Starting phenix.real_space_refine
on Mon Apr 28 16:29:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6irt_9722/04_2025/6irt_9722_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6irt_9722/04_2025/6irt_9722.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6irt_9722/04_2025/6irt_9722.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6irt_9722/04_2025/6irt_9722.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6irt_9722/04_2025/6irt_9722_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6irt_9722/04_2025/6irt_9722_neut.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.006
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      27      5.16       5
     C    4815      2.51       5
     N    1173      2.21       5
     O    1331      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 7348
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 3650
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 469, 3650
          Classifications: {'peptide': 469}
          Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 446}
    Chain: "B"
      Number of atoms: 3479
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 457, 3479
          Classifications: {'peptide': 457}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 432}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 52
          Unresolved non-hydrogen angles: 67
          Unresolved non-hydrogen dihedrals: 42
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 31
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 107
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 107
          Unusual residues: {'3PH': 2, 'AUU': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 5.28, per 1000 atoms: 0.72
  Number of scatterers: 7348
  At special positions: 0
  Unit cell: (82.916, 84.007, 124.374, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      27     16.00
     P       2     15.00
     O    1331      8.00
     N    1173      7.00
     C    4815      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 211 " - pdb=" SG  CYS B 164 " distance=2.03

  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: 2.00
  Conformation dependent library (CDL) restraints added in 951.6 milliseconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 3 sheets defined
      58.4% alpha, 5.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.67
  Creating SS restraints...
    Processing helix  chain 'A' and resid 168 through 175
      removed outlier: 3.604A  pdb=" N   LYS A 172 " --> pdb=" O   GLU A 168 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   VAL A 173 " --> pdb=" O   GLU A 169 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   ALA A 174 " --> pdb=" O   LEU A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 180 through 185
    Processing helix  chain 'A' and resid 185 through 208
      removed outlier: 3.616A  pdb=" N   PHE A 190 " --> pdb=" O   LEU A 186 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   TRP A 191 " --> pdb=" O   LEU A 187 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   MET A 197 " --> pdb=" O   GLY A 193 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   GLY A 200 " --> pdb=" O   GLY A 196 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   VAL A 203 " --> pdb=" O   ALA A 199 " (cutoff:3.500A)
      removed outlier: 4.401A  pdb=" N   ILE A 204 " --> pdb=" O   GLY A 200 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   ILE A 205 " --> pdb=" O   ALA A 201 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 218 through 222
      removed outlier: 3.735A  pdb=" N   HIS A 221 " --> pdb=" O   LYS A 218 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   THR A 222 " --> pdb=" O   TRP A 219 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 218 through 222'
    Processing helix  chain 'A' and resid 230 through 235
    Processing helix  chain 'A' and resid 241 through 246
    Processing helix  chain 'A' and resid 248 through 256
      removed outlier: 3.876A  pdb=" N   SER A 254 " --> pdb=" O   ASP A 250 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 301
      removed outlier: 3.866A  pdb=" N   LYS A 301 " --> pdb=" O   SER A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 342
      removed outlier: 4.203A  pdb=" N   GLU A 336 " --> pdb=" O   LYS A 332 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   LEU A 339 " --> pdb=" O   LEU A 335 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   GLN A 340 " --> pdb=" O   GLU A 336 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 350 through 354
    Processing helix  chain 'A' and resid 356 through 370
      removed outlier: 3.768A  pdb=" N   PHE A 360 " --> pdb=" O   ASP A 356 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   LEU A 361 " --> pdb=" O   ALA A 357 " (cutoff:3.500A)
      removed outlier: 4.329A  pdb=" N   ALA A 362 " --> pdb=" O   SER A 358 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   GLU A 363 " --> pdb=" O   SER A 359 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 393
      removed outlier: 3.665A  pdb=" N   LEU A 392 " --> pdb=" O   GLN A 388 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 412 through 428
      removed outlier: 3.787A  pdb=" N   GLN A 422 " --> pdb=" O   SER A 418 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 450 through 461
      removed outlier: 3.522A  pdb=" N   GLN A 455 " --> pdb=" O   LEU A 451 " (cutoff:3.500A)
      removed outlier: 4.451A  pdb=" N   LEU A 456 " --> pdb=" O   ARG A 452 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   MET A 457 " --> pdb=" O   LEU A 453 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 493 through 497
      removed outlier: 4.405A  pdb=" N   PHE A 497 " --> pdb=" O   GLU A 494 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 509 through 514
    Processing helix  chain 'A' and resid 519 through 532
      removed outlier: 3.595A  pdb=" N   ARG A 526 " --> pdb=" O   SER A 522 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   SER A 532 " --> pdb=" O   SER A 528 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 534 through 540
      removed outlier: 3.784A  pdb=" N   HIS A 539 " --> pdb=" O   ARG A 535 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 52 through 63
      removed outlier: 4.369A  pdb=" N   ALA B  57 " --> pdb=" O   LEU B  53 " (cutoff:3.500A)
      removed outlier: 4.213A  pdb=" N   ILE B  58 " --> pdb=" O   ASN B  54 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   ILE B  59 " --> pdb=" O   GLY B  55 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   ILE B  63 " --> pdb=" O   ILE B  59 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 66 through 74
      removed outlier: 4.759A  pdb=" N   THR B  71 " --> pdb=" O   ILE B  68 " (cutoff:3.500A)
      Proline residue:  B  72  - end of helix
    Processing helix  chain 'B' and resid 81 through 110
      removed outlier: 3.607A  pdb=" N   LEU B  86 " --> pdb=" O   PRO B  82 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   VAL B  87 " --> pdb=" O   GLY B  83 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   TRP B  89 " --> pdb=" O   ALA B  85 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   GLY B  93 " --> pdb=" O   TRP B  89 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   THR B 108 " --> pdb=" O   ALA B 104 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   ILE B 110 " --> pdb=" O   LEU B 106 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 117 through 124
      removed outlier: 3.569A  pdb=" N   VAL B 123 " --> pdb=" O   TYR B 119 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 126 through 139
    Processing helix  chain 'B' and resid 139 through 158
      removed outlier: 3.581A  pdb=" N   SER B 143 " --> pdb=" O   ILE B 139 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   GLN B 145 " --> pdb=" O   ARG B 141 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   ILE B 147 " --> pdb=" O   SER B 143 " (cutoff:3.500A)
      removed outlier: 4.347A  pdb=" N   VAL B 148 " --> pdb=" O   SER B 144 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   ALA B 153 " --> pdb=" O   ALA B 149 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   LEU B 156 " --> pdb=" O   PHE B 152 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 167 through 187
      removed outlier: 4.333A  pdb=" N   LEU B 173 " --> pdb=" O   GLU B 169 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   VAL B 174 " --> pdb=" O   ALA B 170 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   ALA B 175 " --> pdb=" O   ALA B 171 " (cutoff:3.500A)
      removed outlier: 4.231A  pdb=" N   LEU B 177 " --> pdb=" O   LEU B 173 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   LEU B 181 " --> pdb=" O   LEU B 177 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   LEU B 182 " --> pdb=" O   CYS B 178 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   ALA B 184 " --> pdb=" O   LEU B 180 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 189 through 199
      removed outlier: 4.151A  pdb=" N   ARG B 195 " --> pdb=" O   LYS B 191 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 201 through 222
      removed outlier: 3.544A  pdb=" N   LEU B 213 " --> pdb=" O   ALA B 209 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   GLN B 218 " --> pdb=" O   LEU B 214 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   ILE B 219 " --> pdb=" O   GLY B 215 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   GLY B 222 " --> pdb=" O   GLN B 218 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 230 through 235
      removed outlier: 4.399A  pdb=" N   GLU B 234 " --> pdb=" O   PHE B 231 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   GLY B 235 " --> pdb=" O   SER B 232 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 243 through 251
      removed outlier: 3.633A  pdb=" N   SER B 249 " --> pdb=" O   LEU B 245 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 260 through 263
      removed outlier: 3.727A  pdb=" N   VAL B 263 " --> pdb=" O   LEU B 260 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 260 through 263'
    Processing helix  chain 'B' and resid 264 through 269
      removed outlier: 4.079A  pdb=" N   ILE B 268 " --> pdb=" O   THR B 264 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 273 through 300
      removed outlier: 3.694A  pdb=" N   ALA B 277 " --> pdb=" O   ASN B 273 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   ILE B 279 " --> pdb=" O   PRO B 275 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   ILE B 280 " --> pdb=" O   LEU B 276 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   LEU B 282 " --> pdb=" O   ILE B 278 " (cutoff:3.500A)
      Proline residue:  B 283  - end of helix
      removed outlier: 3.730A  pdb=" N   ASN B 293 " --> pdb=" O   TYR B 289 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   THR B 299 " --> pdb=" O   ALA B 295 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 303 through 308
    Processing helix  chain 'B' and resid 310 through 320
      removed outlier: 4.029A  pdb=" N   ASP B 314 " --> pdb=" O   ALA B 310 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   HIS B 319 " --> pdb=" O   PHE B 315 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   LEU B 320 " --> pdb=" O   GLY B 316 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 326 through 333
    Processing helix  chain 'B' and resid 334 through 339
      removed outlier: 3.550A  pdb=" N   VAL B 339 " --> pdb=" O   CYS B 335 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 340 through 343
    Processing helix  chain 'B' and resid 344 through 355
      removed outlier: 3.954A  pdb=" N   ARG B 348 " --> pdb=" O   PHE B 344 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   LEU B 349 " --> pdb=" O   THR B 345 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   PHE B 350 " --> pdb=" O   SER B 346 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   PHE B 351 " --> pdb=" O   SER B 347 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   VAL B 352 " --> pdb=" O   ARG B 348 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ARG B 355 " --> pdb=" O   PHE B 351 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 373 through 386
      removed outlier: 3.675A  pdb=" N   PHE B 379 " --> pdb=" O   PRO B 375 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 387 through 390
    Processing helix  chain 'B' and resid 393 through 421
      removed outlier: 3.509A  pdb=" N   PHE B 399 " --> pdb=" O   SER B 395 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   PHE B 402 " --> pdb=" O   ASN B 398 " (cutoff:3.500A)
      removed outlier: 4.263A  pdb=" N   PHE B 403 " --> pdb=" O   PHE B 399 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   TRP B 405 " --> pdb=" O   SER B 401 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   ILE B 412 " --> pdb=" O   VAL B 408 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   ARG B 419 " --> pdb=" O   MET B 415 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 434 through 453
      removed outlier: 3.808A  pdb=" N   ALA B 442 " --> pdb=" O   PHE B 438 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   PHE B 445 " --> pdb=" O   LEU B 441 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   LEU B 446 " --> pdb=" O   ALA B 442 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   ILE B 447 " --> pdb=" O   CYS B 443 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   SER B 450 " --> pdb=" O   LEU B 446 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   PHE B 451 " --> pdb=" O   ILE B 447 " (cutoff:3.500A)
      removed outlier: 4.274A  pdb=" N   TRP B 452 " --> pdb=" O   ALA B 448 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 454 through 466
      removed outlier: 4.293A  pdb=" N   CYS B 458 " --> pdb=" O   THR B 454 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   ILE B 460 " --> pdb=" O   VAL B 456 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 469 through 476
    Processing helix  chain 'B' and resid 484 through 501
      removed outlier: 3.950A  pdb=" N   PHE B 490 " --> pdb=" O   LEU B 486 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 400 through 401
      removed outlier: 6.562A  pdb=" N   PHE A 346 " --> pdb=" O   ILE A 378 " (cutoff:3.500A)
      removed outlier: 7.136A  pdb=" N   VAL A 305 " --> pdb=" O   GLY A 345 " (cutoff:3.500A)
      removed outlier: 8.275A  pdb=" N   GLN A 347 " --> pdb=" O   VAL A 305 " (cutoff:3.500A)
      removed outlier: 6.472A  pdb=" N   LEU A 307 " --> pdb=" O   GLN A 347 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   TYR A 226 " --> pdb=" O   GLY A 259 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 266 through 268
    Processing sheet with id=AA3, first strand: chain 'A' and resid 541 through 545
      removed outlier: 4.700A  pdb=" N   SER A 553 " --> pdb=" O   PHE A 545 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   ARG A 556 " --> pdb=" O   PHE A 564 " (cutoff:3.500A)
      removed outlier: 5.498A  pdb=" N   ARG A 626 " --> pdb=" O   LEU A 596 " (cutoff:3.500A)
      removed outlier: 4.815A  pdb=" N   LEU A 596 " --> pdb=" O   ARG A 626 " (cutoff:3.500A)

    297 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: 1.89

  Time building geometry restraints manager: 2.32 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: 2069
        1.33 -     1.45: 1333
        1.45 -     1.57: 4077
        1.57 -     1.69: 3
        1.69 -     1.81: 42
  Bond restraints: 7524
  Sorted by residual:
  bond pdb=" C06 AUU B 603 "
       pdb=" C08 AUU B 603 "
    ideal  model  delta    sigma   weight residual
    1.531  1.707 -0.176 2.00e-02 2.50e+03 7.77e+01
  bond pdb=" C04 AUU B 603 "
       pdb=" C09 AUU B 603 "
    ideal  model  delta    sigma   weight residual
    1.535  1.362  0.173 2.00e-02 2.50e+03 7.53e+01
  bond pdb=" C04 AUU B 603 "
       pdb=" C08 AUU B 603 "
    ideal  model  delta    sigma   weight residual
    1.533  1.699 -0.166 2.00e-02 2.50e+03 6.89e+01
  bond pdb=" C06 AUU B 603 "
       pdb=" C07 AUU B 603 "
    ideal  model  delta    sigma   weight residual
    1.534  1.370  0.164 2.00e-02 2.50e+03 6.71e+01
  bond pdb=" C06 AUU B 603 "
       pdb=" C11 AUU B 603 "
    ideal  model  delta    sigma   weight residual
    1.537  1.383  0.154 2.00e-02 2.50e+03 5.94e+01
  ... (remaining 7519 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.19: 9548
        2.19 -     4.39: 554
        4.39 -     6.58: 79
        6.58 -     8.78: 35
        8.78 -    10.97: 13
  Bond angle restraints: 10229
  Sorted by residual:
  angle pdb=" N   HIS B 319 "
        pdb=" CA  HIS B 319 "
        pdb=" C   HIS B 319 "
      ideal   model   delta    sigma   weight residual
     111.36  122.33  -10.97 1.09e+00 8.42e-01 1.01e+02
  angle pdb=" C   SER A 176 "
        pdb=" N   PRO A 177 "
        pdb=" CA  PRO A 177 "
      ideal   model   delta    sigma   weight residual
     119.84  128.89   -9.05 1.25e+00 6.40e-01 5.24e+01
  angle pdb=" N   LEU B 320 "
        pdb=" CA  LEU B 320 "
        pdb=" C   LEU B 320 "
      ideal   model   delta    sigma   weight residual
     108.34  116.69   -8.35 1.31e+00 5.83e-01 4.07e+01
  angle pdb=" C   PHE B 161 "
        pdb=" N   PRO B 162 "
        pdb=" CD  PRO B 162 "
      ideal   model   delta    sigma   weight residual
     120.60  109.75   10.85 2.20e+00 2.07e-01 2.43e+01
  angle pdb=" CA  LEU B 469 "
        pdb=" C   LEU B 469 "
        pdb=" N   PRO B 470 "
      ideal   model   delta    sigma   weight residual
     120.81  116.58    4.23 8.60e-01 1.35e+00 2.42e+01
  ... (remaining 10224 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.14: 4295
       21.14 -    42.28: 211
       42.28 -    63.42: 34
       63.42 -    84.56: 12
       84.56 -   105.70: 10
  Dihedral angle restraints: 4562
    sinusoidal: 1909
      harmonic: 2653
  Sorted by residual:
  dihedral pdb=" CB  CYS A 211 "
           pdb=" SG  CYS A 211 "
           pdb=" SG  CYS B 164 "
           pdb=" CB  CYS B 164 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -157.02   71.02     1      1.00e+01 1.00e-02 6.48e+01
  dihedral pdb=" CA  VAL B 322 "
           pdb=" C   VAL B 322 "
           pdb=" N   MET B 323 "
           pdb=" CA  MET B 323 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.31   26.69     0      5.00e+00 4.00e-02 2.85e+01
  dihedral pdb=" CA  GLN A 323 "
           pdb=" C   GLN A 323 "
           pdb=" N   VAL A 324 "
           pdb=" CA  VAL A 324 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -154.11  -25.89     0      5.00e+00 4.00e-02 2.68e+01
  ... (remaining 4559 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.277: 1194
       0.277 -    0.553: 7
       0.553 -    0.830: 0
       0.830 -    1.106: 0
       1.106 -    1.383: 2
  Chirality restraints: 1203
  Sorted by residual:
  chirality pdb=" C1  NAG C   1 "
            pdb=" ND2 ASN A 507 "
            pdb=" C2  NAG C   1 "
            pdb=" O5  NAG C   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.02   -1.38 2.00e-01 2.50e+01 4.78e+01
  chirality pdb=" C1  NAG E   1 "
            pdb=" ND2 ASN A 382 "
            pdb=" C2  NAG E   1 "
            pdb=" O5  NAG E   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.10   -1.30 2.00e-01 2.50e+01 4.22e+01
  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   -2.88    0.48 2.00e-01 2.50e+01 5.74e+00
  ... (remaining 1200 not shown)

  Planarity restraints: 1259
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 366 "    0.102 2.00e-02 2.50e+03   2.65e-01 8.75e+02
        pdb=" CG  ASN A 366 "   -0.080 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 366 "    0.153 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 366 "   -0.471 2.00e-02 2.50e+03
        pdb=" C1  NAG D   1 "    0.296 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 382 "   -0.123 2.00e-02 2.50e+03   2.00e-01 5.00e+02
        pdb=" CG  ASN A 382 "    0.059 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 382 "   -0.058 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 382 "    0.353 2.00e-02 2.50e+03
        pdb=" C1  NAG E   1 "   -0.231 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 507 "   -0.072 2.00e-02 2.50e+03   8.36e-02 8.74e+01
        pdb=" CG  ASN A 507 "    0.031 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 507 "    0.001 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 507 "    0.139 2.00e-02 2.50e+03
        pdb=" C1  NAG C   1 "   -0.098 2.00e-02 2.50e+03
  ... (remaining 1256 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1762
        2.77 -     3.30: 6596
        3.30 -     3.84: 11683
        3.84 -     4.37: 13661
        4.37 -     4.90: 22977
  Nonbonded interactions: 56679
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 460 "
            pdb=" OH  TYR A 554 "
     model   vdw
     2.241 3.040
  nonbonded pdb=" OG  SER A 599 "
            pdb=" OE2 GLU A 621 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" O   ASP A 516 "
            pdb=" OG  SER A 522 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" O   THR A 460 "
            pdb=" NH1 ARG A 556 "
     model   vdw
     2.291 3.120
  nonbonded pdb=" O   GLY B 107 "
            pdb=" OG  SER B 111 "
     model   vdw
     2.300 3.040
  ... (remaining 56674 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.510
  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:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     20.510
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.390
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
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      :  0.012   0.176   7533  Z= 0.539
  Angle     :  1.297  17.404  10255  Z= 0.657
  Chirality :  0.088   1.383   1203
  Planarity :  0.008   0.063   1255
  Dihedral  : 14.319 105.703   2855
  Min Nonbonded Distance : 2.241

Molprobity Statistics.
  All-atom Clashscore : 10.46
  Ramachandran Plot:
    Outliers :  0.76 %
    Allowed  :  9.22 %
    Favored  : 90.02 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  :  6.54 %
    Favored  : 90.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.53 (0.19), residues: 922
  helix: -4.19 (0.12), residues: 470
  sheet: -1.95 (0.65), residues: 49
  loop : -3.07 (0.26), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.004   TRP B 417 
 HIS   0.009   0.004   HIS A 620 
 PHE   0.024   0.003   PHE A 552 
 TYR   0.036   0.004   TYR A 454 
 ARG   0.012   0.001   ARG A 227 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.05936 (    4)
  link_NAG-ASN         : angle      11.21040 (   12)
  link_BETA1-4         : bond        0.01414 (    4)
  link_BETA1-4         : angle       3.79315 (   12)
  hydrogen bonds       : bond        0.31282 (  297)
  hydrogen bonds       : angle      10.07666 (  852)
  SS BOND              : bond        0.00530 (    1)
  SS BOND              : angle       1.23577 (    2)
  covalent geometry    : bond        0.01162 ( 7524)
  covalent geometry    : angle       1.23364 (10229)

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

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 226
  time to evaluate  : 0.812 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  534 GLU cc_start: 0.7413 (mm-30) cc_final: 0.7076 (mm-30)
REVERT: B  146 TYR cc_start: 0.8686 (t80) cc_final: 0.8121 (t80)
REVERT: B  195 ARG cc_start: 0.8020 (mtm110) cc_final: 0.7737 (ptt180)
REVERT: B  218 GLN cc_start: 0.8445 (tp40) cc_final: 0.8213 (tp40)
REVERT: B  315 PHE cc_start: 0.8297 (t80) cc_final: 0.8064 (t80)
REVERT: B  419 ARG cc_start: 0.8107 (mtp85) cc_final: 0.7342 (mmp-170)
REVERT: B  440 ILE cc_start: 0.9232 (mt) cc_final: 0.9008 (mt)
REVERT: B  466 LEU cc_start: 0.8515 (mp) cc_final: 0.8275 (tp)
REVERT: B  478 TRP cc_start: 0.6616 (t-100) cc_final: 0.6280 (t-100)
REVERT: B  501 GLN cc_start: 0.8096 (tt0) cc_final: 0.7827 (tm-30)
  outliers start: 23
  outliers final: 5
  residues processed: 234
  average time/residue: 0.2132
  time to fit residues: 64.9254
Evaluate side-chains
  139 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 134
  time to evaluate  : 0.758 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  456 LEU
Chi-restraints excluded: chain A residue  485 MET
Chi-restraints excluded: chain A residue  490 MET
Chi-restraints excluded: chain B residue   63 ILE
Chi-restraints excluded: chain B residue  131 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 76 optimal weight:    0.9980
   chunk 68 optimal weight:    4.9990
   chunk 38 optimal weight:    0.6980
   chunk 23 optimal weight:    0.6980
   chunk 46 optimal weight:    0.6980
   chunk 36 optimal weight:    0.6980
   chunk 71 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 43 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 217 GLN
A 221 HIS
A 232 GLN
A 268 ASN
A 388 GLN
A 483 GLN
A 561 ASN
A 620 HIS
B 293 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.122200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.095201 restraints weight = 13335.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.098895 restraints weight = 6843.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.101350 restraints weight = 4691.842|
|-----------------------------------------------------------------------------|
r_work (final): 0.3379
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8002
moved from start:          0.2966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7533  Z= 0.167
  Angle     :  0.872  13.079  10255  Z= 0.413
  Chirality :  0.051   0.679   1203
  Planarity :  0.006   0.043   1255
  Dihedral  : 12.781  90.249   1274
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  7.70 %
    Favored  : 92.08 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 13.74 %
    Favored  : 83.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.02 (0.22), residues: 922
  helix: -2.57 (0.17), residues: 489
  sheet: -1.89 (0.62), residues: 60
  loop : -2.76 (0.29), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 134 
 HIS   0.005   0.001   HIS B 319 
 PHE   0.021   0.002   PHE B  95 
 TYR   0.013   0.002   TYR B 318 
 ARG   0.010   0.001   ARG B 355 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00893 (    4)
  link_NAG-ASN         : angle       6.86544 (   12)
  link_BETA1-4         : bond        0.00866 (    4)
  link_BETA1-4         : angle       2.44016 (   12)
  hydrogen bonds       : bond        0.06226 (  297)
  hydrogen bonds       : angle       5.58922 (  852)
  SS BOND              : bond        0.00191 (    1)
  SS BOND              : angle       0.93905 (    2)
  covalent geometry    : bond        0.00354 ( 7524)
  covalent geometry    : angle       0.83657 (10229)

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

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 173
  time to evaluate  : 0.752 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 MET cc_start: 0.7836 (ttp) cc_final: 0.7570 (mmp)
REVERT: A  279 LEU cc_start: 0.8087 (pp) cc_final: 0.7799 (pp)
REVERT: B  120 MET cc_start: 0.9081 (tpp) cc_final: 0.8822 (tpp)
REVERT: B  146 TYR cc_start: 0.8627 (t80) cc_final: 0.8117 (t80)
REVERT: B  195 ARG cc_start: 0.8065 (mtm110) cc_final: 0.7756 (ptt180)
REVERT: B  218 GLN cc_start: 0.8690 (tp40) cc_final: 0.8414 (tp-100)
REVERT: B  254 TYR cc_start: 0.8740 (m-80) cc_final: 0.8297 (m-80)
REVERT: B  352 VAL cc_start: 0.9387 (t) cc_final: 0.9067 (t)
REVERT: B  466 LEU cc_start: 0.8632 (mp) cc_final: 0.8302 (tp)
REVERT: B  478 TRP cc_start: 0.6521 (t-100) cc_final: 0.6235 (t-100)
REVERT: B  499 LEU cc_start: 0.9122 (tt) cc_final: 0.8886 (tt)
  outliers start: 20
  outliers final: 10
  residues processed: 185
  average time/residue: 0.1608
  time to fit residues: 41.8564
Evaluate side-chains
  151 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 141
  time to evaluate  : 0.907 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  485 MET
Chi-restraints excluded: chain A residue  504 VAL
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  393 ILE
Chi-restraints excluded: chain B residue  416 ILE
Chi-restraints excluded: chain B residue  467 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 9 optimal weight:    3.9990
   chunk 77 optimal weight:    2.9990
   chunk 78 optimal weight:    0.6980
   chunk 44 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9990
   chunk 45 optimal weight:    6.9990
   chunk 2 optimal weight:    0.0040
   chunk 70 optimal weight:    4.9990
   chunk 17 optimal weight:    0.9990
   chunk 30 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9990
   overall best weight:    0.6796

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

Flipped N/Q/H residues before XYZ refinement:
B 317 ASN
B 497 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.119477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.092388 restraints weight = 13778.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.096108 restraints weight = 7066.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.098504 restraints weight = 4817.346|
|-----------------------------------------------------------------------------|
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
moved from start:          0.3614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7533  Z= 0.140
  Angle     :  0.766  10.776  10255  Z= 0.362
  Chirality :  0.046   0.431   1203
  Planarity :  0.005   0.039   1255
  Dihedral  : 10.716  89.437   1267
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  7.48 %
    Favored  : 92.30 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 15.45 %
    Favored  : 80.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.73 (0.25), residues: 922
  helix: -1.28 (0.21), residues: 490
  sheet: -1.04 (0.66), residues: 55
  loop : -2.57 (0.29), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 405 
 HIS   0.005   0.001   HIS B 367 
 PHE   0.021   0.001   PHE B  95 
 TYR   0.017   0.002   TYR A 405 
 ARG   0.004   0.000   ARG B 272 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00783 (    4)
  link_NAG-ASN         : angle       5.92805 (   12)
  link_BETA1-4         : bond        0.00674 (    4)
  link_BETA1-4         : angle       2.57797 (   12)
  hydrogen bonds       : bond        0.04850 (  297)
  hydrogen bonds       : angle       4.97648 (  852)
  SS BOND              : bond        0.00187 (    1)
  SS BOND              : angle       0.65697 (    2)
  covalent geometry    : bond        0.00307 ( 7524)
  covalent geometry    : angle       0.73472 (10229)

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

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 155
  time to evaluate  : 0.834 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 MET cc_start: 0.7883 (ttp) cc_final: 0.7579 (mmp)
REVERT: A  534 GLU cc_start: 0.6999 (mm-30) cc_final: 0.6378 (mt-10)
REVERT: A  555 ILE cc_start: 0.9132 (mt) cc_final: 0.8866 (pt)
REVERT: B  146 TYR cc_start: 0.8635 (t80) cc_final: 0.8089 (t80)
REVERT: B  195 ARG cc_start: 0.7999 (mtm110) cc_final: 0.7672 (ptt180)
REVERT: B  218 GLN cc_start: 0.8741 (tp40) cc_final: 0.8476 (tp-100)
REVERT: B  254 TYR cc_start: 0.8747 (m-80) cc_final: 0.8241 (m-80)
REVERT: B  318 TYR cc_start: 0.6911 (t80) cc_final: 0.6615 (t80)
REVERT: B  352 VAL cc_start: 0.9236 (t) cc_final: 0.8409 (t)
REVERT: B  356 GLU cc_start: 0.7365 (mp0) cc_final: 0.7156 (mp0)
REVERT: B  466 LEU cc_start: 0.8623 (mp) cc_final: 0.8281 (tp)
  outliers start: 28
  outliers final: 12
  residues processed: 170
  average time/residue: 0.1754
  time to fit residues: 42.9162
Evaluate side-chains
  151 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 139
  time to evaluate  : 0.747 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  414 GLU
Chi-restraints excluded: chain A residue  504 VAL
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  208 LEU
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  416 ILE
Chi-restraints excluded: chain B residue  427 ARG
Chi-restraints excluded: chain B residue  467 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 44 optimal weight:    8.9990
   chunk 24 optimal weight:    0.0470
   chunk 79 optimal weight:    0.3980
   chunk 30 optimal weight:    0.5980
   chunk 57 optimal weight:    0.3980
   chunk 8 optimal weight:    7.9990
   chunk 15 optimal weight:    0.0050
   chunk 34 optimal weight:    0.2980
   chunk 16 optimal weight:    5.9990
   chunk 82 optimal weight:    4.9990
   chunk 14 optimal weight:    0.9990
   overall best weight:    0.2292

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

Flipped N/Q/H residues before XYZ refinement:
B 317 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.127795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.100326 restraints weight = 13173.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.104373 restraints weight = 6494.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.106988 restraints weight = 4355.075|
|-----------------------------------------------------------------------------|
r_work (final): 0.3460
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7957
moved from start:          0.4047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7533  Z= 0.121
  Angle     :  0.730   9.926  10255  Z= 0.341
  Chirality :  0.045   0.435   1203
  Planarity :  0.004   0.038   1255
  Dihedral  :  9.515  89.166   1262
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  6.72 %
    Favored  : 93.06 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 16.62 %
    Favored  : 80.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.10 (0.26), residues: 922
  helix: -0.66 (0.22), residues: 497
  sheet: -0.79 (0.67), residues: 55
  loop : -2.47 (0.30), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 405 
 HIS   0.003   0.001   HIS B 367 
 PHE   0.022   0.001   PHE B  95 
 TYR   0.016   0.001   TYR A 405 
 ARG   0.005   0.000   ARG A 212 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00674 (    4)
  link_NAG-ASN         : angle       5.36276 (   12)
  link_BETA1-4         : bond        0.00742 (    4)
  link_BETA1-4         : angle       2.53554 (   12)
  hydrogen bonds       : bond        0.04081 (  297)
  hydrogen bonds       : angle       4.64291 (  852)
  SS BOND              : bond        0.00082 (    1)
  SS BOND              : angle       0.51149 (    2)
  covalent geometry    : bond        0.00251 ( 7524)
  covalent geometry    : angle       0.70199 (10229)

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

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 148
  time to evaluate  : 0.737 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 MET cc_start: 0.7729 (ttp) cc_final: 0.7529 (mmp)
REVERT: A  534 GLU cc_start: 0.6932 (mm-30) cc_final: 0.6371 (mt-10)
REVERT: B  120 MET cc_start: 0.9166 (mmm) cc_final: 0.8800 (tpp)
REVERT: B  146 TYR cc_start: 0.8597 (t80) cc_final: 0.8113 (t80)
REVERT: B  195 ARG cc_start: 0.7924 (mtm110) cc_final: 0.7598 (ptt180)
REVERT: B  254 TYR cc_start: 0.8700 (m-80) cc_final: 0.8288 (m-80)
REVERT: B  265 GLU cc_start: 0.7623 (tm-30) cc_final: 0.7090 (tm-30)
REVERT: B  318 TYR cc_start: 0.6959 (t80) cc_final: 0.6673 (t80)
REVERT: B  352 VAL cc_start: 0.9238 (t) cc_final: 0.8407 (t)
REVERT: B  466 LEU cc_start: 0.8754 (mp) cc_final: 0.8401 (tp)
REVERT: B  500 MET cc_start: 0.8693 (mtt) cc_final: 0.8436 (mtp)
REVERT: B  501 GLN cc_start: 0.8646 (tm-30) cc_final: 0.7749 (tm-30)
  outliers start: 23
  outliers final: 13
  residues processed: 161
  average time/residue: 0.1465
  time to fit residues: 34.3924
Evaluate side-chains
  149 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 136
  time to evaluate  : 0.900 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  290 ASP
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  485 MET
Chi-restraints excluded: chain A residue  504 VAL
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  208 LEU
Chi-restraints excluded: chain B residue  416 ILE
Chi-restraints excluded: chain B residue  467 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 53 optimal weight:    0.0770
   chunk 74 optimal weight:    0.4980
   chunk 48 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9990
   chunk 47 optimal weight:    0.6980
   chunk 82 optimal weight:    0.7980
   chunk 79 optimal weight:    3.9990
   chunk 62 optimal weight:    0.6980
   chunk 86 optimal weight:    0.6980
   chunk 63 optimal weight:    0.9990
   overall best weight:    0.5338

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

Flipped N/Q/H residues before XYZ refinement:
B 218 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.126955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.099178 restraints weight = 13221.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.103189 restraints weight = 6615.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.105777 restraints weight = 4482.249|
|-----------------------------------------------------------------------------|
r_work (final): 0.3441
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7979
moved from start:          0.4262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.072   7533  Z= 0.126
  Angle     :  0.713   9.336  10255  Z= 0.334
  Chirality :  0.045   0.414   1203
  Planarity :  0.004   0.038   1255
  Dihedral  :  8.936  87.626   1262
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  6.94 %
    Favored  : 92.84 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 16.75 %
    Favored  : 79.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.70 (0.27), residues: 922
  helix: -0.32 (0.23), residues: 490
  sheet: -0.11 (0.67), residues: 52
  loop : -2.36 (0.30), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 405 
 HIS   0.002   0.000   HIS B 420 
 PHE   0.024   0.001   PHE B  95 
 TYR   0.016   0.001   TYR A 405 
 ARG   0.003   0.000   ARG A 227 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00562 (    4)
  link_NAG-ASN         : angle       4.97934 (   12)
  link_BETA1-4         : bond        0.00723 (    4)
  link_BETA1-4         : angle       2.54932 (   12)
  hydrogen bonds       : bond        0.03849 (  297)
  hydrogen bonds       : angle       4.53788 (  852)
  SS BOND              : bond        0.00204 (    1)
  SS BOND              : angle       0.36487 (    2)
  covalent geometry    : bond        0.00286 ( 7524)
  covalent geometry    : angle       0.68791 (10229)

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

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 152
  time to evaluate  : 0.699 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 MET cc_start: 0.7755 (ttp) cc_final: 0.7552 (mmp)
REVERT: A  249 LEU cc_start: 0.9226 (mt) cc_final: 0.8895 (mt)
REVERT: A  534 GLU cc_start: 0.7106 (mm-30) cc_final: 0.6519 (mt-10)
REVERT: B  146 TYR cc_start: 0.8656 (t80) cc_final: 0.8186 (t80)
REVERT: B  195 ARG cc_start: 0.7911 (mtm110) cc_final: 0.7587 (ptt180)
REVERT: B  254 TYR cc_start: 0.8723 (m-80) cc_final: 0.8251 (m-80)
REVERT: B  265 GLU cc_start: 0.7587 (tm-30) cc_final: 0.7088 (tm-30)
REVERT: B  438 PHE cc_start: 0.8093 (t80) cc_final: 0.7739 (t80)
REVERT: B  466 LEU cc_start: 0.8586 (mp) cc_final: 0.8309 (tp)
  outliers start: 27
  outliers final: 19
  residues processed: 161
  average time/residue: 0.2486
  time to fit residues: 60.2855
Evaluate side-chains
  153 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 134
  time to evaluate  : 1.739 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  485 MET
Chi-restraints excluded: chain A residue  504 VAL
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue  208 LEU
Chi-restraints excluded: chain B residue  213 LEU
Chi-restraints excluded: chain B residue  218 GLN
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  383 MET
Chi-restraints excluded: chain B residue  386 LEU
Chi-restraints excluded: chain B residue  413 ILE
Chi-restraints excluded: chain B residue  416 ILE
Chi-restraints excluded: chain B residue  467 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 8 optimal weight:    5.9990
   chunk 72 optimal weight:    0.8980
   chunk 88 optimal weight:    0.9980
   chunk 18 optimal weight:    0.8980
   chunk 83 optimal weight:    0.0970
   chunk 54 optimal weight:    0.9980
   chunk 45 optimal weight:    5.9990
   chunk 43 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 46 optimal weight:    0.0370
   overall best weight:    0.5856

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

Flipped N/Q/H residues before XYZ refinement:
B 218 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.126581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.098969 restraints weight = 13346.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.103014 restraints weight = 6675.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.105583 restraints weight = 4508.865|
|-----------------------------------------------------------------------------|
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7984
moved from start:          0.4455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   7533  Z= 0.126
  Angle     :  0.713   8.813  10255  Z= 0.334
  Chirality :  0.045   0.410   1203
  Planarity :  0.004   0.040   1255
  Dihedral  :  8.603  87.181   1262
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  6.94 %
    Favored  : 92.73 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 17.54 %
    Favored  : 78.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.50 (0.27), residues: 922
  helix: -0.11 (0.23), residues: 490
  sheet:  0.00 (0.68), residues: 52
  loop : -2.33 (0.30), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 405 
 HIS   0.006   0.001   HIS B 367 
 PHE   0.024   0.001   PHE B  95 
 TYR   0.017   0.001   TYR A 405 
 ARG   0.003   0.000   ARG A 227 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00540 (    4)
  link_NAG-ASN         : angle       4.81543 (   12)
  link_BETA1-4         : bond        0.00724 (    4)
  link_BETA1-4         : angle       2.50749 (   12)
  hydrogen bonds       : bond        0.03709 (  297)
  hydrogen bonds       : angle       4.52964 (  852)
  SS BOND              : bond        0.00158 (    1)
  SS BOND              : angle       0.37221 (    2)
  covalent geometry    : bond        0.00285 ( 7524)
  covalent geometry    : angle       0.68882 (10229)

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

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 142
  time to evaluate  : 0.828 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 MET cc_start: 0.7773 (ttp) cc_final: 0.7550 (mmp)
REVERT: A  249 LEU cc_start: 0.9199 (mt) cc_final: 0.8882 (mt)
REVERT: A  272 ASP cc_start: 0.7843 (t0) cc_final: 0.7557 (p0)
REVERT: A  534 GLU cc_start: 0.7055 (mm-30) cc_final: 0.6492 (mt-10)
REVERT: B  120 MET cc_start: 0.9047 (tpp) cc_final: 0.8679 (tpp)
REVERT: B  146 TYR cc_start: 0.8667 (t80) cc_final: 0.8203 (t80)
REVERT: B  195 ARG cc_start: 0.7920 (mtm110) cc_final: 0.7602 (ptt180)
REVERT: B  254 TYR cc_start: 0.8735 (m-80) cc_final: 0.8266 (m-80)
REVERT: B  438 PHE cc_start: 0.8119 (t80) cc_final: 0.7742 (t80)
REVERT: B  453 LYS cc_start: 0.8359 (tptm) cc_final: 0.7914 (mmtt)
REVERT: B  466 LEU cc_start: 0.8586 (mp) cc_final: 0.8358 (tp)
  outliers start: 30
  outliers final: 23
  residues processed: 155
  average time/residue: 0.1606
  time to fit residues: 36.1058
Evaluate side-chains
  155 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 132
  time to evaluate  : 1.091 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  485 MET
Chi-restraints excluded: chain A residue  504 VAL
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain B residue  208 LEU
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  213 LEU
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  359 LEU
Chi-restraints excluded: chain B residue  383 MET
Chi-restraints excluded: chain B residue  386 LEU
Chi-restraints excluded: chain B residue  413 ILE
Chi-restraints excluded: chain B residue  416 ILE
Chi-restraints excluded: chain B residue  467 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 4 optimal weight:    0.6980
   chunk 72 optimal weight:    0.8980
   chunk 80 optimal weight:    0.8980
   chunk 82 optimal weight:    3.9990
   chunk 23 optimal weight:    0.8980
   chunk 9 optimal weight:    0.5980
   chunk 60 optimal weight:    3.9990
   chunk 64 optimal weight:   20.0000
   chunk 47 optimal weight:    0.9980
   chunk 54 optimal weight:    0.8980
   chunk 2 optimal weight:    2.9990
   overall best weight:    0.7980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.125915 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.098065 restraints weight = 13309.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.102085 restraints weight = 6670.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.104664 restraints weight = 4528.647|
|-----------------------------------------------------------------------------|
r_work (final): 0.3430
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.4531

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7533  Z= 0.134
  Angle     :  0.709   8.537  10255  Z= 0.333
  Chirality :  0.045   0.400   1203
  Planarity :  0.004   0.038   1255
  Dihedral  :  8.317  86.351   1262
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  7.05 %
    Favored  : 92.62 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 19.11 %
    Favored  : 77.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.28 (0.27), residues: 922
  helix:  0.09 (0.24), residues: 491
  sheet:  0.08 (0.67), residues: 59
  loop : -2.30 (0.30), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B 405 
 HIS   0.004   0.001   HIS B 367 
 PHE   0.024   0.001   PHE B  95 
 TYR   0.015   0.001   TYR A 405 
 ARG   0.004   0.000   ARG A 227 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00469 (    4)
  link_NAG-ASN         : angle       4.71049 (   12)
  link_BETA1-4         : bond        0.00683 (    4)
  link_BETA1-4         : angle       2.47197 (   12)
  hydrogen bonds       : bond        0.03590 (  297)
  hydrogen bonds       : angle       4.47594 (  852)
  SS BOND              : bond        0.00113 (    1)
  SS BOND              : angle       0.46020 (    2)
  covalent geometry    : bond        0.00307 ( 7524)
  covalent geometry    : angle       0.68638 (10229)

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

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 135
  time to evaluate  : 0.730 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 MET cc_start: 0.7767 (ttp) cc_final: 0.7551 (mmp)
REVERT: A  249 LEU cc_start: 0.9196 (mt) cc_final: 0.8886 (mt)
REVERT: A  534 GLU cc_start: 0.7073 (mm-30) cc_final: 0.6511 (mt-10)
REVERT: B  146 TYR cc_start: 0.8670 (t80) cc_final: 0.8273 (t80)
REVERT: B  195 ARG cc_start: 0.7911 (mtm110) cc_final: 0.7606 (ptt180)
REVERT: B  206 LEU cc_start: 0.9015 (tt) cc_final: 0.8799 (pp)
REVERT: B  254 TYR cc_start: 0.8776 (m-80) cc_final: 0.8276 (m-80)
REVERT: B  265 GLU cc_start: 0.7652 (tm-30) cc_final: 0.7134 (tm-30)
REVERT: B  365 MET cc_start: 0.8821 (mmm) cc_final: 0.8356 (mtp)
REVERT: B  438 PHE cc_start: 0.8117 (t80) cc_final: 0.7848 (t80)
REVERT: B  453 LYS cc_start: 0.8381 (tptm) cc_final: 0.7928 (mmtt)
REVERT: B  466 LEU cc_start: 0.8717 (mp) cc_final: 0.8517 (tp)
REVERT: B  500 MET cc_start: 0.8704 (mtt) cc_final: 0.8314 (mtp)
REVERT: B  501 GLN cc_start: 0.8691 (tm-30) cc_final: 0.7948 (tm-30)
  outliers start: 27
  outliers final: 22
  residues processed: 148
  average time/residue: 0.1617
  time to fit residues: 34.8397
Evaluate side-chains
  154 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 132
  time to evaluate  : 0.765 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  205 ILE
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  485 MET
Chi-restraints excluded: chain A residue  504 VAL
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain B residue  208 LEU
Chi-restraints excluded: chain B residue  213 LEU
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  359 LEU
Chi-restraints excluded: chain B residue  386 LEU
Chi-restraints excluded: chain B residue  413 ILE
Chi-restraints excluded: chain B residue  416 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 29 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 35 optimal weight:    6.9990
   chunk 25 optimal weight:    1.9990
   chunk 86 optimal weight:    0.0060
   chunk 49 optimal weight:    2.9990
   chunk 7 optimal weight:    5.9990
   chunk 82 optimal weight:    0.7980
   chunk 88 optimal weight:    0.4980
   chunk 71 optimal weight:    3.9990
   chunk 84 optimal weight:    0.8980
   overall best weight:    0.6396

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.126830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.098897 restraints weight = 13364.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.102973 restraints weight = 6633.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.105578 restraints weight = 4477.640|
|-----------------------------------------------------------------------------|
r_work (final): 0.3439
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
moved from start:          0.4689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7533  Z= 0.127
  Angle     :  0.719  12.186  10255  Z= 0.334
  Chirality :  0.045   0.404   1203
  Planarity :  0.004   0.039   1255
  Dihedral  :  8.081  86.586   1262
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  7.05 %
    Favored  : 92.62 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 20.55 %
    Favored  : 76.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.24 (0.27), residues: 922
  helix:  0.09 (0.23), residues: 499
  sheet: -0.03 (0.65), residues: 59
  loop : -2.26 (0.31), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B 405 
 HIS   0.005   0.001   HIS B 367 
 PHE   0.028   0.001   PHE A 346 
 TYR   0.015   0.001   TYR A 405 
 ARG   0.003   0.000   ARG A 227 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00463 (    4)
  link_NAG-ASN         : angle       4.68003 (   12)
  link_BETA1-4         : bond        0.00716 (    4)
  link_BETA1-4         : angle       2.42782 (   12)
  hydrogen bonds       : bond        0.03469 (  297)
  hydrogen bonds       : angle       4.44908 (  852)
  SS BOND              : bond        0.00100 (    1)
  SS BOND              : angle       0.31449 (    2)
  covalent geometry    : bond        0.00288 ( 7524)
  covalent geometry    : angle       0.69710 (10229)

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

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 142
  time to evaluate  : 1.146 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  249 LEU cc_start: 0.9193 (mt) cc_final: 0.8891 (mt)
REVERT: A  272 ASP cc_start: 0.7877 (t0) cc_final: 0.7586 (p0)
REVERT: A  534 GLU cc_start: 0.7055 (mm-30) cc_final: 0.6487 (mt-10)
REVERT: B  146 TYR cc_start: 0.8664 (t80) cc_final: 0.8281 (t80)
REVERT: B  195 ARG cc_start: 0.7943 (mtm110) cc_final: 0.7627 (ptt180)
REVERT: B  254 TYR cc_start: 0.8765 (m-80) cc_final: 0.8257 (m-80)
REVERT: B  265 GLU cc_start: 0.7613 (tm-30) cc_final: 0.7119 (tm-30)
REVERT: B  365 MET cc_start: 0.8746 (mmm) cc_final: 0.8438 (mtp)
REVERT: B  438 PHE cc_start: 0.8107 (t80) cc_final: 0.7887 (t80)
REVERT: B  453 LYS cc_start: 0.8403 (tptm) cc_final: 0.7972 (mmtt)
REVERT: B  501 GLN cc_start: 0.8954 (tm-30) cc_final: 0.8191 (tm-30)
  outliers start: 22
  outliers final: 20
  residues processed: 152
  average time/residue: 0.1988
  time to fit residues: 44.4514
Evaluate side-chains
  153 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 133
  time to evaluate  : 1.014 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  504 VAL
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain B residue  108 THR
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  173 LEU
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain B residue  208 LEU
Chi-restraints excluded: chain B residue  213 LEU
Chi-restraints excluded: chain B residue  359 LEU
Chi-restraints excluded: chain B residue  386 LEU
Chi-restraints excluded: chain B residue  413 ILE
Chi-restraints excluded: chain B residue  416 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 20 optimal weight:    0.0170
   chunk 35 optimal weight:    0.2980
   chunk 16 optimal weight:    0.0870
   chunk 14 optimal weight:    0.7980
   chunk 0 optimal weight:    7.9990
   chunk 6 optimal weight:    3.9990
   chunk 39 optimal weight:    3.9990
   chunk 46 optimal weight:    4.9990
   chunk 1 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 33 optimal weight:    4.9990
   overall best weight:    0.8398

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

Flipped N/Q/H residues before XYZ refinement:
B 293 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.126168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.097987 restraints weight = 13496.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.102014 restraints weight = 6701.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.104552 restraints weight = 4563.524|
|-----------------------------------------------------------------------------|
r_work (final): 0.3423
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8004
moved from start:          0.4746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7533  Z= 0.136
  Angle     :  0.738  11.760  10255  Z= 0.344
  Chirality :  0.045   0.398   1203
  Planarity :  0.004   0.038   1255
  Dihedral  :  7.952  86.335   1262
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  6.72 %
    Favored  : 92.95 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 21.34 %
    Favored  : 75.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.15 (0.27), residues: 922
  helix:  0.16 (0.23), residues: 501
  sheet: -0.04 (0.65), residues: 59
  loop : -2.21 (0.31), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B 405 
 HIS   0.004   0.001   HIS B 367 
 PHE   0.024   0.002   PHE B  95 
 TYR   0.014   0.001   TYR A 405 
 ARG   0.003   0.000   ARG A 227 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00400 (    4)
  link_NAG-ASN         : angle       4.63110 (   12)
  link_BETA1-4         : bond        0.00735 (    4)
  link_BETA1-4         : angle       2.38366 (   12)
  hydrogen bonds       : bond        0.03481 (  297)
  hydrogen bonds       : angle       4.43503 (  852)
  SS BOND              : bond        0.00099 (    1)
  SS BOND              : angle       0.49576 (    2)
  covalent geometry    : bond        0.00316 ( 7524)
  covalent geometry    : angle       0.71738 (10229)

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

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 138
  time to evaluate  : 1.370 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  249 LEU cc_start: 0.9192 (mt) cc_final: 0.8893 (mt)
REVERT: A  534 GLU cc_start: 0.7084 (mm-30) cc_final: 0.6518 (mt-10)
REVERT: B  146 TYR cc_start: 0.8688 (t80) cc_final: 0.8335 (t80)
REVERT: B  195 ARG cc_start: 0.7943 (mtm110) cc_final: 0.7622 (ptt180)
REVERT: B  254 TYR cc_start: 0.8798 (m-80) cc_final: 0.8270 (m-80)
REVERT: B  265 GLU cc_start: 0.7644 (tm-30) cc_final: 0.7142 (tm-30)
REVERT: B  365 MET cc_start: 0.8835 (mmm) cc_final: 0.8503 (mtp)
REVERT: B  438 PHE cc_start: 0.8103 (t80) cc_final: 0.7898 (t80)
REVERT: B  453 LYS cc_start: 0.8418 (tptm) cc_final: 0.8006 (mmtt)
REVERT: B  501 GLN cc_start: 0.8979 (tm-30) cc_final: 0.8218 (tm-30)
  outliers start: 22
  outliers final: 19
  residues processed: 148
  average time/residue: 0.1978
  time to fit residues: 43.7271
Evaluate side-chains
  149 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 130
  time to evaluate  : 0.847 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  504 VAL
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  173 LEU
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain B residue  208 LEU
Chi-restraints excluded: chain B residue  213 LEU
Chi-restraints excluded: chain B residue  359 LEU
Chi-restraints excluded: chain B residue  386 LEU
Chi-restraints excluded: chain B residue  413 ILE
Chi-restraints excluded: chain B residue  416 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 53 optimal weight:    0.2980
   chunk 49 optimal weight:    8.9990
   chunk 13 optimal weight:    0.7980
   chunk 89 optimal weight:    0.8980
   chunk 8 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 52 optimal weight:    0.9980
   chunk 47 optimal weight:    1.9990
   chunk 70 optimal weight:    2.9990
   overall best weight:    0.7580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.126479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.098163 restraints weight = 13490.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.102145 restraints weight = 6658.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.104735 restraints weight = 4556.492|
|-----------------------------------------------------------------------------|
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.4838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7533  Z= 0.134
  Angle     :  0.747  12.093  10255  Z= 0.346
  Chirality :  0.046   0.402   1203
  Planarity :  0.004   0.039   1255
  Dihedral  :  7.832  86.604   1262
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  6.72 %
    Favored  : 92.95 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 20.68 %
    Favored  : 76.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.25 (0.27), residues: 922
  helix:  0.08 (0.23), residues: 509
  sheet: -0.03 (0.65), residues: 59
  loop : -2.31 (0.30), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B 405 
 HIS   0.004   0.001   HIS B 367 
 PHE   0.025   0.001   PHE B  95 
 TYR   0.014   0.001   TYR A 405 
 ARG   0.003   0.000   ARG A 227 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00394 (    4)
  link_NAG-ASN         : angle       4.62129 (   12)
  link_BETA1-4         : bond        0.00690 (    4)
  link_BETA1-4         : angle       2.34281 (   12)
  hydrogen bonds       : bond        0.03456 (  297)
  hydrogen bonds       : angle       4.40473 (  852)
  SS BOND              : bond        0.00108 (    1)
  SS BOND              : angle       0.35828 (    2)
  covalent geometry    : bond        0.00315 ( 7524)
  covalent geometry    : angle       0.72690 (10229)

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

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 138
  time to evaluate  : 0.760 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  249 LEU cc_start: 0.9195 (mt) cc_final: 0.8904 (mt)
REVERT: A  272 ASP cc_start: 0.7985 (t0) cc_final: 0.7678 (p0)
REVERT: A  534 GLU cc_start: 0.7075 (mm-30) cc_final: 0.6511 (mt-10)
REVERT: B  146 TYR cc_start: 0.8683 (t80) cc_final: 0.8321 (t80)
REVERT: B  195 ARG cc_start: 0.7927 (mtm110) cc_final: 0.7596 (ptt180)
REVERT: B  254 TYR cc_start: 0.8801 (m-80) cc_final: 0.8324 (m-80)
REVERT: B  265 GLU cc_start: 0.7636 (tm-30) cc_final: 0.7138 (tm-30)
REVERT: B  365 MET cc_start: 0.8839 (mmm) cc_final: 0.8489 (mtp)
REVERT: B  453 LYS cc_start: 0.8410 (tptm) cc_final: 0.8011 (mmtt)
REVERT: B  501 GLN cc_start: 0.9010 (tm-30) cc_final: 0.8741 (tm-30)
  outliers start: 23
  outliers final: 20
  residues processed: 149
  average time/residue: 0.1473
  time to fit residues: 32.4582
Evaluate side-chains
  150 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 130
  time to evaluate  : 0.780 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  504 VAL
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain B residue   97 ILE
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  173 LEU
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain B residue  208 LEU
Chi-restraints excluded: chain B residue  213 LEU
Chi-restraints excluded: chain B residue  359 LEU
Chi-restraints excluded: chain B residue  386 LEU
Chi-restraints excluded: chain B residue  413 ILE
Chi-restraints excluded: chain B residue  416 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 79 optimal weight:    0.9980
   chunk 68 optimal weight:    0.0570
   chunk 90 optimal weight:    0.9980
   chunk 6 optimal weight:    0.2980
   chunk 69 optimal weight:    5.9990
   chunk 39 optimal weight:    1.9990
   chunk 7 optimal weight:    0.0770
   chunk 36 optimal weight:    0.7980
   chunk 10 optimal weight:    0.6980
   chunk 18 optimal weight:    0.8980
   overall best weight:    0.3856

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.127940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.099805 restraints weight = 13227.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.103881 restraints weight = 6550.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.106466 restraints weight = 4446.693|
|-----------------------------------------------------------------------------|
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7969
moved from start:          0.5007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7533  Z= 0.122
  Angle     :  0.743  12.362  10255  Z= 0.342
  Chirality :  0.045   0.408   1203
  Planarity :  0.004   0.036   1255
  Dihedral  :  7.658  87.700   1262
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  6.94 %
    Favored  : 92.73 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 21.20 %
    Favored  : 76.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.18 (0.27), residues: 922
  helix:  0.18 (0.23), residues: 498
  sheet: -0.33 (0.60), residues: 65
  loop : -2.24 (0.30), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B 405 
 HIS   0.004   0.001   HIS B 367 
 PHE   0.043   0.002   PHE B 438 
 TYR   0.013   0.001   TYR A 405 
 ARG   0.003   0.000   ARG A 227 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00456 (    4)
  link_NAG-ASN         : angle       4.61583 (   12)
  link_BETA1-4         : bond        0.00700 (    4)
  link_BETA1-4         : angle       2.30046 (   12)
  hydrogen bonds       : bond        0.03254 (  297)
  hydrogen bonds       : angle       4.28033 (  852)
  SS BOND              : bond        0.00103 (    1)
  SS BOND              : angle       0.21653 (    2)
  covalent geometry    : bond        0.00278 ( 7524)
  covalent geometry    : angle       0.72271 (10229)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3090.39 seconds
wall clock time: 56 minutes 49.50 seconds (3409.50 seconds total)