Starting phenix.real_space_refine
on Tue Mar  3 17:41:12 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7cmi_30407/03_2026/7cmi_30407.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7cmi_30407/03_2026/7cmi_30407.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7cmi_30407/03_2026/7cmi_30407.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7cmi_30407/03_2026/7cmi_30407.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7cmi_30407/03_2026/7cmi_30407.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7cmi_30407/03_2026/7cmi_30407.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.003
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    4814      2.51       5
     N    1176      2.21       5
     O    1334      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7353
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 3650
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 469, 3650
          Classifications: {'peptide': 469}
          Link IDs: {'PTRANS': 22, 'TRANS': 446}
    Chain: "B"
      Number of atoms: 3480
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 458, 3480
          Classifications: {'peptide': 458}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 25, 'TRANS': 432}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 76
          Unresolved non-hydrogen angles: 99
          Unresolved non-hydrogen dihedrals: 70
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 4, 'TYR:plan': 1, 'PHE:plan': 3, 'TRP:plan': 1, 'ASN:plan1': 2, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 60
    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: 9
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 9
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
    Chain: "B"
      Number of atoms: 102
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 102
          Unusual residues: {'3PH': 2}
          Classifications: {'undetermined': 2, 'water': 6}
          Link IDs: {None: 7}
  Time building chain proxies: 1.69, per 1000 atoms: 0.23
  Number of scatterers: 7353
  At special positions: 0
  Unit cell: (82.612, 86.96, 125.005, 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    1334      8.00
     N    1176      7.00
     C    4814      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 154 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  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: 0.53
  Conformation dependent library (CDL) restraints added in 260.4 milliseconds
  

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1700

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 3 sheets defined
      55.4% alpha, 5.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing helix  chain 'A' and resid 167 through 175
      removed outlier: 4.142A  pdb=" N   LYS A 172 " --> pdb=" O   GLU A 168 " (cutoff:3.500A)
      removed outlier: 4.207A  pdb=" N   VAL A 173 " --> pdb=" O   GLU A 169 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ALA A 174 " --> pdb=" O   LEU A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 178 through 183
      removed outlier: 3.879A  pdb=" N   THR A 182 " --> pdb=" O   GLY A 178 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 208
      removed outlier: 3.781A  pdb=" N   LEU A 187 " --> pdb=" O   ARG A 183 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   LEU A 189 " --> pdb=" O   ALA A 185 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   VAL A 203 " --> pdb=" O   ALA A 199 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   ILE A 204 " --> pdb=" O   GLY A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 236
      removed outlier: 3.521A  pdb=" N   GLN A 235 " --> pdb=" O   LEU A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 237 through 240
      removed outlier: 3.599A  pdb=" N   GLY A 240 " --> pdb=" O   HIS A 237 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 237 through 240'
    Processing helix  chain 'A' and resid 243 through 247
    Processing helix  chain 'A' and resid 248 through 255
    Processing helix  chain 'A' and resid 287 through 301
      removed outlier: 3.793A  pdb=" N   SER A 293 " --> pdb=" O   GLU A 289 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   LYS A 299 " --> pdb=" O   LEU A 295 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   LYS A 300 " --> pdb=" O   GLN A 296 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   LYS A 301 " --> pdb=" O   SER A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 325 through 342
      removed outlier: 3.564A  pdb=" N   ALA A 334 " --> pdb=" O   LYS A 330 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   GLU A 336 " --> pdb=" O   LYS A 332 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   PHE A 337 " --> pdb=" O   ASP A 333 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   GLN A 340 " --> pdb=" O   GLU A 336 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 356 through 372
      removed outlier: 4.269A  pdb=" N   ALA A 362 " --> pdb=" O   SER A 358 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   GLU A 363 " --> pdb=" O   SER A 359 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   ILE A 367 " --> pdb=" O   GLU A 363 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   SER A 372 " --> pdb=" O   THR A 368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 391
      removed outlier: 3.598A  pdb=" N   ILE A 389 " --> pdb=" O   ASP A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 412 through 427
      removed outlier: 4.013A  pdb=" N   THR A 416 " --> pdb=" O   THR A 412 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   TYR A 423 " --> pdb=" O   LEU A 419 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ASN A 425 " --> pdb=" O   THR A 421 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 452 through 459
      removed outlier: 3.506A  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 532
      removed outlier: 4.514A  pdb=" N   GLN A 530 " --> pdb=" O   ARG A 526 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 534 through 539
    Processing helix  chain 'B' and resid 42 through 54
      removed outlier: 3.858A  pdb=" N   GLY B  47 " --> pdb=" O   VAL B  43 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   ILE B  48 " --> pdb=" O   SER B  44 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   ILE B  49 " --> pdb=" O   ALA B  45 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 61 through 70
      removed outlier: 3.671A  pdb=" N   ASN B  68 " --> pdb=" O   GLY B  64 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   ALA B  69 " --> pdb=" O   VAL B  65 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 71 through 100
      removed outlier: 3.629A  pdb=" N   ALA B  75 " --> pdb=" O   SER B  71 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ILE B  77 " --> pdb=" O   GLY B  73 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   ILE B  80 " --> pdb=" O   LEU B  76 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   GLY B  83 " --> pdb=" O   TRP B  79 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   VAL B  87 " --> pdb=" O   GLY B  83 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   CYS B  92 " --> pdb=" O   VAL B  88 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   TYR B  93 " --> pdb=" O   GLY B  89 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   LEU B  96 " --> pdb=" O   CYS B  92 " (cutoff:3.500A)
      removed outlier: 4.105A  pdb=" N   VAL B  98 " --> pdb=" O   ALA B  94 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 105 through 113
      removed outlier: 3.634A  pdb=" N   TYR B 109 " --> pdb=" O   GLY B 105 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   VAL B 110 " --> pdb=" O   ASP B 106 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   LYS B 111 " --> pdb=" O   TYR B 107 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 116 through 129
      removed outlier: 3.802A  pdb=" N   PHE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 129 through 147
      removed outlier: 3.671A  pdb=" N   ILE B 138 " --> pdb=" O   ASN B 134 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   SER B 143 " --> pdb=" O   ALA B 139 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 157 through 178
      removed outlier: 3.636A  pdb=" N   ARG B 162 " --> pdb=" O   GLU B 158 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   LEU B 163 " --> pdb=" O   SER B 159 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ILE B 167 " --> pdb=" O   LEU B 163 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   CYS B 168 " --> pdb=" O   LEU B 164 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   TRP B 174 " --> pdb=" O   LEU B 170 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 179 through 186
      removed outlier: 3.733A  pdb=" N   ALA B 183 " --> pdb=" O   SER B 179 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   THR B 184 " --> pdb=" O   VAL B 180 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 188 through 210
      removed outlier: 3.545A  pdb=" N   GLY B 193 " --> pdb=" O   ILE B 189 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   LYS B 194 " --> pdb=" O   PHE B 190 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   VAL B 207 " --> pdb=" O   ILE B 203 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   GLN B 208 " --> pdb=" O   MET B 204 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 233 through 242
      removed outlier: 3.524A  pdb=" N   ALA B 237 " --> pdb=" O   LEU B 233 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   LEU B 239 " --> pdb=" O   ALA B 235 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   GLN B 240 " --> pdb=" O   LEU B 236 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 254 through 258
      removed outlier: 4.099A  pdb=" N   GLU B 257 " --> pdb=" O   VAL B 254 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 265 through 289
      removed outlier: 3.631A  pdb=" N   ILE B 269 " --> pdb=" O   LEU B 265 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   PHE B 270 " --> pdb=" O   PRO B 266 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   ILE B 271 " --> pdb=" O   ARG B 267 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   ILE B 273 " --> pdb=" O   ILE B 269 " (cutoff:3.500A)
      Proline residue:  B 274  - end of helix
      removed outlier: 3.562A  pdb=" N   TYR B 287 " --> pdb=" O   ALA B 283 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   VAL B 288 " --> pdb=" O   ASN B 284 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   THR B 289 " --> pdb=" O   VAL B 285 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 292 through 297
    Processing helix  chain 'B' and resid 301 through 309
      removed outlier: 3.645A  pdb=" N   LYS B 309 " --> pdb=" O   THR B 305 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 313 through 336
      removed outlier: 3.701A  pdb=" N   ILE B 317 " --> pdb=" O   VAL B 313 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   MET B 318 " --> pdb=" O   MET B 314 " (cutoff:3.500A)
      Proline residue:  B 319  - end of helix
      removed outlier: 3.535A  pdb=" N   GLY B 328 " --> pdb=" O   LEU B 324 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   PHE B 335 " --> pdb=" O   ASN B 331 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   THR B 336 " --> pdb=" O   GLY B 332 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 338 through 346
      removed outlier: 3.532A  pdb=" N   ARG B 346 " --> pdb=" O   PHE B 342 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 364 through 378
      removed outlier: 3.533A  pdb=" N   PHE B 370 " --> pdb=" O   PRO B 366 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   THR B 371 " --> pdb=" O   ALA B 367 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   SER B 374 " --> pdb=" O   PHE B 370 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   THR B 375 " --> pdb=" O   THR B 371 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 385 through 412
      removed outlier: 3.953A  pdb=" N   ILE B 394 " --> pdb=" O   TYR B 390 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   TYR B 396 " --> pdb=" O   GLY B 392 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   PHE B 398 " --> pdb=" O   ILE B 394 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   VAL B 401 " --> pdb=" O   LEU B 397 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   THR B 402 " --> pdb=" O   PHE B 398 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   VAL B 403 " --> pdb=" O   TYR B 399 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   ARG B 410 " --> pdb=" O   GLN B 406 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 425 through 445
      removed outlier: 3.798A  pdb=" N   ILE B 429 " --> pdb=" O   LEU B 425 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   TYR B 430 " --> pdb=" O   PHE B 426 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   VAL B 439 " --> pdb=" O   ALA B 435 " (cutoff:3.500A)
      removed outlier: 4.280A  pdb=" N   PHE B 440 " --> pdb=" O   PHE B 436 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   TRP B 443 " --> pdb=" O   VAL B 439 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 445 through 467
      removed outlier: 3.692A  pdb=" N   ILE B 451 " --> pdb=" O   VAL B 447 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   GLY B 452 " --> pdb=" O   VAL B 448 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   LEU B 453 " --> pdb=" O   CYS B 449 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   ILE B 455 " --> pdb=" O   ILE B 451 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   MET B 456 " --> pdb=" O   GLY B 452 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   VAL B 460 " --> pdb=" O   MET B 456 " (cutoff:3.500A)
      Proline residue:  B 461  - end of helix
      removed outlier: 3.729A  pdb=" N   PHE B 464 " --> pdb=" O   VAL B 460 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 473 through 491
      removed outlier: 3.524A  pdb=" N   ASP B 478 " --> pdb=" O   LYS B 474 " (cutoff:3.500A)
      removed outlier: 4.985A  pdb=" N   PHE B 479 " --> pdb=" O   CYS B 475 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   ILE B 480 " --> pdb=" O   PHE B 476 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   GLU B 481 " --> pdb=" O   SER B 477 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   CYS B 491 " --> pdb=" O   SER B 487 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 400 through 402
      removed outlier: 3.552A  pdb=" N   LEU A 400 " --> pdb=" O   LEU A 377 " (cutoff:3.500A)
      removed outlier: 6.603A  pdb=" N   PHE A 346 " --> pdb=" O   ILE A 378 " (cutoff:3.500A)
      removed outlier: 8.359A  pdb=" N   GLY A 380 " --> pdb=" O   PHE A 346 " (cutoff:3.500A)
      removed outlier: 7.045A  pdb=" N   VAL A 348 " --> pdb=" O   GLY A 380 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   GLY A 345 " --> pdb=" O   VAL A 305 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   LEU A 307 " --> pdb=" O   GLY A 345 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   GLN A 347 " --> pdb=" O   LEU A 307 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   ASP A 308 " --> pdb=" O   LEU A 262 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   TYR A 226 " --> pdb=" O   GLY A 259 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 541 through 545
      removed outlier: 4.624A  pdb=" N   SER A 553 " --> pdb=" O   PHE A 545 " (cutoff:3.500A)
      removed outlier: 7.012A  pdb=" N   GLY A 622 " --> pdb=" O   SER A 599 " (cutoff:3.500A)
      removed outlier: 4.730A  pdb=" N   SER A 599 " --> pdb=" O   GLY A 622 " (cutoff:3.500A)
      removed outlier: 6.869A  pdb=" N   LEU A 624 " --> pdb=" O   LEU A 597 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 357 through 358

    292 hydrogen bonds defined for protein.
    852 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: 0.71

  Time building geometry restraints manager: 0.74 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1834
        1.33 -     1.45: 1445
        1.45 -     1.57: 4199
        1.57 -     1.69: 2
        1.69 -     1.81: 41
  Bond restraints: 7521
  Sorted by residual:
  bond pdb=" C31 3PH B 602 "
       pdb=" O31 3PH B 602 "
    ideal  model  delta    sigma   weight residual
    1.325  1.454 -0.129 2.00e-02 2.50e+03 4.14e+01
  bond pdb=" C31 3PH B 603 "
       pdb=" O31 3PH B 603 "
    ideal  model  delta    sigma   weight residual
    1.325  1.449 -0.124 2.00e-02 2.50e+03 3.83e+01
  bond pdb=" C21 3PH B 603 "
       pdb=" O21 3PH B 603 "
    ideal  model  delta    sigma   weight residual
    1.328  1.451 -0.123 2.00e-02 2.50e+03 3.77e+01
  bond pdb=" C21 3PH B 602 "
       pdb=" O21 3PH B 602 "
    ideal  model  delta    sigma   weight residual
    1.328  1.449 -0.121 2.00e-02 2.50e+03 3.67e+01
  bond pdb=" O11 3PH B 603 "
       pdb=" P   3PH B 603 "
    ideal  model  delta    sigma   weight residual
    1.703  1.607  0.096 2.00e-02 2.50e+03 2.31e+01
  ... (remaining 7516 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.65: 9953
        2.65 -     5.30: 224
        5.30 -     7.96: 38
        7.96 -    10.61: 8
       10.61 -    13.26: 2
  Bond angle restraints: 10225
  Sorted by residual:
  angle pdb=" C   LEU B 265 "
        pdb=" N   PRO B 266 "
        pdb=" CA  PRO B 266 "
      ideal   model   delta    sigma   weight residual
     119.64  114.12    5.52 1.01e+00 9.80e-01 2.98e+01
  angle pdb=" N   TYR B 385 "
        pdb=" CA  TYR B 385 "
        pdb=" C   TYR B 385 "
      ideal   model   delta    sigma   weight residual
     113.50  107.10    6.40 1.23e+00 6.61e-01 2.70e+01
  angle pdb=" N   GLY B 115 "
        pdb=" CA  GLY B 115 "
        pdb=" C   GLY B 115 "
      ideal   model   delta    sigma   weight residual
     112.49  118.69   -6.20 1.21e+00 6.83e-01 2.63e+01
  angle pdb=" N   THR B 386 "
        pdb=" CA  THR B 386 "
        pdb=" C   THR B 386 "
      ideal   model   delta    sigma   weight residual
     112.23  105.86    6.37 1.26e+00 6.30e-01 2.55e+01
  angle pdb=" N   SER B 179 "
        pdb=" CA  SER B 179 "
        pdb=" C   SER B 179 "
      ideal   model   delta    sigma   weight residual
     111.02  117.09   -6.07 1.25e+00 6.40e-01 2.36e+01
  ... (remaining 10220 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.27: 4152
       22.27 -    44.54: 313
       44.54 -    66.80: 54
       66.80 -    89.07: 9
       89.07 -   111.34: 8
  Dihedral angle restraints: 4536
    sinusoidal: 1884
      harmonic: 2652
  Sorted by residual:
  dihedral pdb=" CA  SER B 178 "
           pdb=" C   SER B 178 "
           pdb=" N   SER B 179 "
           pdb=" CA  SER B 179 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.28   28.72     0      5.00e+00 4.00e-02 3.30e+01
  dihedral pdb=" CA  SER A 176 "
           pdb=" C   SER A 176 "
           pdb=" N   PRO A 177 "
           pdb=" CA  PRO A 177 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.21   25.79     0      5.00e+00 4.00e-02 2.66e+01
  dihedral pdb=" CA  PHE B 114 "
           pdb=" C   PHE B 114 "
           pdb=" N   GLY B 115 "
           pdb=" CA  GLY B 115 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.10  -23.90     0      5.00e+00 4.00e-02 2.29e+01
  ... (remaining 4533 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.134: 1178
       0.134 -    0.269: 20
       0.269 -    0.403: 2
       0.403 -    0.538: 0
       0.538 -    0.672: 1
  Chirality restraints: 1201
  Sorted by residual:
  chirality pdb=" C1  NAG D   1 "
            pdb=" ND2 ASN A 366 "
            pdb=" C2  NAG D   1 "
            pdb=" O5  NAG D   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.73   -0.67 2.00e-01 2.50e+01 1.13e+01
  chirality pdb=" CB  VAL B 493 "
            pdb=" CA  VAL B 493 "
            pdb=" CG1 VAL B 493 "
            pdb=" CG2 VAL B 493 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.33   -0.30 2.00e-01 2.50e+01 2.31e+00
  chirality pdb=" C1  NAG F   1 "
            pdb=" ND2 ASN A 425 "
            pdb=" C2  NAG F   1 "
            pdb=" O5  NAG F   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.11   -0.29 2.00e-01 2.50e+01 2.17e+00
  ... (remaining 1198 not shown)

  Planarity restraints: 1262
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU B 228 "   -0.056 5.00e-02 4.00e+02   8.33e-02 1.11e+01
        pdb=" N   PRO B 229 "    0.144 5.00e-02 4.00e+02
        pdb=" CA  PRO B 229 "   -0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO B 229 "   -0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 618 "   -0.041 5.00e-02 4.00e+02   6.23e-02 6.22e+00
        pdb=" N   PRO A 619 "    0.108 5.00e-02 4.00e+02
        pdb=" CA  PRO A 619 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A 619 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR B 131 "   -0.035 5.00e-02 4.00e+02   5.23e-02 4.38e+00
        pdb=" N   PRO B 132 "    0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO B 132 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO B 132 "   -0.030 5.00e-02 4.00e+02
  ... (remaining 1259 not shown)

  Histogram of nonbonded interaction distances:
        1.90 -     2.50: 35
        2.50 -     3.10: 4426
        3.10 -     3.70: 10892
        3.70 -     4.30: 15771
        4.30 -     4.90: 25638
  Nonbonded interactions: 56762
  Sorted by model distance:
  nonbonded pdb=" O   THR B 381 "
            pdb=" O   SER B 382 "
     model   vdw
     1.904 3.040
  nonbonded pdb=" OG1 THR B 381 "
            pdb=" N   SER B 382 "
     model   vdw
     2.246 3.120
  nonbonded pdb=" O   PHE B 243 "
            pdb=" CB  LEU B 601 "
     model   vdw
     2.248 3.440
  nonbonded pdb=" O   LEU B 379 "
            pdb=" N   THR B 381 "
     model   vdw
     2.258 3.120
  nonbonded pdb=" OH  TYR B 396 "
            pdb=" O   HOH B 701 "
     model   vdw
     2.262 3.040
  ... (remaining 56757 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:             1.120
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     7.200
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  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:7.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.550
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6582
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.129   7530  Z= 0.321
  Angle     :  1.028  13.260  10251  Z= 0.552
  Chirality :  0.055   0.672   1201
  Planarity :  0.006   0.083   1258
  Dihedral  : 16.611 111.339   2833
  Min Nonbonded Distance : 1.904

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  1.41 %
    Allowed  :  7.15 %
    Favored  : 91.44 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  :  6.95 %
    Favored  : 91.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.99 (0.17), residues: 923
  helix: -4.51 (0.10), residues: 471
  sheet: -1.07 (0.58), residues: 72
  loop : -3.68 (0.22), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 349 
 TYR   0.016   0.002   TYR A 313 
 PHE   0.023   0.002   PHE B 335 
 TRP   0.021   0.002   TRP B 124 
 HIS   0.006   0.001   HIS B 358 

Details of bonding type rmsd
  covalent geometry    : bond        0.00635 ( 7521)
  covalent geometry    : angle       1.01217 (10225)
  SS BOND              : bond        0.00165 (    1)
  SS BOND              : angle       1.79920 (    2)
  hydrogen bonds       : bond        0.34454 (  292)
  hydrogen bonds       : angle      10.33981 (  852)
  link_BETA1-4         : bond        0.01223 (    4)
  link_BETA1-4         : angle       3.25152 (   12)
  link_NAG-ASN         : bond        0.00364 (    4)
  link_NAG-ASN         : angle       4.39518 (   12)

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

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

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 253
  time to evaluate  : 0.191 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  500 ILE cc_start: 0.6211 (mt) cc_final: 0.6000 (mt)
REVERT: B   99 THR cc_start: 0.6872 (m) cc_final: 0.6403 (m)
  outliers start: 11
  outliers final: 4
  residues processed: 258
  average time/residue: 0.3314
  time to fit residues: 92.8475
Evaluate side-chains
  148 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 144
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain B residue  262 TYR
Chi-restraints excluded: chain B residue  382 SER
Chi-restraints excluded: chain B residue  601 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    0.4980
   chunk 33 optimal weight:    0.0870
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    0.6980
   chunk 45 optimal weight:    4.9990
   chunk 74 optimal weight:    0.7980
   overall best weight:    0.5358

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

Flipped N/Q/H residues before XYZ refinement:
A 217 GLN
A 275 GLN
A 296 GLN
** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 560 GLN
A 561 ASN
B 134 ASN
B 264 ASN
B 406 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.110235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.086586 restraints weight = 12904.625|
|-----------------------------------------------------------------------------|
r_work (start): 0.3175 rms_B_bonded: 3.23
r_work: 0.3042 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7422
moved from start:          0.3664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   7530  Z= 0.175
  Angle     :  0.825  10.787  10251  Z= 0.404
  Chirality :  0.047   0.314   1201
  Planarity :  0.006   0.067   1258
  Dihedral  : 13.410  92.407   1249
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  6.93 %
    Favored  : 92.96 %
  Rotamer:
    Outliers :  4.46 %
    Allowed  : 19.66 %
    Favored  : 75.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.97 (0.22), residues: 923
  helix: -2.56 (0.18), residues: 470
  sheet: -0.39 (0.61), residues: 67
  loop : -3.06 (0.26), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 346 
 TYR   0.018   0.002   TYR B  93 
 PHE   0.030   0.002   PHE B 250 
 TRP   0.017   0.002   TRP A 338 
 HIS   0.003   0.001   HIS B 349 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 ( 7521)
  covalent geometry    : angle       0.81590 (10225)
  SS BOND              : bond        0.00487 (    1)
  SS BOND              : angle       2.86668 (    2)
  hydrogen bonds       : bond        0.05771 (  292)
  hydrogen bonds       : angle       4.99883 (  852)
  link_BETA1-4         : bond        0.00429 (    4)
  link_BETA1-4         : angle       1.97529 (   12)
  link_NAG-ASN         : bond        0.00333 (    4)
  link_NAG-ASN         : angle       3.07347 (   12)

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

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

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 160
  time to evaluate  : 0.184 
Fit side-chains
   revert: symmetry clash
REVERT: A  360 PHE cc_start: 0.8041 (m-80) cc_final: 0.7747 (m-80)
REVERT: B  314 MET cc_start: 0.7130 (ptt) cc_final: 0.6649 (pmm)
REVERT: B  347 GLU cc_start: 0.8454 (tp30) cc_final: 0.8127 (tp30)
REVERT: B  380 VAL cc_start: 0.6121 (m) cc_final: 0.5648 (p)
  outliers start: 34
  outliers final: 11
  residues processed: 183
  average time/residue: 0.3225
  time to fit residues: 64.3700
Evaluate side-chains
  144 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 133
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  509 THR
Chi-restraints excluded: chain B residue   54 ILE
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  163 LEU
Chi-restraints excluded: chain B residue  262 TYR
Chi-restraints excluded: chain B residue  321 SER
Chi-restraints excluded: chain B residue  326 THR
Chi-restraints excluded: chain B residue  465 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 61 optimal weight:    2.9990
   chunk 53 optimal weight:    0.1980
   chunk 22 optimal weight:    0.6980
   chunk 76 optimal weight:    3.9990
   chunk 58 optimal weight:    0.6980
   chunk 26 optimal weight:    0.0000
   chunk 33 optimal weight:    0.0570
   chunk 83 optimal weight:    2.9990
   chunk 55 optimal weight:    0.0980
   chunk 62 optimal weight:    0.6980
   chunk 7 optimal weight:    4.9990
   overall best weight:    0.2102

-------------------------------------------------------------------------------
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**
A 580 GLN
B 240 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.111517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.087750 restraints weight = 12840.468|
|-----------------------------------------------------------------------------|
r_work (start): 0.3205 rms_B_bonded: 3.24
r_work: 0.3075 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3075
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7508
moved from start:          0.4215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7530  Z= 0.127
  Angle     :  0.679   7.901  10251  Z= 0.329
  Chirality :  0.044   0.319   1201
  Planarity :  0.004   0.061   1258
  Dihedral  : 11.980  83.163   1244
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  6.72 %
    Favored  : 93.17 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 21.36 %
    Favored  : 73.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.72 (0.25), residues: 923
  helix: -1.28 (0.22), residues: 478
  sheet:  0.18 (0.65), residues: 53
  loop : -2.74 (0.27), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 440 
 TYR   0.030   0.002   TYR B 253 
 PHE   0.012   0.001   PHE A 337 
 TRP   0.018   0.001   TRP B 124 
 HIS   0.002   0.001   HIS A 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 7521)
  covalent geometry    : angle       0.66881 (10225)
  SS BOND              : bond        0.00318 (    1)
  SS BOND              : angle       2.35393 (    2)
  hydrogen bonds       : bond        0.04603 (  292)
  hydrogen bonds       : angle       4.48004 (  852)
  link_BETA1-4         : bond        0.00548 (    4)
  link_BETA1-4         : angle       2.15537 (   12)
  link_NAG-ASN         : bond        0.00393 (    4)
  link_NAG-ASN         : angle       2.74511 (   12)

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

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

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 146
  time to evaluate  : 0.260 
Fit side-chains
REVERT: B  171 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8238 (tm)
REVERT: B  314 MET cc_start: 0.7036 (ptt) cc_final: 0.6614 (pmm)
REVERT: B  347 GLU cc_start: 0.8400 (tp30) cc_final: 0.8130 (tp30)
REVERT: B  410 ARG cc_start: 0.8015 (mmt90) cc_final: 0.7789 (mmm-85)
REVERT: B  426 PHE cc_start: 0.8256 (OUTLIER) cc_final: 0.7708 (t80)
  outliers start: 36
  outliers final: 12
  residues processed: 168
  average time/residue: 0.3510
  time to fit residues: 64.1467
Evaluate side-chains
  140 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 126
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain A residue  435 SER
Chi-restraints excluded: chain A residue  568 LEU
Chi-restraints excluded: chain B residue   99 THR
Chi-restraints excluded: chain B residue  163 LEU
Chi-restraints excluded: chain B residue  164 LEU
Chi-restraints excluded: chain B residue  171 LEU
Chi-restraints excluded: chain B residue  259 VAL
Chi-restraints excluded: chain B residue  321 SER
Chi-restraints excluded: chain B residue  426 PHE
Chi-restraints excluded: chain B residue  465 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 9 optimal weight:    0.7980
   chunk 8 optimal weight:    0.7980
   chunk 45 optimal weight:    3.9990
   chunk 5 optimal weight:    0.1980
   chunk 10 optimal weight:    0.0470
   chunk 71 optimal weight:    2.9990
   chunk 23 optimal weight:    3.9990
   chunk 39 optimal weight:    3.9990
   chunk 18 optimal weight:    2.9990
   chunk 60 optimal weight:    0.8980
   chunk 30 optimal weight:    0.5980
   overall best weight:    0.4878

-------------------------------------------------------------------------------
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**
A 530 GLN
A 569 ASN
B 406 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.111937 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.088005 restraints weight = 12989.010|
|-----------------------------------------------------------------------------|
r_work (start): 0.3206 rms_B_bonded: 3.28
r_work: 0.3075 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.3075
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7819
moved from start:          0.5414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7530  Z= 0.138
  Angle     :  0.700   8.611  10251  Z= 0.337
  Chirality :  0.046   0.300   1201
  Planarity :  0.004   0.057   1258
  Dihedral  : 10.376  65.758   1242
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  6.18 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  5.90 %
    Allowed  : 22.41 %
    Favored  : 71.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.80 (0.26), residues: 923
  helix: -0.46 (0.23), residues: 487
  sheet:  0.31 (0.66), residues: 53
  loop : -2.37 (0.29), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 346 
 TYR   0.029   0.002   TYR B 253 
 PHE   0.023   0.002   PHE A 627 
 TRP   0.014   0.001   TRP B 124 
 HIS   0.003   0.001   HIS A 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 7521)
  covalent geometry    : angle       0.68963 (10225)
  SS BOND              : bond        0.00363 (    1)
  SS BOND              : angle       2.11774 (    2)
  hydrogen bonds       : bond        0.04024 (  292)
  hydrogen bonds       : angle       4.24719 (  852)
  link_BETA1-4         : bond        0.00538 (    4)
  link_BETA1-4         : angle       2.11050 (   12)
  link_NAG-ASN         : bond        0.00386 (    4)
  link_NAG-ASN         : angle       2.94938 (   12)

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

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

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 132
  time to evaluate  : 0.261 
Fit side-chains
REVERT: A  165 LEU cc_start: 0.5701 (pt) cc_final: 0.5066 (pp)
REVERT: B   52 ASN cc_start: 0.8596 (OUTLIER) cc_final: 0.8367 (t160)
REVERT: B  314 MET cc_start: 0.7192 (ptt) cc_final: 0.6815 (pmm)
REVERT: B  327 PHE cc_start: 0.8328 (OUTLIER) cc_final: 0.8084 (t80)
REVERT: B  426 PHE cc_start: 0.8538 (OUTLIER) cc_final: 0.7991 (t80)
REVERT: B  432 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8421 (mm)
REVERT: B  440 PHE cc_start: 0.8332 (m-80) cc_final: 0.8052 (m-10)
REVERT: B  456 MET cc_start: 0.8936 (ttp) cc_final: 0.8617 (ttt)
  outliers start: 45
  outliers final: 10
  residues processed: 163
  average time/residue: 0.3722
  time to fit residues: 65.6553
Evaluate side-chains
  122 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 108
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  435 SER
Chi-restraints excluded: chain B residue   52 ASN
Chi-restraints excluded: chain B residue   98 VAL
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  259 VAL
Chi-restraints excluded: chain B residue  260 ASP
Chi-restraints excluded: chain B residue  316 TRP
Chi-restraints excluded: chain B residue  321 SER
Chi-restraints excluded: chain B residue  327 PHE
Chi-restraints excluded: chain B residue  426 PHE
Chi-restraints excluded: chain B residue  432 LEU
Chi-restraints excluded: chain B residue  465 LEU
Chi-restraints excluded: chain B residue  487 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 48 optimal weight:    0.9980
   chunk 64 optimal weight:   20.0000
   chunk 1 optimal weight:    0.0870
   chunk 0 optimal weight:    4.9990
   chunk 50 optimal weight:    0.9980
   chunk 18 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 9 optimal weight:    0.3980
   chunk 55 optimal weight:    0.9990
   chunk 4 optimal weight:    0.6980
   chunk 84 optimal weight:    0.5980
   overall best weight:    0.5558

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

Flipped N/Q/H residues before XYZ refinement:
** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 240 GLN
B 331 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.111313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.087126 restraints weight = 12989.814|
|-----------------------------------------------------------------------------|
r_work (start): 0.3188 rms_B_bonded: 3.32
r_work: 0.3056 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7993
moved from start:          0.6377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   7530  Z= 0.136
  Angle     :  0.688   8.130  10251  Z= 0.325
  Chirality :  0.045   0.308   1201
  Planarity :  0.004   0.056   1258
  Dihedral  :  9.235  59.439   1242
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  6.72 %
    Favored  : 93.17 %
  Rotamer:
    Outliers :  5.37 %
    Allowed  : 23.59 %
    Favored  : 71.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.28 (0.27), residues: 923
  helix: -0.01 (0.24), residues: 485
  sheet:  0.60 (0.65), residues: 53
  loop : -2.17 (0.30), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 346 
 TYR   0.027   0.002   TYR A 629 
 PHE   0.025   0.001   PHE B 250 
 TRP   0.014   0.001   TRP B 124 
 HIS   0.003   0.001   HIS B 358 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 7521)
  covalent geometry    : angle       0.67531 (10225)
  SS BOND              : bond        0.02080 (    1)
  SS BOND              : angle       2.44085 (    2)
  hydrogen bonds       : bond        0.03967 (  292)
  hydrogen bonds       : angle       4.12543 (  852)
  link_BETA1-4         : bond        0.00574 (    4)
  link_BETA1-4         : angle       2.37627 (   12)
  link_NAG-ASN         : bond        0.00343 (    4)
  link_NAG-ASN         : angle       2.93885 (   12)

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

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

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 119
  time to evaluate  : 0.209 
Fit side-chains
REVERT: A  611 GLU cc_start: 0.7776 (pm20) cc_final: 0.7432 (pp20)
REVERT: B   95 GLU cc_start: 0.8785 (tp30) cc_final: 0.8582 (tp30)
REVERT: B  162 ARG cc_start: 0.8290 (mtm-85) cc_final: 0.7929 (mtt180)
REVERT: B  314 MET cc_start: 0.7529 (ptt) cc_final: 0.7050 (pmm)
REVERT: B  327 PHE cc_start: 0.8670 (OUTLIER) cc_final: 0.8325 (t80)
REVERT: B  383 ASP cc_start: 0.7544 (OUTLIER) cc_final: 0.7233 (p0)
REVERT: B  396 TYR cc_start: 0.8759 (m-80) cc_final: 0.8522 (m-80)
REVERT: B  426 PHE cc_start: 0.8730 (OUTLIER) cc_final: 0.8255 (t80)
REVERT: B  456 MET cc_start: 0.8946 (ttp) cc_final: 0.8485 (ttt)
  outliers start: 41
  outliers final: 17
  residues processed: 149
  average time/residue: 0.3437
  time to fit residues: 55.6425
Evaluate side-chains
  126 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 106
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  510 VAL
Chi-restraints excluded: chain A residue  587 SER
Chi-restraints excluded: chain A residue  596 LEU
Chi-restraints excluded: chain A residue  597 LEU
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain B residue   88 VAL
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue  164 LEU
Chi-restraints excluded: chain B residue  259 VAL
Chi-restraints excluded: chain B residue  260 ASP
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  316 TRP
Chi-restraints excluded: chain B residue  321 SER
Chi-restraints excluded: chain B residue  327 PHE
Chi-restraints excluded: chain B residue  349 HIS
Chi-restraints excluded: chain B residue  374 SER
Chi-restraints excluded: chain B residue  383 ASP
Chi-restraints excluded: chain B residue  386 THR
Chi-restraints excluded: chain B residue  426 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 82 optimal weight:    1.9990
   chunk 86 optimal weight:    0.7980
   chunk 77 optimal weight:    0.0070
   chunk 14 optimal weight:    0.8980
   chunk 20 optimal weight:    2.9990
   chunk 23 optimal weight:    3.9990
   chunk 31 optimal weight:    3.9990
   chunk 76 optimal weight:    1.9990
   chunk 10 optimal weight:    0.1980
   chunk 28 optimal weight:    2.9990
   chunk 44 optimal weight:    0.6980
   overall best weight:    0.5198

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

Flipped N/Q/H residues before XYZ refinement:
** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 483 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 = 0.3553 r_free = 0.3553 target = 0.111229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.086783 restraints weight = 12858.791|
|-----------------------------------------------------------------------------|
r_work (start): 0.3181 rms_B_bonded: 3.20
r_work: 0.3047 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.3047
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
moved from start:          0.6988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   7530  Z= 0.129
  Angle     :  0.684   9.406  10251  Z= 0.324
  Chirality :  0.044   0.306   1201
  Planarity :  0.004   0.056   1258
  Dihedral  :  8.753  59.372   1242
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  6.61 %
    Favored  : 93.28 %
  Rotamer:
    Outliers :  5.24 %
    Allowed  : 24.38 %
    Favored  : 70.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.98 (0.27), residues: 923
  helix:  0.32 (0.24), residues: 486
  sheet:  0.56 (0.63), residues: 53
  loop : -2.14 (0.30), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 346 
 TYR   0.019   0.001   TYR B 253 
 PHE   0.022   0.001   PHE B 250 
 TRP   0.013   0.001   TRP B 124 
 HIS   0.001   0.001   HIS A 620 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 7521)
  covalent geometry    : angle       0.67162 (10225)
  SS BOND              : bond        0.00208 (    1)
  SS BOND              : angle       2.53744 (    2)
  hydrogen bonds       : bond        0.03707 (  292)
  hydrogen bonds       : angle       4.09095 (  852)
  link_BETA1-4         : bond        0.00493 (    4)
  link_BETA1-4         : angle       2.29751 (   12)
  link_NAG-ASN         : bond        0.00313 (    4)
  link_NAG-ASN         : angle       3.03813 (   12)

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

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

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 114
  time to evaluate  : 0.280 
Fit side-chains
REVERT: A  197 MET cc_start: 0.8981 (mtm) cc_final: 0.8781 (mtm)
REVERT: A  490 MET cc_start: 0.8546 (tpt) cc_final: 0.7708 (tpt)
REVERT: A  572 ASP cc_start: 0.8503 (m-30) cc_final: 0.8266 (p0)
REVERT: A  611 GLU cc_start: 0.7838 (pm20) cc_final: 0.7514 (pp20)
REVERT: B   52 ASN cc_start: 0.8737 (OUTLIER) cc_final: 0.8522 (t160)
REVERT: B   95 GLU cc_start: 0.8781 (tp30) cc_final: 0.8507 (tp30)
REVERT: B  162 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.8086 (mtt180)
REVERT: B  185 ARG cc_start: 0.8673 (mmm160) cc_final: 0.7976 (ptt180)
REVERT: B  203 ILE cc_start: 0.8837 (pt) cc_final: 0.8636 (mp)
REVERT: B  314 MET cc_start: 0.7520 (ptt) cc_final: 0.7196 (pmm)
REVERT: B  327 PHE cc_start: 0.8719 (OUTLIER) cc_final: 0.8290 (t80)
REVERT: B  383 ASP cc_start: 0.7388 (OUTLIER) cc_final: 0.7182 (p0)
REVERT: B  396 TYR cc_start: 0.8813 (m-80) cc_final: 0.8562 (m-80)
REVERT: B  426 PHE cc_start: 0.8813 (OUTLIER) cc_final: 0.8409 (t80)
REVERT: B  456 MET cc_start: 0.8949 (ttp) cc_final: 0.8507 (ttt)
  outliers start: 40
  outliers final: 14
  residues processed: 141
  average time/residue: 0.3795
  time to fit residues: 58.0099
Evaluate side-chains
  121 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 102
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  293 SER
Chi-restraints excluded: chain A residue  510 VAL
Chi-restraints excluded: chain B residue   52 ASN
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain B residue   98 VAL
Chi-restraints excluded: chain B residue  162 ARG
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain B residue  209 ILE
Chi-restraints excluded: chain B residue  259 VAL
Chi-restraints excluded: chain B residue  260 ASP
Chi-restraints excluded: chain B residue  316 TRP
Chi-restraints excluded: chain B residue  321 SER
Chi-restraints excluded: chain B residue  327 PHE
Chi-restraints excluded: chain B residue  383 ASP
Chi-restraints excluded: chain B residue  426 PHE
Chi-restraints excluded: chain B residue  487 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 34 optimal weight:    0.5980
   chunk 37 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9980
   chunk 16 optimal weight:    0.7980
   chunk 43 optimal weight:    0.7980
   chunk 50 optimal weight:    0.6980
   chunk 10 optimal weight:    0.0040
   chunk 87 optimal weight:    0.0670
   chunk 72 optimal weight:    1.9990
   chunk 26 optimal weight:    0.3980
   chunk 0 optimal weight:    5.9990
   overall best weight:    0.3530

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

Flipped N/Q/H residues before XYZ refinement:
** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 240 GLN
B 349 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.111795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.087237 restraints weight = 12841.821|
|-----------------------------------------------------------------------------|
r_work (start): 0.3189 rms_B_bonded: 3.19
r_work: 0.3057 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8197
moved from start:          0.7317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   7530  Z= 0.115
  Angle     :  0.689   9.269  10251  Z= 0.323
  Chirality :  0.044   0.304   1201
  Planarity :  0.004   0.056   1258
  Dihedral  :  8.289  57.060   1242
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  6.83 %
    Favored  : 93.07 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 24.90 %
    Favored  : 70.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.74 (0.28), residues: 923
  helix:  0.57 (0.24), residues: 487
  sheet:  0.57 (0.66), residues: 51
  loop : -2.08 (0.30), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 346 
 TYR   0.019   0.001   TYR A 469 
 PHE   0.020   0.001   PHE B 250 
 TRP   0.016   0.001   TRP B 124 
 HIS   0.003   0.001   HIS B 349 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 7521)
  covalent geometry    : angle       0.67634 (10225)
  SS BOND              : bond        0.00176 (    1)
  SS BOND              : angle       2.30133 (    2)
  hydrogen bonds       : bond        0.03397 (  292)
  hydrogen bonds       : angle       4.02163 (  852)
  link_BETA1-4         : bond        0.00588 (    4)
  link_BETA1-4         : angle       2.42490 (   12)
  link_NAG-ASN         : bond        0.00334 (    4)
  link_NAG-ASN         : angle       3.02513 (   12)

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

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

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 109
  time to evaluate  : 0.260 
Fit side-chains
REVERT: A  325 ASP cc_start: 0.8946 (m-30) cc_final: 0.8268 (p0)
REVERT: A  451 LEU cc_start: 0.8861 (tt) cc_final: 0.8609 (tp)
REVERT: A  490 MET cc_start: 0.8628 (tpt) cc_final: 0.7770 (tpt)
REVERT: A  572 ASP cc_start: 0.8532 (m-30) cc_final: 0.8248 (p0)
REVERT: A  611 GLU cc_start: 0.7846 (pm20) cc_final: 0.7597 (pp20)
REVERT: B   95 GLU cc_start: 0.8782 (tp30) cc_final: 0.8528 (tp30)
REVERT: B  162 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.8089 (mtt180)
REVERT: B  185 ARG cc_start: 0.8701 (mmm160) cc_final: 0.8033 (ptt180)
REVERT: B  314 MET cc_start: 0.7467 (ptt) cc_final: 0.7188 (pmm)
REVERT: B  327 PHE cc_start: 0.8668 (OUTLIER) cc_final: 0.8290 (t80)
REVERT: B  426 PHE cc_start: 0.8859 (OUTLIER) cc_final: 0.8460 (t80)
REVERT: B  456 MET cc_start: 0.8934 (ttp) cc_final: 0.8593 (ttt)
  outliers start: 36
  outliers final: 15
  residues processed: 134
  average time/residue: 0.3619
  time to fit residues: 52.8280
Evaluate side-chains
  118 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 100
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  504 VAL
Chi-restraints excluded: chain A residue  510 VAL
Chi-restraints excluded: chain A residue  579 LEU
Chi-restraints excluded: chain A residue  587 SER
Chi-restraints excluded: chain A residue  597 LEU
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue   98 VAL
Chi-restraints excluded: chain B residue  162 ARG
Chi-restraints excluded: chain B residue  168 CYS
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain B residue  260 ASP
Chi-restraints excluded: chain B residue  316 TRP
Chi-restraints excluded: chain B residue  321 SER
Chi-restraints excluded: chain B residue  327 PHE
Chi-restraints excluded: chain B residue  426 PHE
Chi-restraints excluded: chain B residue  487 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 54 optimal weight:    3.9990
   chunk 18 optimal weight:    1.9990
   chunk 35 optimal weight:    0.0170
   chunk 30 optimal weight:    0.7980
   chunk 88 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9980
   chunk 42 optimal weight:    6.9990
   chunk 79 optimal weight:    0.0570
   chunk 50 optimal weight:    0.6980
   chunk 27 optimal weight:    0.0370
   overall best weight:    0.3214

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

Flipped N/Q/H residues before XYZ refinement:
** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 208 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.110632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.086682 restraints weight = 13147.778|
|-----------------------------------------------------------------------------|
r_work (start): 0.3162 rms_B_bonded: 3.29
r_work: 0.3025 rms_B_bonded: 3.78 restraints_weight: 0.5000
r_work (final): 0.3025
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
moved from start:          0.7657

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   7530  Z= 0.113
  Angle     :  0.682   9.178  10251  Z= 0.321
  Chirality :  0.043   0.302   1201
  Planarity :  0.004   0.056   1258
  Dihedral  :  7.901  57.371   1242
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  6.61 %
    Favored  : 93.28 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 25.56 %
    Favored  : 70.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.58 (0.28), residues: 923
  helix:  0.74 (0.24), residues: 487
  sheet:  0.46 (0.66), residues: 51
  loop : -2.03 (0.30), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 346 
 TYR   0.017   0.001   TYR B 253 
 PHE   0.015   0.001   PHE B 250 
 TRP   0.015   0.001   TRP B 124 
 HIS   0.003   0.001   HIS B 349 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 7521)
  covalent geometry    : angle       0.66911 (10225)
  SS BOND              : bond        0.00242 (    1)
  SS BOND              : angle       2.15987 (    2)
  hydrogen bonds       : bond        0.03308 (  292)
  hydrogen bonds       : angle       3.97390 (  852)
  link_BETA1-4         : bond        0.00526 (    4)
  link_BETA1-4         : angle       2.33895 (   12)
  link_NAG-ASN         : bond        0.00318 (    4)
  link_NAG-ASN         : angle       3.08698 (   12)

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

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

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 104
  time to evaluate  : 0.239 
Fit side-chains
REVERT: A  165 LEU cc_start: 0.5523 (pt) cc_final: 0.5187 (pt)
REVERT: A  325 ASP cc_start: 0.9042 (m-30) cc_final: 0.8358 (p0)
REVERT: A  451 LEU cc_start: 0.8861 (tt) cc_final: 0.8654 (tp)
REVERT: A  572 ASP cc_start: 0.8672 (m-30) cc_final: 0.8290 (p0)
REVERT: A  611 GLU cc_start: 0.7921 (pm20) cc_final: 0.7587 (pp20)
REVERT: B   95 GLU cc_start: 0.8802 (tp30) cc_final: 0.8436 (tp30)
REVERT: B  162 ARG cc_start: 0.8324 (mtm-85) cc_final: 0.7994 (mtt180)
REVERT: B  185 ARG cc_start: 0.8731 (mmm160) cc_final: 0.8073 (ptt180)
REVERT: B  314 MET cc_start: 0.7363 (ptt) cc_final: 0.7083 (pmm)
REVERT: B  327 PHE cc_start: 0.8629 (OUTLIER) cc_final: 0.8127 (t80)
REVERT: B  347 GLU cc_start: 0.8298 (tt0) cc_final: 0.7870 (tp30)
REVERT: B  456 MET cc_start: 0.8810 (ttp) cc_final: 0.8470 (ttt)
  outliers start: 31
  outliers final: 12
  residues processed: 126
  average time/residue: 0.3975
  time to fit residues: 54.0805
Evaluate side-chains
  104 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 91
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  510 VAL
Chi-restraints excluded: chain A residue  579 LEU
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain B residue   98 VAL
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain B residue  259 VAL
Chi-restraints excluded: chain B residue  260 ASP
Chi-restraints excluded: chain B residue  316 TRP
Chi-restraints excluded: chain B residue  327 PHE
Chi-restraints excluded: chain B residue  487 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 82 optimal weight:    1.9990
   chunk 57 optimal weight:    0.0020
   chunk 15 optimal weight:    0.4980
   chunk 69 optimal weight:    0.6980
   chunk 42 optimal weight:    3.9990
   chunk 14 optimal weight:    0.8980
   chunk 67 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9990
   chunk 31 optimal weight:    5.9990
   chunk 60 optimal weight:    1.9990
   chunk 39 optimal weight:    4.9990
   overall best weight:    0.6190

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

Flipped N/Q/H residues before XYZ refinement:
** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 483 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 = 0.3514 r_free = 0.3514 target = 0.109082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.084933 restraints weight = 12893.256|
|-----------------------------------------------------------------------------|
r_work (start): 0.3134 rms_B_bonded: 3.23
r_work: 0.2998 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.2998
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8246
moved from start:          0.8018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7530  Z= 0.130
  Angle     :  0.718   8.848  10251  Z= 0.343
  Chirality :  0.045   0.309   1201
  Planarity :  0.004   0.056   1258
  Dihedral  :  7.756  56.968   1242
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  6.39 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 27.00 %
    Favored  : 70.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.51 (0.28), residues: 923
  helix:  0.79 (0.24), residues: 488
  sheet:  0.40 (0.67), residues: 51
  loop : -1.99 (0.31), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 346 
 TYR   0.018   0.001   TYR A 469 
 PHE   0.014   0.001   PHE B 250 
 TRP   0.012   0.001   TRP B 124 
 HIS   0.008   0.001   HIS B 358 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 7521)
  covalent geometry    : angle       0.70593 (10225)
  SS BOND              : bond        0.00312 (    1)
  SS BOND              : angle       2.15782 (    2)
  hydrogen bonds       : bond        0.03509 (  292)
  hydrogen bonds       : angle       3.97468 (  852)
  link_BETA1-4         : bond        0.00580 (    4)
  link_BETA1-4         : angle       2.28437 (   12)
  link_NAG-ASN         : bond        0.00323 (    4)
  link_NAG-ASN         : angle       3.17205 (   12)

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

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

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 100
  time to evaluate  : 0.244 
Fit side-chains
   revert: symmetry clash
REVERT: A  292 ASP cc_start: 0.9061 (t0) cc_final: 0.8541 (m-30)
REVERT: A  325 ASP cc_start: 0.9031 (m-30) cc_final: 0.8343 (p0)
REVERT: A  583 ASP cc_start: 0.8627 (m-30) cc_final: 0.7726 (p0)
REVERT: A  611 GLU cc_start: 0.7992 (pm20) cc_final: 0.7662 (pp20)
REVERT: B   95 GLU cc_start: 0.8784 (tp30) cc_final: 0.8299 (tp30)
REVERT: B  162 ARG cc_start: 0.8449 (mtm-85) cc_final: 0.8200 (mtt180)
REVERT: B  185 ARG cc_start: 0.8779 (mmm160) cc_final: 0.8135 (ptt180)
REVERT: B  314 MET cc_start: 0.7402 (ptt) cc_final: 0.7135 (pmm)
REVERT: B  426 PHE cc_start: 0.8898 (OUTLIER) cc_final: 0.8510 (t80)
REVERT: B  456 MET cc_start: 0.8864 (ttp) cc_final: 0.8556 (ttt)
  outliers start: 21
  outliers final: 13
  residues processed: 114
  average time/residue: 0.4042
  time to fit residues: 49.7555
Evaluate side-chains
  107 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 93
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  510 VAL
Chi-restraints excluded: chain A residue  597 LEU
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain B residue   98 VAL
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  260 ASP
Chi-restraints excluded: chain B residue  316 TRP
Chi-restraints excluded: chain B residue  327 PHE
Chi-restraints excluded: chain B residue  426 PHE
Chi-restraints excluded: chain B residue  487 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 74 optimal weight:    2.9990
   chunk 84 optimal weight:    0.4980
   chunk 27 optimal weight:    5.9990
   chunk 21 optimal weight:    0.6980
   chunk 89 optimal weight:    6.9990
   chunk 28 optimal weight:    0.0000
   chunk 72 optimal weight:    0.7980
   chunk 82 optimal weight:    0.9990
   chunk 52 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 78 optimal weight:    2.9990
   overall best weight:    0.5986

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

Flipped N/Q/H residues before XYZ refinement:
** A 268 ASN ** 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 = 0.3510 r_free = 0.3510 target = 0.108756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.084588 restraints weight = 12950.606|
|-----------------------------------------------------------------------------|
r_work (start): 0.3129 rms_B_bonded: 3.25
r_work: 0.2994 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.2994
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8255
moved from start:          0.8295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7530  Z= 0.126
  Angle     :  0.715   9.790  10251  Z= 0.340
  Chirality :  0.044   0.302   1201
  Planarity :  0.004   0.056   1258
  Dihedral  :  7.678  55.228   1242
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  6.72 %
    Favored  : 93.17 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 27.52 %
    Favored  : 69.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.40 (0.28), residues: 923
  helix:  0.92 (0.24), residues: 489
  sheet:  0.31 (0.68), residues: 51
  loop : -1.99 (0.30), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 346 
 TYR   0.015   0.001   TYR B 253 
 PHE   0.014   0.001   PHE B 250 
 TRP   0.012   0.001   TRP B 124 
 HIS   0.002   0.000   HIS B 358 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 7521)
  covalent geometry    : angle       0.70108 (10225)
  SS BOND              : bond        0.00304 (    1)
  SS BOND              : angle       2.08046 (    2)
  hydrogen bonds       : bond        0.03432 (  292)
  hydrogen bonds       : angle       3.94567 (  852)
  link_BETA1-4         : bond        0.00661 (    4)
  link_BETA1-4         : angle       2.24032 (   12)
  link_NAG-ASN         : bond        0.00373 (    4)
  link_NAG-ASN         : angle       3.50062 (   12)

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

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

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1846 Ramachandran restraints generated.
    923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 95
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
REVERT: A  167 LYS cc_start: 0.7888 (tmmt) cc_final: 0.7567 (pptt)
REVERT: A  292 ASP cc_start: 0.9075 (t0) cc_final: 0.8577 (m-30)
REVERT: A  366 ASN cc_start: 0.6383 (t0) cc_final: 0.6058 (t0)
REVERT: A  583 ASP cc_start: 0.8549 (m-30) cc_final: 0.7726 (p0)
REVERT: A  611 GLU cc_start: 0.8081 (pm20) cc_final: 0.7728 (pp20)
REVERT: B   95 GLU cc_start: 0.8760 (tp30) cc_final: 0.8340 (tp30)
REVERT: B  162 ARG cc_start: 0.8450 (mtm-85) cc_final: 0.8169 (mtt180)
REVERT: B  185 ARG cc_start: 0.8745 (mmm160) cc_final: 0.8151 (ptt180)
REVERT: B  347 GLU cc_start: 0.8338 (tt0) cc_final: 0.7865 (tp30)
REVERT: B  426 PHE cc_start: 0.8936 (OUTLIER) cc_final: 0.8592 (t80)
REVERT: B  456 MET cc_start: 0.8866 (ttp) cc_final: 0.8548 (ttt)
  outliers start: 19
  outliers final: 9
  residues processed: 108
  average time/residue: 0.4325
  time to fit residues: 50.2906
Evaluate side-chains
  100 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 90
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  510 VAL
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain B residue   98 VAL
Chi-restraints excluded: chain B residue  186 VAL
Chi-restraints excluded: chain B residue  260 ASP
Chi-restraints excluded: chain B residue  316 TRP
Chi-restraints excluded: chain B residue  426 PHE
Chi-restraints excluded: chain B residue  487 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 41 optimal weight:    6.9990
   chunk 58 optimal weight:    3.9990
   chunk 43 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9990
   chunk 35 optimal weight:    4.9990
   chunk 10 optimal weight:    0.0980
   chunk 69 optimal weight:    0.5980
   chunk 12 optimal weight:    0.5980
   chunk 11 optimal weight:    0.8980
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A 268 ASN ** 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 = 0.3502 r_free = 0.3502 target = 0.108252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.084045 restraints weight = 12968.464|
|-----------------------------------------------------------------------------|
r_work (start): 0.3119 rms_B_bonded: 3.22
r_work: 0.2986 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.2986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8297
moved from start:          0.8468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7530  Z= 0.128
  Angle     :  0.732  12.703  10251  Z= 0.344
  Chirality :  0.045   0.304   1201
  Planarity :  0.004   0.056   1258
  Dihedral  :  7.570  54.970   1242
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  6.39 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 28.57 %
    Favored  : 69.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.33 (0.28), residues: 923
  helix:  0.98 (0.24), residues: 490
  sheet:  0.29 (0.69), residues: 51
  loop : -1.95 (0.30), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 346 
 TYR   0.015   0.001   TYR B 253 
 PHE   0.014   0.001   PHE B 250 
 TRP   0.012   0.001   TRP B 124 
 HIS   0.002   0.000   HIS B 358 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 7521)
  covalent geometry    : angle       0.71916 (10225)
  SS BOND              : bond        0.00311 (    1)
  SS BOND              : angle       2.08463 (    2)
  hydrogen bonds       : bond        0.03436 (  292)
  hydrogen bonds       : angle       3.91234 (  852)
  link_BETA1-4         : bond        0.00542 (    4)
  link_BETA1-4         : angle       2.23082 (   12)
  link_NAG-ASN         : bond        0.00278 (    4)
  link_NAG-ASN         : angle       3.29329 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2151.62 seconds
wall clock time: 37 minutes 22.02 seconds (2242.02 seconds total)