  593 LYS cc_start: 0.8120 (mttp) cc_final: 0.7771 (ttpt)
REVERT: A  614 ARG cc_start: 0.7963 (tpp80) cc_final: 0.7627 (mtp85)
REVERT: B  137 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7803 (mt)
REVERT: B  191 LYS cc_start: 0.7575 (tmtt) cc_final: 0.7309 (tmtt)
REVERT: B  210 LEU cc_start: 0.8783 (tt) cc_final: 0.8427 (tt)
REVERT: B  320 LEU cc_start: 0.7191 (tp) cc_final: 0.6702 (tp)
  outliers start: 24
  outliers final: 8
  residues processed: 174
  average time/residue: 0.2000
  time to fit residues: 46.3114
Evaluate side-chains
  135 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 124
  time to evaluate  : 0.776 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 SER
Chi-restraints excluded: chain A residue  458 LEU
Chi-restraints excluded: chain A residue  485 MET
Chi-restraints excluded: chain B residue   63 ILE
Chi-restraints excluded: chain B residue  105 GLU
Chi-restraints excluded: chain B residue  106 LEU
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  163 THR
Chi-restraints excluded: chain B residue  245 LEU
Chi-restraints excluded: chain B residue  278 ILE
Chi-restraints excluded: chain B residue  376 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 52 optimal weight:    6.9990
   chunk 20 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9990
   chunk 37 optimal weight:    1.9990
   chunk 10 optimal weight:    0.8980
   chunk 32 optimal weight:    3.9990
   chunk 90 optimal weight:    0.9990
   chunk 4 optimal weight:    5.9990
   chunk 13 optimal weight:    0.9990
   chunk 77 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.9788

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

Flipped N/Q/H residues before XYZ refinement:
** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.132622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.101957 restraints weight = 12188.202|
|-----------------------------------------------------------------------------|
r_work (start): 0.3391 rms_B_bonded: 3.05
r_work: 0.3261 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.3261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7902
moved from start:          0.3599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7521  Z= 0.160
  Angle     :  0.795  15.436  10236  Z= 0.373
  Chirality :  0.046   0.208   1200
  Planarity :  0.005   0.043   1254
  Dihedral  : 11.503  84.236   1244
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  7.70 %
    Favored  : 92.19 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 17.41 %
    Favored  : 78.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    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: -2.98 (0.25), residues: 922
  helix: -1.38 (0.20), residues: 503
  sheet: -0.62 (0.76), residues: 52
  loop : -2.98 (0.29), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 405 
 HIS   0.009   0.002   HIS B 319 
 PHE   0.019   0.002   PHE B 474 
 TYR   0.020   0.002   TYR A 629 
 ARG   0.004   0.000   ARG A 314 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00536 (    4)
  link_NAG-ASN         : angle       7.97128 (   12)
  link_BETA1-4         : bond        0.00437 (    4)
  link_BETA1-4         : angle       2.51103 (   12)
  hydrogen bonds       : bond        0.04654 (  311)
  hydrogen bonds       : angle       4.88242 (  915)
  SS BOND              : bond        0.00199 (    1)
  SS BOND              : angle       0.34152 (    2)
  covalent geometry    : bond        0.00361 ( 7512)
  covalent geometry    : angle       0.74311 (10210)

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 138
  time to evaluate  : 0.785 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  191 TRP cc_start: 0.7829 (m100) cc_final: 0.7437 (m-10)
REVERT: A  192 LEU cc_start: 0.8743 (mm) cc_final: 0.8498 (mm)
REVERT: A  290 ASP cc_start: 0.8327 (m-30) cc_final: 0.7900 (t0)
REVERT: A  397 LYS cc_start: 0.7668 (mttt) cc_final: 0.7403 (ptmt)
REVERT: A  458 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8600 (mp)
REVERT: A  511 LYS cc_start: 0.8304 (mmtt) cc_final: 0.7958 (mmtt)
REVERT: B  124 TYR cc_start: 0.7034 (m-80) cc_final: 0.6671 (m-80)
REVERT: B  137 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7864 (mt)
REVERT: B  191 LYS cc_start: 0.7601 (tmtt) cc_final: 0.7389 (tmtt)
REVERT: B  210 LEU cc_start: 0.8769 (tt) cc_final: 0.8479 (tt)
REVERT: B  320 LEU cc_start: 0.7181 (tp) cc_final: 0.6749 (tp)
REVERT: B  421 ARG cc_start: 0.7334 (mmp80) cc_final: 0.7015 (mmp80)
REVERT: B  444 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.9026 (tp)
  outliers start: 30
  outliers final: 16
  residues processed: 155
  average time/residue: 0.2117
  time to fit residues: 44.6743
Evaluate side-chains
  136 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 117
  time to evaluate  : 0.765 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  254 SER
Chi-restraints excluded: chain A residue  317 ASN
Chi-restraints excluded: chain A residue  458 LEU
Chi-restraints excluded: chain A residue  489 VAL
Chi-restraints excluded: chain A residue  497 PHE
Chi-restraints excluded: chain A residue  539 HIS
Chi-restraints excluded: chain A residue  621 GLU
Chi-restraints excluded: chain B residue  105 GLU
Chi-restraints excluded: chain B residue  106 LEU
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  244 VAL
Chi-restraints excluded: chain B residue  245 LEU
Chi-restraints excluded: chain B residue  263 VAL
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  367 HIS
Chi-restraints excluded: chain B residue  376 SER
Chi-restraints excluded: chain B residue  440 ILE
Chi-restraints excluded: chain B residue  444 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 35 optimal weight:    4.9990
   chunk 84 optimal weight:    0.9990
   chunk 69 optimal weight:    1.9990
   chunk 71 optimal weight:    3.9990
   chunk 29 optimal weight:    0.8980
   chunk 58 optimal weight:    0.7980
   chunk 34 optimal weight:    0.8980
   chunk 45 optimal weight:    0.1980
   chunk 77 optimal weight:    0.9980
   chunk 0 optimal weight:    7.9990
   chunk 13 optimal weight:    2.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 323 GLN
** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 487 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.132910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.102322 restraints weight = 12102.063|
|-----------------------------------------------------------------------------|
r_work (start): 0.3401 rms_B_bonded: 3.05
r_work: 0.3270 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
moved from start:          0.3975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7521  Z= 0.135
  Angle     :  0.745  15.316  10236  Z= 0.346
  Chirality :  0.044   0.219   1200
  Planarity :  0.005   0.043   1254
  Dihedral  : 10.826  81.662   1240
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  7.59 %
    Favored  : 92.30 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 20.16 %
    Favored  : 76.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    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: -2.37 (0.26), residues: 922
  helix: -0.78 (0.22), residues: 504
  sheet: -0.47 (0.77), residues: 52
  loop : -2.87 (0.29), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 434 
 HIS   0.005   0.001   HIS B 319 
 PHE   0.016   0.001   PHE B 451 
 TYR   0.016   0.001   TYR B 103 
 ARG   0.003   0.000   ARG A 314 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00558 (    4)
  link_NAG-ASN         : angle       7.38498 (   12)
  link_BETA1-4         : bond        0.00481 (    4)
  link_BETA1-4         : angle       2.48453 (   12)
  hydrogen bonds       : bond        0.04027 (  311)
  hydrogen bonds       : angle       4.58134 (  915)
  SS BOND              : bond        0.00161 (    1)
  SS BOND              : angle       0.57446 (    2)
  covalent geometry    : bond        0.00297 ( 7512)
  covalent geometry    : angle       0.69671 (10210)

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 127
  time to evaluate  : 0.820 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  191 TRP cc_start: 0.7857 (m100) cc_final: 0.7469 (m-10)
REVERT: A  192 LEU cc_start: 0.8775 (mm) cc_final: 0.8556 (mm)
REVERT: A  290 ASP cc_start: 0.8304 (m-30) cc_final: 0.7874 (t0)
REVERT: A  300 LYS cc_start: 0.8683 (mmtt) cc_final: 0.8452 (mmtt)
REVERT: A  374 ASP cc_start: 0.7876 (t0) cc_final: 0.7628 (t0)
REVERT: A  397 LYS cc_start: 0.7919 (mttt) cc_final: 0.7515 (ptmt)
REVERT: A  458 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8777 (mp)
REVERT: A  511 LYS cc_start: 0.8340 (mmtt) cc_final: 0.8089 (mmtt)
REVERT: B  124 TYR cc_start: 0.6956 (m-80) cc_final: 0.6546 (m-80)
REVERT: B  210 LEU cc_start: 0.8739 (tt) cc_final: 0.8387 (tt)
REVERT: B  213 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8847 (pp)
REVERT: B  421 ARG cc_start: 0.7447 (mmp80) cc_final: 0.7237 (mmp80)
REVERT: B  444 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8973 (tp)
  outliers start: 29
  outliers final: 13
  residues processed: 144
  average time/residue: 0.2064
  time to fit residues: 39.9470
Evaluate side-chains
  132 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 116
  time to evaluate  : 0.808 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  254 SER
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  458 LEU
Chi-restraints excluded: chain A residue  489 VAL
Chi-restraints excluded: chain A residue  539 HIS
Chi-restraints excluded: chain B residue   63 ILE
Chi-restraints excluded: chain B residue  105 GLU
Chi-restraints excluded: chain B residue  213 LEU
Chi-restraints excluded: chain B residue  245 LEU
Chi-restraints excluded: chain B residue  263 VAL
Chi-restraints excluded: chain B residue  344 PHE
Chi-restraints excluded: chain B residue  367 HIS
Chi-restraints excluded: chain B residue  376 SER
Chi-restraints excluded: chain B residue  386 LEU
Chi-restraints excluded: chain B residue  440 ILE
Chi-restraints excluded: chain B residue  444 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 21 optimal weight:    0.0980
   chunk 71 optimal weight:    0.8980
   chunk 10 optimal weight:    4.9990
   chunk 80 optimal weight:    0.4980
   chunk 19 optimal weight:    0.3980
   chunk 28 optimal weight:    0.8980
   chunk 70 optimal weight:    0.6980
   chunk 54 optimal weight:    1.9990
   chunk 62 optimal weight:    3.9990
   chunk 63 optimal weight:    8.9990
   chunk 36 optimal weight:    0.9990
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
A 269 GLN
** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.133742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.103405 restraints weight = 11991.251|
|-----------------------------------------------------------------------------|
r_work (start): 0.3414 rms_B_bonded: 3.05
r_work: 0.3286 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7859
moved from start:          0.4268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7521  Z= 0.121
  Angle     :  0.720  14.543  10236  Z= 0.331
  Chirality :  0.043   0.236   1200
  Planarity :  0.005   0.064   1254
  Dihedral  : 10.029  78.695   1238
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  7.92 %
    Favored  : 91.97 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 22.38 %
    Favored  : 74.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    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: -1.84 (0.26), residues: 922
  helix: -0.26 (0.22), residues: 502
  sheet: -0.48 (0.76), residues: 52
  loop : -2.72 (0.29), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 405 
 HIS   0.004   0.001   HIS B 367 
 PHE   0.013   0.001   PHE B 451 
 TYR   0.022   0.001   TYR A 629 
 ARG   0.015   0.001   ARG B 272 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00608 (    4)
  link_NAG-ASN         : angle       6.83381 (   12)
  link_BETA1-4         : bond        0.00538 (    4)
  link_BETA1-4         : angle       2.56813 (   12)
  hydrogen bonds       : bond        0.03579 (  311)
  hydrogen bonds       : angle       4.31304 (  915)
  SS BOND              : bond        0.00105 (    1)
  SS BOND              : angle       0.48722 (    2)
  covalent geometry    : bond        0.00266 ( 7512)
  covalent geometry    : angle       0.67625 (10210)

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 130
  time to evaluate  : 0.775 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  191 TRP cc_start: 0.7883 (m100) cc_final: 0.7440 (m-10)
REVERT: A  214 LEU cc_start: 0.7840 (mt) cc_final: 0.7609 (mt)
REVERT: A  290 ASP cc_start: 0.8304 (m-30) cc_final: 0.7798 (t0)
REVERT: A  300 LYS cc_start: 0.8658 (mmtt) cc_final: 0.8436 (mmtt)
REVERT: A  374 ASP cc_start: 0.7781 (t0) cc_final: 0.7325 (t0)
REVERT: A  397 LYS cc_start: 0.7891 (mttt) cc_final: 0.7497 (ptmt)
REVERT: A  454 TYR cc_start: 0.8469 (m-80) cc_final: 0.8140 (m-80)
REVERT: A  511 LYS cc_start: 0.8360 (mmtt) cc_final: 0.8096 (mmtt)
REVERT: A  535 ARG cc_start: 0.7118 (OUTLIER) cc_final: 0.6844 (ttp-170)
REVERT: B   54 ASN cc_start: 0.8567 (m-40) cc_final: 0.8233 (p0)
REVERT: B  124 TYR cc_start: 0.6571 (m-80) cc_final: 0.6107 (m-80)
REVERT: B  191 LYS cc_start: 0.7374 (tmtt) cc_final: 0.7077 (tptm)
REVERT: B  210 LEU cc_start: 0.8810 (tt) cc_final: 0.8431 (tt)
REVERT: B  212 ILE cc_start: 0.8241 (mm) cc_final: 0.8025 (mm)
REVERT: B  213 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8826 (pp)
  outliers start: 22
  outliers final: 14
  residues processed: 142
  average time/residue: 0.2139
  time to fit residues: 40.9342
Evaluate side-chains
  132 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 116
  time to evaluate  : 0.903 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  254 SER
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  535 ARG
Chi-restraints excluded: chain A residue  621 GLU
Chi-restraints excluded: chain B residue   63 ILE
Chi-restraints excluded: chain B residue  105 GLU
Chi-restraints excluded: chain B residue  213 LEU
Chi-restraints excluded: chain B residue  245 LEU
Chi-restraints excluded: chain B residue  263 VAL
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  344 PHE
Chi-restraints excluded: chain B residue  367 HIS
Chi-restraints excluded: chain B residue  376 SER
Chi-restraints excluded: chain B residue  386 LEU
Chi-restraints excluded: chain B residue  440 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 56 optimal weight:    0.6980
   chunk 37 optimal weight:    2.9990
   chunk 46 optimal weight:    0.4980
   chunk 38 optimal weight:    7.9990
   chunk 33 optimal weight:    0.0270
   chunk 51 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 75 optimal weight:    4.9990
   chunk 48 optimal weight:    0.8980
   chunk 19 optimal weight:    0.0470
   chunk 24 optimal weight:    0.6980
   overall best weight:    0.3936

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

Flipped N/Q/H residues before XYZ refinement:
** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.135624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.106060 restraints weight = 12083.821|
|-----------------------------------------------------------------------------|
r_work (start): 0.3432 rms_B_bonded: 3.00
r_work: 0.3297 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.3297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.4481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   7521  Z= 0.114
  Angle     :  0.705  14.107  10236  Z= 0.324
  Chirality :  0.043   0.260   1200
  Planarity :  0.004   0.043   1254
  Dihedral  :  9.458  76.161   1236
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  6.62 %
    Favored  : 93.28 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 21.99 %
    Favored  : 74.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    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: -1.40 (0.27), residues: 922
  helix:  0.15 (0.23), residues: 506
  sheet: -0.49 (0.75), residues: 52
  loop : -2.58 (0.30), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 405 
 HIS   0.003   0.001   HIS B 367 
 PHE   0.013   0.001   PHE B 439 
 TYR   0.016   0.001   TYR B 103 
 ARG   0.005   0.000   ARG B 421 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00672 (    4)
  link_NAG-ASN         : angle       6.50134 (   12)
  link_BETA1-4         : bond        0.00470 (    4)
  link_BETA1-4         : angle       2.56465 (   12)
  hydrogen bonds       : bond        0.03401 (  311)
  hydrogen bonds       : angle       4.19726 (  915)
  SS BOND              : bond        0.00089 (    1)
  SS BOND              : angle       0.46296 (    2)
  covalent geometry    : bond        0.00246 ( 7512)
  covalent geometry    : angle       0.66437 (10210)

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 126
  time to evaluate  : 0.783 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  191 TRP cc_start: 0.7663 (m100) cc_final: 0.7337 (m-10)
REVERT: A  290 ASP cc_start: 0.8218 (m-30) cc_final: 0.7761 (t0)
REVERT: A  300 LYS cc_start: 0.8640 (mmtt) cc_final: 0.8436 (mmtt)
REVERT: A  454 TYR cc_start: 0.8475 (m-80) cc_final: 0.8144 (m-80)
REVERT: A  511 LYS cc_start: 0.8503 (mmtt) cc_final: 0.8220 (mmtt)
REVERT: A  535 ARG cc_start: 0.7150 (OUTLIER) cc_final: 0.6869 (ttp-170)
REVERT: B   54 ASN cc_start: 0.8545 (m-40) cc_final: 0.8259 (p0)
REVERT: B  124 TYR cc_start: 0.6580 (m-80) cc_final: 0.6109 (m-80)
REVERT: B  191 LYS cc_start: 0.7413 (tmtt) cc_final: 0.7112 (tptm)
REVERT: B  210 LEU cc_start: 0.8765 (tt) cc_final: 0.8395 (tt)
REVERT: B  212 ILE cc_start: 0.8093 (mm) cc_final: 0.7883 (mm)
REVERT: B  213 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8802 (pp)
  outliers start: 27
  outliers final: 20
  residues processed: 143
  average time/residue: 0.2091
  time to fit residues: 39.6450
Evaluate side-chains
  136 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 114
  time to evaluate  : 0.747 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  254 SER
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  535 ARG
Chi-restraints excluded: chain A residue  559 ASP
Chi-restraints excluded: chain A residue  621 GLU
Chi-restraints excluded: chain B residue   63 ILE
Chi-restraints excluded: chain B residue  105 GLU
Chi-restraints excluded: chain B residue  213 LEU
Chi-restraints excluded: chain B residue  245 LEU
Chi-restraints excluded: chain B residue  263 VAL
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  324 SER
Chi-restraints excluded: chain B residue  339 VAL
Chi-restraints excluded: chain B residue  344 PHE
Chi-restraints excluded: chain B residue  367 HIS
Chi-restraints excluded: chain B residue  376 SER
Chi-restraints excluded: chain B residue  386 LEU
Chi-restraints excluded: chain B residue  433 LEU
Chi-restraints excluded: chain B residue  440 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 62 optimal weight:    0.8980
   chunk 7 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9990
   chunk 39 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9990
   chunk 28 optimal weight:    0.0170
   chunk 74 optimal weight:    1.9990
   chunk 76 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 12 optimal weight:    0.1980
   chunk 67 optimal weight:    0.8980
   overall best weight:    0.5418

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

Flipped N/Q/H residues before XYZ refinement:
** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.134658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.104212 restraints weight = 12032.103|
|-----------------------------------------------------------------------------|
r_work (start): 0.3428 rms_B_bonded: 3.09
r_work: 0.3294 rms_B_bonded: 3.78 restraints_weight: 0.5000
r_work (final): 0.3294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7859
moved from start:          0.4620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7521  Z= 0.119
  Angle     :  0.702  13.193  10236  Z= 0.324
  Chirality :  0.043   0.279   1200
  Planarity :  0.004   0.044   1254
  Dihedral  :  9.066  73.923   1236
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  7.27 %
    Favored  : 92.62 %
  Rotamer:
    Outliers :  4.32 %
    Allowed  : 21.34 %
    Favored  : 74.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.14 (0.27), residues: 922
  helix:  0.41 (0.23), residues: 506
  sheet: -0.41 (0.80), residues: 47
  loop : -2.52 (0.30), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 405 
 HIS   0.003   0.001   HIS B 367 
 PHE   0.013   0.001   PHE B 451 
 TYR   0.016   0.001   TYR B 103 
 ARG   0.003   0.000   ARG A 440 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00657 (    4)
  link_NAG-ASN         : angle       6.29436 (   12)
  link_BETA1-4         : bond        0.00485 (    4)
  link_BETA1-4         : angle       2.53797 (   12)
  hydrogen bonds       : bond        0.03378 (  311)
  hydrogen bonds       : angle       4.10556 (  915)
  SS BOND              : bond        0.00033 (    1)
  SS BOND              : angle       1.27773 (    2)
  covalent geometry    : bond        0.00264 ( 7512)
  covalent geometry    : angle       0.66305 (10210)

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 125
  time to evaluate  : 0.779 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  191 TRP cc_start: 0.7779 (m100) cc_final: 0.7393 (m-10)
REVERT: A  290 ASP cc_start: 0.8303 (m-30) cc_final: 0.7797 (t0)
REVERT: A  300 LYS cc_start: 0.8645 (mmtt) cc_final: 0.8419 (mmtt)
REVERT: A  397 LYS cc_start: 0.7872 (mttt) cc_final: 0.7451 (ptmt)
REVERT: A  415 HIS cc_start: 0.7542 (OUTLIER) cc_final: 0.7135 (t-170)
REVERT: A  454 TYR cc_start: 0.8524 (m-80) cc_final: 0.8193 (m-80)
REVERT: A  511 LYS cc_start: 0.8549 (mmtt) cc_final: 0.8270 (mmtt)
REVERT: A  535 ARG cc_start: 0.7236 (OUTLIER) cc_final: 0.6968 (ttp-170)
REVERT: B   54 ASN cc_start: 0.8590 (m-40) cc_final: 0.8269 (p0)
REVERT: B  124 TYR cc_start: 0.6489 (m-80) cc_final: 0.6047 (m-80)
REVERT: B  191 LYS cc_start: 0.7384 (tmtt) cc_final: 0.7090 (tptm)
REVERT: B  210 LEU cc_start: 0.8761 (tt) cc_final: 0.8374 (tt)
REVERT: B  212 ILE cc_start: 0.8115 (mm) cc_final: 0.7907 (mm)
REVERT: B  213 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8750 (pp)
  outliers start: 33
  outliers final: 22
  residues processed: 146
  average time/residue: 0.2338
  time to fit residues: 45.8896
Evaluate side-chains
  141 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 116
  time to evaluate  : 0.870 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  254 SER
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  293 SER
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  415 HIS
Chi-restraints excluded: chain A residue  522 SER
Chi-restraints excluded: chain A residue  535 ARG
Chi-restraints excluded: chain A residue  553 SER
Chi-restraints excluded: chain A residue  621 GLU
Chi-restraints excluded: chain B residue   63 ILE
Chi-restraints excluded: chain B residue  105 GLU
Chi-restraints excluded: chain B residue  213 LEU
Chi-restraints excluded: chain B residue  245 LEU
Chi-restraints excluded: chain B residue  263 VAL
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  329 VAL
Chi-restraints excluded: chain B residue  344 PHE
Chi-restraints excluded: chain B residue  367 HIS
Chi-restraints excluded: chain B residue  376 SER
Chi-restraints excluded: chain B residue  386 LEU
Chi-restraints excluded: chain B residue  433 LEU
Chi-restraints excluded: chain B residue  437 VAL
Chi-restraints excluded: chain B residue  440 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 76 optimal weight:    1.9990
   chunk 85 optimal weight:    0.7980
   chunk 48 optimal weight:    0.8980
   chunk 61 optimal weight:    0.7980
   chunk 32 optimal weight:    0.6980
   chunk 38 optimal weight:    1.9990
   chunk 19 optimal weight:    5.9990
   chunk 44 optimal weight:    0.5980
   chunk 71 optimal weight:    0.0870
   chunk 16 optimal weight:    0.9990
   chunk 26 optimal weight:    0.3980
   overall best weight:    0.5158

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

Flipped N/Q/H residues before XYZ refinement:
** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 358 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.134878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.104666 restraints weight = 12212.071|
|-----------------------------------------------------------------------------|
r_work (start): 0.3432 rms_B_bonded: 3.08
r_work: 0.3300 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
moved from start:          0.4743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7521  Z= 0.118
  Angle     :  0.701  13.212  10236  Z= 0.324
  Chirality :  0.043   0.287   1200
  Planarity :  0.004   0.043   1254
  Dihedral  :  8.891  71.564   1236
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  7.16 %
    Favored  : 92.73 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 22.51 %
    Favored  : 73.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    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 (0.27), residues: 922
  helix:  0.53 (0.23), residues: 506
  sheet: -0.34 (0.79), residues: 47
  loop : -2.51 (0.30), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 405 
 HIS   0.003   0.001   HIS B 367 
 PHE   0.028   0.001   PHE B 474 
 TYR   0.016   0.001   TYR B 103 
 ARG   0.004   0.000   ARG A 440 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00656 (    4)
  link_NAG-ASN         : angle       6.09384 (   12)
  link_BETA1-4         : bond        0.00501 (    4)
  link_BETA1-4         : angle       2.51427 (   12)
  hydrogen bonds       : bond        0.03323 (  311)
  hydrogen bonds       : angle       4.11990 (  915)
  SS BOND              : bond        0.00064 (    1)
  SS BOND              : angle       1.01276 (    2)
  covalent geometry    : bond        0.00263 ( 7512)
  covalent geometry    : angle       0.66487 (10210)

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 122
  time to evaluate  : 0.745 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  191 TRP cc_start: 0.7783 (m100) cc_final: 0.7421 (m-10)
REVERT: A  290 ASP cc_start: 0.8188 (m-30) cc_final: 0.7579 (t0)
REVERT: A  300 LYS cc_start: 0.8628 (mmtt) cc_final: 0.8417 (mmtt)
REVERT: A  316 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8224 (pt0)
REVERT: A  415 HIS cc_start: 0.7477 (OUTLIER) cc_final: 0.7082 (t-170)
REVERT: A  454 TYR cc_start: 0.8507 (m-80) cc_final: 0.8207 (m-80)
REVERT: A  511 LYS cc_start: 0.8525 (mmtt) cc_final: 0.8244 (mmtt)
REVERT: A  535 ARG cc_start: 0.7190 (OUTLIER) cc_final: 0.6916 (ttp-170)
REVERT: B   54 ASN cc_start: 0.8579 (m-40) cc_final: 0.8238 (p0)
REVERT: B  124 TYR cc_start: 0.6372 (m-80) cc_final: 0.5931 (m-80)
REVERT: B  191 LYS cc_start: 0.7398 (tmtt) cc_final: 0.7100 (tptm)
REVERT: B  210 LEU cc_start: 0.8831 (tt) cc_final: 0.8445 (tt)
REVERT: B  212 ILE cc_start: 0.8215 (mm) cc_final: 0.7984 (mm)
REVERT: B  213 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8764 (pp)
REVERT: B  453 LYS cc_start: 0.7801 (mmmt) cc_final: 0.7481 (mmmt)
  outliers start: 28
  outliers final: 22
  residues processed: 138
  average time/residue: 0.2071
  time to fit residues: 39.2733
Evaluate side-chains
  138 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 113
  time to evaluate  : 0.823 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  254 SER
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  293 SER
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  415 HIS
Chi-restraints excluded: chain A residue  522 SER
Chi-restraints excluded: chain A residue  535 ARG
Chi-restraints excluded: chain A residue  553 SER
Chi-restraints excluded: chain A residue  621 GLU
Chi-restraints excluded: chain B residue   63 ILE
Chi-restraints excluded: chain B residue  105 GLU
Chi-restraints excluded: chain B residue  213 LEU
Chi-restraints excluded: chain B residue  245 LEU
Chi-restraints excluded: chain B residue  263 VAL
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  329 VAL
Chi-restraints excluded: chain B residue  344 PHE
Chi-restraints excluded: chain B residue  367 HIS
Chi-restraints excluded: chain B residue  376 SER
Chi-restraints excluded: chain B residue  386 LEU
Chi-restraints excluded: chain B residue  433 LEU
Chi-restraints excluded: chain B residue  440 ILE
Chi-restraints excluded: chain B residue  444 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 34 optimal weight:    0.0770
   chunk 19 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9990
   chunk 52 optimal weight:    0.3980
   chunk 36 optimal weight:    0.7980
   chunk 80 optimal weight:    0.9990
   chunk 39 optimal weight:    4.9990
   chunk 76 optimal weight:    0.9980
   chunk 25 optimal weight:    2.9990
   chunk 81 optimal weight:    0.9990
   chunk 9 optimal weight:    3.9990
   overall best weight:    0.6540

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

Flipped N/Q/H residues before XYZ refinement:
** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.134356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.104152 restraints weight = 12197.788|
|-----------------------------------------------------------------------------|
r_work (start): 0.3425 rms_B_bonded: 3.09
r_work: 0.3294 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.3294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7866
moved from start:          0.4817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7521  Z= 0.124
  Angle     :  0.716  13.917  10236  Z= 0.331
  Chirality :  0.043   0.294   1200
  Planarity :  0.004   0.044   1254
  Dihedral  :  8.839  69.088   1236
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  7.48 %
    Favored  : 92.41 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 23.30 %
    Favored  : 73.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    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: -0.92 (0.27), residues: 922
  helix:  0.63 (0.23), residues: 507
  sheet: -0.30 (0.78), residues: 47
  loop : -2.51 (0.30), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 405 
 HIS   0.003   0.001   HIS B 367 
 PHE   0.025   0.001   PHE B 474 
 TYR   0.018   0.001   TYR B 103 
 ARG   0.004   0.000   ARG A 440 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00396 (    4)
  link_NAG-ASN         : angle       6.16443 (   12)
  link_BETA1-4         : bond        0.00508 (    4)
  link_BETA1-4         : angle       2.47741 (   12)
  hydrogen bonds       : bond        0.03347 (  311)
  hydrogen bonds       : angle       4.08758 (  915)
  SS BOND              : bond        0.00089 (    1)
  SS BOND              : angle       0.96273 (    2)
  covalent geometry    : bond        0.00279 ( 7512)
  covalent geometry    : angle       0.67969 (10210)

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 115
  time to evaluate  : 2.689 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  191 TRP cc_start: 0.7674 (m100) cc_final: 0.7358 (m-10)
REVERT: A  290 ASP cc_start: 0.8159 (m-30) cc_final: 0.7536 (t0)
REVERT: A  316 GLU cc_start: 0.8459 (mt-10) cc_final: 0.8192 (pt0)
REVERT: A  397 LYS cc_start: 0.7881 (mttt) cc_final: 0.7463 (ptmt)
REVERT: A  454 TYR cc_start: 0.8651 (m-80) cc_final: 0.8294 (m-80)
REVERT: A  511 LYS cc_start: 0.8524 (mmtt) cc_final: 0.8236 (mmtt)
REVERT: A  535 ARG cc_start: 0.7174 (OUTLIER) cc_final: 0.6907 (ttp-170)
REVERT: B   54 ASN cc_start: 0.8598 (m-40) cc_final: 0.8247 (p0)
REVERT: B  124 TYR cc_start: 0.6416 (m-80) cc_final: 0.5980 (m-80)
REVERT: B  191 LYS cc_start: 0.7422 (tmtt) cc_final: 0.7126 (tptm)
REVERT: B  210 LEU cc_start: 0.8789 (tt) cc_final: 0.8400 (tt)
REVERT: B  212 ILE cc_start: 0.8208 (mm) cc_final: 0.7979 (mm)
REVERT: B  213 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8760 (pp)
REVERT: B  453 LYS cc_start: 0.7833 (mmmt) cc_final: 0.7503 (mmmt)
  outliers start: 25
  outliers final: 22
  residues processed: 130
  average time/residue: 0.3885
  time to fit residues: 72.4093
Evaluate side-chains
  136 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 112
  time to evaluate  : 1.604 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  254 SER
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  293 SER
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  522 SER
Chi-restraints excluded: chain A residue  535 ARG
Chi-restraints excluded: chain A residue  553 SER
Chi-restraints excluded: chain A residue  621 GLU
Chi-restraints excluded: chain B residue   63 ILE
Chi-restraints excluded: chain B residue  105 GLU
Chi-restraints excluded: chain B residue  213 LEU
Chi-restraints excluded: chain B residue  245 LEU
Chi-restraints excluded: chain B residue  263 VAL
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  329 VAL
Chi-restraints excluded: chain B residue  344 PHE
Chi-restraints excluded: chain B residue  367 HIS
Chi-restraints excluded: chain B residue  376 SER
Chi-restraints excluded: chain B residue  386 LEU
Chi-restraints excluded: chain B residue  433 LEU
Chi-restraints excluded: chain B residue  440 ILE
Chi-restraints excluded: chain B residue  444 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 63 optimal weight:    8.9990
   chunk 11 optimal weight:    0.7980
   chunk 57 optimal weight:    4.9990
   chunk 36 optimal weight:    0.6980
   chunk 28 optimal weight:    3.9990
   chunk 21 optimal weight:    4.9990
   chunk 58 optimal weight:    2.9990
   chunk 22 optimal weight:    0.8980
   chunk 39 optimal weight:    2.9990
   chunk 79 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
A 268 ASN
** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.130421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.100216 restraints weight = 12361.507|
|-----------------------------------------------------------------------------|
r_work (start): 0.3350 rms_B_bonded: 3.06
r_work: 0.3217 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.3217
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7938
moved from start:          0.4754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7521  Z= 0.180
  Angle     :  0.768  12.977  10236  Z= 0.361
  Chirality :  0.046   0.285   1200
  Planarity :  0.005   0.041   1254
  Dihedral  :  9.146  68.562   1236
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  7.92 %
    Favored  : 91.97 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 23.43 %
    Favored  : 73.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.20 (0.27), residues: 922
  helix:  0.32 (0.22), residues: 513
  sheet: -0.47 (0.73), residues: 52
  loop : -2.55 (0.31), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 405 
 HIS   0.004   0.002   HIS B 319 
 PHE   0.023   0.002   PHE B 474 
 TYR   0.027   0.002   TYR B 103 
 ARG   0.004   0.001   ARG A 440 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00534 (    4)
  link_NAG-ASN         : angle       5.98640 (   12)
  link_BETA1-4         : bond        0.00521 (    4)
  link_BETA1-4         : angle       2.34156 (   12)
  hydrogen bonds       : bond        0.03927 (  311)
  hydrogen bonds       : angle       4.37428 (  915)
  SS BOND              : bond        0.00189 (    1)
  SS BOND              : angle       0.63976 (    2)
  covalent geometry    : bond        0.00421 ( 7512)
  covalent geometry    : angle       0.73709 (10210)

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 114
  time to evaluate  : 0.850 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  191 TRP cc_start: 0.7809 (m100) cc_final: 0.7434 (m-10)
REVERT: A  290 ASP cc_start: 0.8126 (m-30) cc_final: 0.7766 (t0)
REVERT: A  316 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8215 (pt0)
REVERT: A  397 LYS cc_start: 0.8110 (mttt) cc_final: 0.7754 (ptmt)
REVERT: A  454 TYR cc_start: 0.8681 (m-80) cc_final: 0.8375 (m-80)
REVERT: A  511 LYS cc_start: 0.8580 (mmtt) cc_final: 0.8348 (mmtt)
REVERT: A  535 ARG cc_start: 0.7301 (OUTLIER) cc_final: 0.7085 (ttp-170)
REVERT: B   54 ASN cc_start: 0.8685 (m-40) cc_final: 0.8424 (p0)
REVERT: B  124 TYR cc_start: 0.6614 (m-80) cc_final: 0.6219 (m-80)
REVERT: B  191 LYS cc_start: 0.7425 (tmtt) cc_final: 0.7174 (tptm)
REVERT: B  210 LEU cc_start: 0.8854 (tt) cc_final: 0.8447 (tt)
REVERT: B  212 ILE cc_start: 0.8173 (mm) cc_final: 0.7959 (mm)
REVERT: B  213 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8891 (pp)
REVERT: B  452 TRP cc_start: 0.6104 (t60) cc_final: 0.5875 (t60)
  outliers start: 22
  outliers final: 18
  residues processed: 127
  average time/residue: 0.2137
  time to fit residues: 37.0784
Evaluate side-chains
  126 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 106
  time to evaluate  : 0.842 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  293 SER
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  522 SER
Chi-restraints excluded: chain A residue  535 ARG
Chi-restraints excluded: chain A residue  553 SER
Chi-restraints excluded: chain A residue  621 GLU
Chi-restraints excluded: chain B residue   63 ILE
Chi-restraints excluded: chain B residue  105 GLU
Chi-restraints excluded: chain B residue  213 LEU
Chi-restraints excluded: chain B residue  245 LEU
Chi-restraints excluded: chain B residue  263 VAL
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  329 VAL
Chi-restraints excluded: chain B residue  376 SER
Chi-restraints excluded: chain B residue  433 LEU
Chi-restraints excluded: chain B residue  440 ILE
Chi-restraints excluded: chain B residue  444 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 5 optimal weight:    0.6980
   chunk 43 optimal weight:    0.2980
   chunk 57 optimal weight:    0.6980
   chunk 54 optimal weight:    0.9990
   chunk 12 optimal weight:    4.9990
   chunk 36 optimal weight:    0.6980
   chunk 63 optimal weight:    6.9990
   chunk 74 optimal weight:    0.5980
   chunk 20 optimal weight:    0.9980
   chunk 38 optimal weight:    2.9990
   chunk 85 optimal weight:    1.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.132929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.102985 restraints weight = 12039.263|
|-----------------------------------------------------------------------------|
r_work (start): 0.3401 rms_B_bonded: 3.02
r_work: 0.3270 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7887
moved from start:          0.4916

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7521  Z= 0.127
  Angle     :  0.735  12.642  10236  Z= 0.345
  Chirality :  0.044   0.291   1200
  Planarity :  0.004   0.041   1254
  Dihedral  :  9.005  64.616   1236
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  7.38 %
    Favored  : 92.52 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 23.56 %
    Favored  : 73.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    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: -0.92 (0.27), residues: 922
  helix:  0.55 (0.23), residues: 510
  sheet: -0.37 (0.73), residues: 52
  loop : -2.40 (0.31), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.049   0.001   TRP B 452 
 HIS   0.007   0.001   HIS B 367 
 PHE   0.024   0.001   PHE B 474 
 TYR   0.020   0.001   TYR B 103 
 ARG   0.003   0.000   ARG A 440 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00493 (    4)
  link_NAG-ASN         : angle       5.90061 (   12)
  link_BETA1-4         : bond        0.00487 (    4)
  link_BETA1-4         : angle       2.38138 (   12)
  hydrogen bonds       : bond        0.03462 (  311)
  hydrogen bonds       : angle       4.18872 (  915)
  SS BOND              : bond        0.00078 (    1)
  SS BOND              : angle       0.80840 (    2)
  covalent geometry    : bond        0.00287 ( 7512)
  covalent geometry    : angle       0.70326 (10210)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4486.24 seconds
wall clock time: 79 minutes 25.55 seconds (4765.55 seconds total)