Starting phenix.real_space_refine
on Thu Jul  2 03:48:19 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8aqt_15589/07_2026/8aqt_15589.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8aqt_15589/07_2026/8aqt_15589.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8aqt_15589/07_2026/8aqt_15589.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8aqt_15589/07_2026/8aqt_15589.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/8aqt_15589/07_2026/8aqt_15589.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8aqt_15589/07_2026/8aqt_15589.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8aqt_15589/07_2026/8aqt_15589.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8aqt_15589/07_2026/8aqt_15589.cif"
  }
  resolution = 4.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.049
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: 4
    Type Number    sf(0)   Gaussians
     S      37      5.16       5
     C    4033      2.51       5
     N    1055      2.21       5
     O    1196      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 6321
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4744
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 584, 4744
          Classifications: {'peptide': 584}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 26, 'TRANS': 557}
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 17
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 12
    Chain: "B"
      Number of atoms: 1535
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 193, 1535
          Classifications: {'peptide': 193}
          Link IDs: {'PTRANS': 10, 'TRANS': 182}
    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 chiralities: 2
    Chain: "B"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 1.04, per 1000 atoms: 0.16
  Number of scatterers: 6321
  At special positions: 0
  Unit cell: (86.086, 91.3836, 116.547, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      37     16.00
     O    1196      8.00
     N    1055      7.00
     C    4033      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 133 " - pdb=" SG  CYS A 141 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 530 " - pdb=" SG  CYS A 542 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 391 " - pdb=" SG  CYS B 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 488 " 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-ASN
      " NAG B1301 " - " ASN B 343 "
      " NAG C   1 " - " ASN A  53 "
  Time building additional restraints: 0.39
  Conformation dependent library (CDL) restraints added in 342.5 milliseconds
  

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1466

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 2 sheets defined
      48.9% alpha, 4.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 23 through 53
    Processing helix  chain 'A' and resid 56 through 80
    Processing helix  chain 'A' and resid 93 through 102
    Processing helix  chain 'A' and resid 111 through 117
      removed outlier: 3.623A  pdb=" N   GLN A 115 " --> pdb=" O   ASP A 111 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 119 through 129
      removed outlier: 4.350A  pdb=" N   ILE A 126 " --> pdb=" O   THR A 122 " (cutoff:3.500A)
      removed outlier: 4.692A  pdb=" N   TYR A 127 " --> pdb=" O   MET A 123 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   SER A 128 " --> pdb=" O   SER A 124 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   THR A 129 " --> pdb=" O   THR A 125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 145 through 153
      removed outlier: 4.222A  pdb=" N   GLU A 150 " --> pdb=" O   PRO A 146 " (cutoff:3.500A)
      removed outlier: 6.004A  pdb=" N   ILE A 151 " --> pdb=" O   GLY A 147 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 165 through 173
      removed outlier: 3.509A  pdb=" N   GLY A 173 " --> pdb=" O   ARG A 169 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 187
      removed outlier: 3.847A  pdb=" N   GLU A 182 " --> pdb=" O   PRO A 178 " (cutoff:3.500A)
      removed outlier: 4.035A  pdb=" N   VAL A 185 " --> pdb=" O   GLU A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 193
    Processing helix  chain 'A' and resid 198 through 205
      removed outlier: 3.827A  pdb=" N   TRP A 203 " --> pdb=" O   TYR A 199 " (cutoff:3.500A)
      removed outlier: 4.144A  pdb=" N   ARG A 204 " --> pdb=" O   GLY A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 220 through 230
      removed outlier: 3.592A  pdb=" N   GLU A 224 " --> pdb=" O   ASN A 220 " (cutoff:3.500A)
      removed outlier: 4.135A  pdb=" N   GLU A 227 " --> pdb=" O   ILE A 223 " (cutoff:3.500A)
      removed outlier: 4.168A  pdb=" N   ARG A 228 " --> pdb=" O   GLU A 224 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   THR A 229 " --> pdb=" O   ASP A 225 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 234 through 239
      removed outlier: 4.030A  pdb=" N   GLU A 238 " --> pdb=" O   LYS A 234 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   HIS A 239 " --> pdb=" O   PRO A 235 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 234 through 239'
    Processing helix  chain 'A' and resid 239 through 252
      removed outlier: 3.756A  pdb=" N   TYR A 243 " --> pdb=" O   HIS A 239 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   VAL A 244 " --> pdb=" O   LEU A 240 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ARG A 245 " --> pdb=" O   HIS A 241 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   ARG A 246 " --> pdb=" O   ALA A 242 " (cutoff:3.500A)
      removed outlier: 4.664A  pdb=" N   LYS A 247 " --> pdb=" O   TYR A 243 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   LEU A 248 " --> pdb=" O   VAL A 244 " (cutoff:3.500A)
      removed outlier: 4.448A  pdb=" N   ASP A 250 " --> pdb=" O   ARG A 246 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   TYR A 252 " --> pdb=" O   LEU A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 292 through 298
    Processing helix  chain 'A' and resid 303 through 308
      removed outlier: 3.503A  pdb=" N   PHE A 308 " --> pdb=" O   ALA A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 308 through 319
      removed outlier: 4.330A  pdb=" N   GLU A 312 " --> pdb=" O   PHE A 308 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   SER A 317 " --> pdb=" O   LYS A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 330
      removed outlier: 3.733A  pdb=" N   TRP A 328 " --> pdb=" O   THR A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 383
      removed outlier: 4.368A  pdb=" N   LEU A 370 " --> pdb=" O   MET A 366 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   HIS A 373 " --> pdb=" O   PHE A 369 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   HIS A 374 " --> pdb=" O   LEU A 370 " (cutoff:3.500A)
      removed outlier: 4.181A  pdb=" N   HIS A 378 " --> pdb=" O   HIS A 374 " (cutoff:3.500A)
      removed outlier: 4.049A  pdb=" N   ILE A 379 " --> pdb=" O   GLU A 375 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   GLN A 380 " --> pdb=" O   MET A 376 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 388 through 393
    Processing helix  chain 'A' and resid 399 through 413
      removed outlier: 4.070A  pdb=" N   GLY A 405 " --> pdb=" O   HIS A 401 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   MET A 408 " --> pdb=" O   VAL A 404 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   SER A 409 " --> pdb=" O   GLY A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 421
      removed outlier: 4.076A  pdb=" N   ILE A 421 " --> pdb=" O   HIS A 417 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 433 through 446
      removed outlier: 3.995A  pdb=" N   ASN A 437 " --> pdb=" O   GLU A 433 " (cutoff:3.500A)
      removed outlier: 4.615A  pdb=" N   LYS A 441 " --> pdb=" O   ASN A 437 " (cutoff:3.500A)
      removed outlier: 4.399A  pdb=" N   GLN A 442 " --> pdb=" O   PHE A 438 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   ILE A 446 " --> pdb=" O   GLN A 442 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 449 through 464
      removed outlier: 3.682A  pdb=" N   LYS A 458 " --> pdb=" O   TYR A 454 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   PHE A 464 " --> pdb=" O   ARG A 460 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 472 through 485
      removed outlier: 3.645A  pdb=" N   LYS A 476 " --> pdb=" O   GLN A 472 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   GLU A 479 " --> pdb=" O   LYS A 475 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 513 through 531
      removed outlier: 4.258A  pdb=" N   ARG A 518 " --> pdb=" O   ARG A 514 " (cutoff:3.500A)
      removed outlier: 5.913A  pdb=" N   THR A 519 " --> pdb=" O   TYR A 515 " (cutoff:3.500A)
      removed outlier: 4.786A  pdb=" N   ILE A 520 " --> pdb=" O   TYR A 516 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   TYR A 521 " --> pdb=" O   THR A 517 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   GLN A 522 " --> pdb=" O   ARG A 518 " (cutoff:3.500A)
      removed outlier: 4.092A  pdb=" N   PHE A 523 " --> pdb=" O   THR A 519 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 548 through 559
      removed outlier: 3.777A  pdb=" N   LYS A 556 " --> pdb=" O   GLN A 552 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   MET A 557 " --> pdb=" O   LYS A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 560 through 564
      removed outlier: 3.968A  pdb=" N   GLU A 564 " --> pdb=" O   GLY A 561 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 574
    Processing helix  chain 'A' and resid 581 through 589
      removed outlier: 3.721A  pdb=" N   PHE A 588 " --> pdb=" O   LEU A 584 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 592 through 598
      removed outlier: 3.934A  pdb=" N   GLN A 598 " --> pdb=" O   TRP A 594 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 337 through 343
      removed outlier: 4.210A  pdb=" N   VAL B 341 " --> pdb=" O   PRO B 337 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 365 through 370
    Processing helix  chain 'B' and resid 383 through 388
      removed outlier: 3.875A  pdb=" N   ASN B 388 " --> pdb=" O   PRO B 384 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 405 through 408
      removed outlier: 4.241A  pdb=" N   ARG B 408 " --> pdb=" O   ASP B 405 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 405 through 408'
    Processing helix  chain 'B' and resid 416 through 422
    Processing helix  chain 'B' and resid 502 through 505
    Processing sheet with id=AA1, first strand: chain 'A' and resid 347 through 349
      removed outlier: 3.885A  pdb=" N   THR A 347 " --> pdb=" O   LYS A 359 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   LYS A 359 " --> pdb=" O   THR A 347 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   TRP A 349 " --> pdb=" O   ARG A 357 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   ARG A 357 " --> pdb=" O   TRP A 349 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'B' and resid 356 through 358
      removed outlier: 3.597A  pdb=" N   LYS B 356 " --> pdb=" O   ALA B 397 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   VAL B 395 " --> pdb=" O   ILE B 358 " (cutoff:3.500A)
      removed outlier: 4.555A  pdb=" N   ASN B 394 " --> pdb=" O   GLU B 516 " (cutoff:3.500A)
      removed outlier: 4.369A  pdb=" N   GLU B 516 " --> pdb=" O   ASN B 394 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   TYR B 396 " --> pdb=" O   SER B 514 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ILE B 402 " --> pdb=" O   TYR B 508 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ILE B 434 " --> pdb=" O   VAL B 511 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   CYS B 432 " --> pdb=" O   LEU B 513 " (cutoff:3.500A)
      removed outlier: 4.269A  pdb=" N   VAL B 433 " --> pdb=" O   LYS B 378 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   LYS B 378 " --> pdb=" O   VAL B 433 " (cutoff:3.500A)

    191 hydrogen bonds defined for protein.
    564 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.62

  Time building geometry restraints manager: 0.55 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: 1476
        1.33 -     1.45: 1554
        1.45 -     1.58: 3405
        1.58 -     1.70: 1
        1.70 -     1.82: 58
  Bond restraints: 6494
  Sorted by residual:
  bond pdb=" C1  NAG B1301 "
       pdb=" O5  NAG B1301 "
    ideal  model  delta    sigma   weight residual
    1.406  1.476 -0.070 2.00e-02 2.50e+03 1.24e+01
  bond pdb=" CA  SER B 477 "
       pdb=" CB  SER B 477 "
    ideal  model  delta    sigma   weight residual
    1.530  1.486  0.044 1.69e-02 3.50e+03 6.75e+00
  bond pdb=" C   PRO B 479 "
       pdb=" O   PRO B 479 "
    ideal  model  delta    sigma   weight residual
    1.235  1.208  0.027 1.30e-02 5.92e+03 4.40e+00
  bond pdb=" CB  PRO A 389 "
       pdb=" CG  PRO A 389 "
    ideal  model  delta    sigma   weight residual
    1.492  1.578 -0.086 5.00e-02 4.00e+02 2.95e+00
  bond pdb=" N   THR B 478 "
       pdb=" CA  THR B 478 "
    ideal  model  delta    sigma   weight residual
    1.457  1.479 -0.022 1.41e-02 5.03e+03 2.44e+00
  ... (remaining 6489 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.27: 8664
        2.27 -     4.53: 133
        4.53 -     6.80: 17
        6.80 -     9.06: 4
        9.06 -    11.33: 1
  Bond angle restraints: 8819
  Sorted by residual:
  angle pdb=" C   PRO B 479 "
        pdb=" CA  PRO B 479 "
        pdb=" CB  PRO B 479 "
      ideal   model   delta    sigma   weight residual
     111.56  100.23   11.33 1.65e+00 3.67e-01 4.71e+01
  angle pdb=" N   PRO B 479 "
        pdb=" CA  PRO B 479 "
        pdb=" C   PRO B 479 "
      ideal   model   delta    sigma   weight residual
     112.47  121.36   -8.89 2.06e+00 2.36e-01 1.86e+01
  angle pdb=" N   GLN A 287 "
        pdb=" CA  GLN A 287 "
        pdb=" C   GLN A 287 "
      ideal   model   delta    sigma   weight residual
     114.31  109.56    4.75 1.29e+00 6.01e-01 1.35e+01
  angle pdb=" N   PRO A 389 "
        pdb=" CA  PRO A 389 "
        pdb=" C   PRO A 389 "
      ideal   model   delta    sigma   weight residual
     112.47  119.46   -6.99 2.06e+00 2.36e-01 1.15e+01
  angle pdb=" C   ILE A 468 "
        pdb=" CA  ILE A 468 "
        pdb=" CB  ILE A 468 "
      ideal   model   delta    sigma   weight residual
     109.33  112.46   -3.13 9.80e-01 1.04e+00 1.02e+01
  ... (remaining 8814 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.94: 3428
       16.94 -    33.88: 314
       33.88 -    50.82: 60
       50.82 -    67.75: 15
       67.75 -    84.69: 5
  Dihedral angle restraints: 3822
    sinusoidal: 1537
      harmonic: 2285
  Sorted by residual:
  dihedral pdb=" CB  CYS A 530 "
           pdb=" SG  CYS A 530 "
           pdb=" SG  CYS A 542 "
           pdb=" CB  CYS A 542 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  156.68  -63.68     1      1.00e+01 1.00e-02 5.34e+01
  dihedral pdb=" CB  CYS B 480 "
           pdb=" SG  CYS B 480 "
           pdb=" SG  CYS B 488 "
           pdb=" CB  CYS B 488 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -139.48   53.48     1      1.00e+01 1.00e-02 3.89e+01
  dihedral pdb=" CB  CYS B 336 "
           pdb=" SG  CYS B 336 "
           pdb=" SG  CYS B 361 "
           pdb=" CB  CYS B 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   39.79   53.21     1      1.00e+01 1.00e-02 3.85e+01
  ... (remaining 3819 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 730
       0.050 -    0.101: 170
       0.101 -    0.151: 26
       0.151 -    0.201: 2
       0.201 -    0.252: 1
  Chirality restraints: 929
  Sorted by residual:
  chirality pdb=" CA  PRO A 389 "
            pdb=" N   PRO A 389 "
            pdb=" C   PRO A 389 "
            pdb=" CB  PRO A 389 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.47    0.25 2.00e-01 2.50e+01 1.58e+00
  chirality pdb=" C2  NAG C   2 "
            pdb=" C1  NAG C   2 "
            pdb=" C3  NAG C   2 "
            pdb=" N2  NAG C   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.33   -0.16 2.00e-01 2.50e+01 6.43e-01
  chirality pdb=" CA  CYS B 480 "
            pdb=" N   CYS B 480 "
            pdb=" C   CYS B 480 "
            pdb=" CB  CYS B 480 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.67   -0.15 2.00e-01 2.50e+01 6.01e-01
  ... (remaining 926 not shown)

  Planarity restraints: 1144
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 388 "    0.081 5.00e-02 4.00e+02   1.22e-01 2.40e+01
        pdb=" N   PRO A 389 "   -0.212 5.00e-02 4.00e+02
        pdb=" CA  PRO A 389 "    0.068 5.00e-02 4.00e+02
        pdb=" CD  PRO A 389 "    0.063 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B 475 "   -0.012 2.00e-02 2.50e+03   2.53e-02 6.39e+00
        pdb=" C   ALA B 475 "    0.044 2.00e-02 2.50e+03
        pdb=" O   ALA B 475 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   GLY B 476 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 468 "    0.036 5.00e-02 4.00e+02   5.49e-02 4.82e+00
        pdb=" N   PRO A 469 "   -0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO A 469 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 469 "    0.030 5.00e-02 4.00e+02
  ... (remaining 1141 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 207
        2.71 -     3.26: 6506
        3.26 -     3.81: 9278
        3.81 -     4.35: 11190
        4.35 -     4.90: 17785
  Nonbonded interactions: 44966
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 370 "
            pdb=" ND1 HIS A 374 "
     model   vdw
     2.165 3.120
  nonbonded pdb=" OH  TYR A  41 "
            pdb=" OG1 THR B 500 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" OE2 GLU A 227 "
            pdb=" OH  TYR A 454 "
     model   vdw
     2.226 3.040
  nonbonded pdb=" O   LEU A 278 "
            pdb=" OG1 THR A 282 "
     model   vdw
     2.239 3.040
  nonbonded pdb=" NZ  LYS A 247 "
            pdb=" O   LEU A 281 "
     model   vdw
     2.240 3.120
  ... (remaining 44961 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=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:             1.310
  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:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     5.860
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.400
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5931
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      :  0.003   0.086   6503  Z= 0.163
  Angle     :  0.705  11.326   8840  Z= 0.395
  Chirality :  0.044   0.252    929
  Planarity :  0.006   0.122   1142
  Dihedral  : 13.668  84.693   2338
  Min Nonbonded Distance : 2.165

Molprobity Statistics.
  All-atom Clashscore : 9.80
  Ramachandran Plot:
    Outliers :  0.78 %
    Allowed  :  5.43 %
    Favored  : 93.79 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  :  0.15 %
    Favored  : 99.41 %
  Cbeta Deviations :  0.14 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.80 (0.29), residues: 773
  helix: -0.56 (0.30), residues: 297
  sheet:  2.44 (1.08), residues: 22
  loop : -1.91 (0.28), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 161 
 TYR   0.009   0.001   TYR A 215 
 PHE   0.016   0.001   PHE A 390 
 TRP   0.016   0.002   TRP A  48 
 HIS   0.006   0.001   HIS A 374 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00314 /  0.16 ( 6494)
  covalent geometry    : angle       0.69510 /  0.39 ( 8819)
  SS BOND              : bond        0.00345 /  0.18 (    6)
  SS BOND              : angle       1.09912 /  0.61 (   12)
  hydrogen bonds       : bond        0.16052 / 10.88 (  191)
  hydrogen bonds       : angle       6.77141 /  5.14 (  564)
  link_BETA1-4         : bond        0.00013 /  0.01 (    1)
  link_BETA1-4         : angle       4.42955 /  2.37 (    3)
  link_NAG-ASN         : bond        0.00396 /  0.19 (    2)
  link_NAG-ASN         : angle       2.98636 /  1.51 (    6)

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 170
  time to evaluate  : 0.186 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 GLN cc_start: 0.8580 (mt0) cc_final: 0.8256 (mt0)
REVERT: A   74 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7625 (tm-30)
REVERT: A  190 MET cc_start: 0.7766 (tpp) cc_final: 0.7411 (ppp)
REVERT: A  461 TRP cc_start: 0.7929 (m-10) cc_final: 0.7545 (m-10)
REVERT: A  539 LEU cc_start: 0.7599 (mt) cc_final: 0.7328 (tp)
REVERT: B  386 LYS cc_start: 0.9115 (pttm) cc_final: 0.8733 (tttm)
REVERT: B  421 TYR cc_start: 0.8677 (m-80) cc_final: 0.8354 (m-80)
REVERT: B  466 ARG cc_start: 0.7743 (ttp-170) cc_final: 0.7392 (mmm160)
  outliers start: 3
  outliers final: 3
  residues processed: 173
  average time/residue: 0.0680
  time to fit residues: 15.3525
Evaluate side-chains
  96 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 93
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.0970
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    8.9990
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    6.9990
   chunk 45 optimal weight:    0.4980
   chunk 74 optimal weight:    7.9990
   overall best weight:    1.1182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 188 ASN
A 508 ASN
** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 422 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4381 r_free = 0.4381 target = 0.141526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.125789 restraints weight = 31499.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.127993 restraints weight = 22704.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4212 r_free = 0.4212 target = 0.129579 restraints weight = 17449.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4230 r_free = 0.4230 target = 0.130760 restraints weight = 14072.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.131641 restraints weight = 11779.659|
|-----------------------------------------------------------------------------|
r_work (final): 0.4218
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6121
moved from start:          0.2756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.085   6503  Z= 0.138
  Angle     :  0.671   9.632   8840  Z= 0.338
  Chirality :  0.048   0.334    929
  Planarity :  0.006   0.122   1142
  Dihedral  :  5.051  41.910    850
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 10.62
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  6.08 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  :  5.34 %
    Favored  : 94.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.65 (0.29), residues: 773
  helix: -0.34 (0.31), residues: 284
  sheet:  1.43 (1.07), residues: 25
  loop : -1.81 (0.28), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 509 
 TYR   0.012   0.001   TYR A 215 
 PHE   0.032   0.002   PHE A 592 
 TRP   0.011   0.001   TRP A 459 
 HIS   0.004   0.001   HIS A 374 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00321 /  0.14 ( 6494)
  covalent geometry    : angle       0.66054 /  0.33 ( 8819)
  SS BOND              : bond        0.00421 /  0.25 (    6)
  SS BOND              : angle       2.38015 /  1.17 (   12)
  hydrogen bonds       : bond        0.03789 /  2.43 (  191)
  hydrogen bonds       : angle       5.50903 /  4.14 (  564)
  link_BETA1-4         : bond        0.00571 /  0.30 (    1)
  link_BETA1-4         : angle       2.87906 /  1.58 (    3)
  link_NAG-ASN         : bond        0.00195 /  0.09 (    2)
  link_NAG-ASN         : angle       2.45548 /  1.19 (    6)

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 119
  time to evaluate  : 0.135 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 ASP cc_start: 0.8029 (m-30) cc_final: 0.7650 (m-30)
REVERT: A   74 GLU cc_start: 0.8358 (tm-30) cc_final: 0.7877 (tm-30)
REVERT: A  522 GLN cc_start: 0.8755 (pt0) cc_final: 0.8539 (pt0)
REVERT: A  539 LEU cc_start: 0.8102 (mt) cc_final: 0.7407 (tp)
REVERT: A  579 MET cc_start: 0.1579 (ttp) cc_final: 0.1351 (ttt)
REVERT: B  390 LEU cc_start: 0.9096 (mt) cc_final: 0.8516 (tp)
  outliers start: 2
  outliers final: 1
  residues processed: 121
  average time/residue: 0.0568
  time to fit residues: 9.1759
Evaluate side-chains
  94 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 93
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 33 optimal weight:    3.9990
   chunk 51 optimal weight:    5.9990
   chunk 26 optimal weight:    1.9990
   chunk 6 optimal weight:    0.2980
   chunk 66 optimal weight:    0.6980
   chunk 67 optimal weight:    1.9990
   chunk 62 optimal weight:    4.9990
   chunk 9 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 50 optimal weight:    0.8980
   overall best weight:    0.9382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  76 GLN
A 368 ASN
A 508 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4369 r_free = 0.4369 target = 0.140442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.125817 restraints weight = 33074.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.127892 restraints weight = 24076.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.129429 restraints weight = 18522.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.130512 restraints weight = 14959.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.4240 r_free = 0.4240 target = 0.131434 restraints weight = 12527.992|
|-----------------------------------------------------------------------------|
r_work (final): 0.4210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6153
moved from start:          0.3451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.086   6503  Z= 0.125
  Angle     :  0.639   9.516   8840  Z= 0.321
  Chirality :  0.047   0.342    929
  Planarity :  0.005   0.120   1142
  Dihedral  :  4.846  39.538    850
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  :  4.92 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  3.41 %
    Favored  : 96.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.74 (0.29), residues: 773
  helix: -0.59 (0.30), residues: 291
  sheet:  1.33 (0.99), residues: 25
  loop : -1.74 (0.28), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 273 
 TYR   0.017   0.001   TYR B 421 
 PHE   0.017   0.002   PHE A 314 
 TRP   0.056   0.002   TRP A 461 
 HIS   0.007   0.001   HIS A 374 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00288 /  0.12 ( 6494)
  covalent geometry    : angle       0.63294 /  0.32 ( 8819)
  SS BOND              : bond        0.00479 /  0.24 (    6)
  SS BOND              : angle       1.36618 /  0.80 (   12)
  hydrogen bonds       : bond        0.03554 /  2.29 (  191)
  hydrogen bonds       : angle       5.20189 /  3.84 (  564)
  link_BETA1-4         : bond        0.00484 /  0.25 (    1)
  link_BETA1-4         : angle       3.15601 /  1.71 (    3)
  link_NAG-ASN         : bond        0.00257 /  0.13 (    2)
  link_NAG-ASN         : angle       2.09774 /  1.01 (    6)

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 118
  time to evaluate  : 0.181 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 ASP cc_start: 0.8146 (m-30) cc_final: 0.7874 (m-30)
REVERT: A   74 GLU cc_start: 0.8338 (tm-30) cc_final: 0.7797 (tm-30)
REVERT: A  539 LEU cc_start: 0.7824 (mt) cc_final: 0.7331 (tp)
REVERT: B  390 LEU cc_start: 0.9119 (mt) cc_final: 0.8417 (tp)
REVERT: B  518 LEU cc_start: 0.8500 (tp) cc_final: 0.8285 (tp)
  outliers start: 1
  outliers final: 1
  residues processed: 119
  average time/residue: 0.0687
  time to fit residues: 10.6576
Evaluate side-chains
  88 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 87
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 45 optimal weight:    0.0870
   chunk 67 optimal weight:    5.9990
   chunk 62 optimal weight:    5.9990
   chunk 10 optimal weight:    5.9990
   chunk 4 optimal weight:    0.9990
   chunk 63 optimal weight:    5.9990
   chunk 31 optimal weight:    0.0970
   chunk 15 optimal weight:    1.9990
   chunk 25 optimal weight:    6.9990
   chunk 65 optimal weight:    2.9990
   chunk 59 optimal weight:    5.9990
   overall best weight:    1.2362

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 368 ASN
A 417 HIS
A 442 GLN
A 508 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4333 r_free = 0.4333 target = 0.137318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.122074 restraints weight = 32038.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.124420 restraints weight = 22530.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.126123 restraints weight = 16898.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.127366 restraints weight = 13286.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.128311 restraints weight = 10899.386|
|-----------------------------------------------------------------------------|
r_work (final): 0.4184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6172
moved from start:          0.4088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.084   6503  Z= 0.131
  Angle     :  0.641   9.382   8840  Z= 0.319
  Chirality :  0.047   0.339    929
  Planarity :  0.005   0.119   1142
  Dihedral  :  4.846  38.280    850
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 9.97
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  5.69 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  4.90 %
    Favored  : 94.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.58 (0.29), residues: 773
  helix: -0.37 (0.30), residues: 286
  sheet:  1.29 (0.95), residues: 25
  loop : -1.69 (0.28), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 273 
 TYR   0.010   0.001   TYR A 215 
 PHE   0.016   0.001   PHE B 374 
 TRP   0.024   0.001   TRP A 461 
 HIS   0.005   0.001   HIS A 374 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00305 /  0.13 ( 6494)
  covalent geometry    : angle       0.63383 /  0.32 ( 8819)
  SS BOND              : bond        0.00445 /  0.23 (    6)
  SS BOND              : angle       1.76535 /  0.71 (   12)
  hydrogen bonds       : bond        0.03270 /  2.08 (  191)
  hydrogen bonds       : angle       5.11527 /  3.79 (  564)
  link_BETA1-4         : bond        0.00234 /  0.12 (    1)
  link_BETA1-4         : angle       3.10034 /  1.68 (    3)
  link_NAG-ASN         : bond        0.00208 /  0.10 (    2)
  link_NAG-ASN         : angle       1.99863 /  0.88 (    6)

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 109
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 ASP cc_start: 0.8074 (m-30) cc_final: 0.7618 (m-30)
REVERT: A   74 GLU cc_start: 0.8366 (tm-30) cc_final: 0.7811 (tm-30)
REVERT: A  190 MET cc_start: 0.7896 (tpp) cc_final: 0.7573 (tpt)
REVERT: A  360 MET cc_start: 0.6590 (mmm) cc_final: 0.6254 (mmm)
REVERT: A  534 LYS cc_start: 0.5976 (mtmm) cc_final: 0.5746 (ttpp)
REVERT: A  539 LEU cc_start: 0.7874 (mt) cc_final: 0.7176 (tp)
REVERT: B  390 LEU cc_start: 0.9065 (mt) cc_final: 0.8365 (tp)
REVERT: B  518 LEU cc_start: 0.8514 (tp) cc_final: 0.8283 (tp)
  outliers start: 1
  outliers final: 1
  residues processed: 110
  average time/residue: 0.0910
  time to fit residues: 13.0728
Evaluate side-chains
  83 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 82
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 73 optimal weight:    6.9990
   chunk 41 optimal weight:    6.9990
   chunk 31 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 29 optimal weight:    0.2980
   chunk 12 optimal weight:   10.0000
   chunk 4 optimal weight:    0.9990
   chunk 39 optimal weight:    4.9990
   chunk 52 optimal weight:    4.9990
   chunk 44 optimal weight:    2.9990
   overall best weight:    2.0588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 239 HIS
A 508 ASN
A 572 ASN
** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.133185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.118021 restraints weight = 32223.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.120247 restraints weight = 22473.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.121748 restraints weight = 16746.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.122934 restraints weight = 13244.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.123726 restraints weight = 10911.076|
|-----------------------------------------------------------------------------|
r_work (final): 0.4107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6414
moved from start:          0.5150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.078   6503  Z= 0.182
  Angle     :  0.742   9.218   8840  Z= 0.375
  Chirality :  0.050   0.362    929
  Planarity :  0.006   0.121   1142
  Dihedral  :  5.250  36.681    850
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 13.78
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  7.24 %
    Favored  : 92.50 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  :  3.26 %
    Favored  : 96.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.85 (0.29), residues: 773
  helix: -0.60 (0.30), residues: 299
  sheet:  1.08 (1.00), residues: 23
  loop : -1.86 (0.29), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 273 
 TYR   0.013   0.002   TYR B 501 
 PHE   0.020   0.002   PHE B 374 
 TRP   0.018   0.002   TRP A 461 
 HIS   0.007   0.002   HIS A 239 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00406 /  0.18 ( 6494)
  covalent geometry    : angle       0.73386 /  0.37 ( 8819)
  SS BOND              : bond        0.01739 /  0.84 (    6)
  SS BOND              : angle       2.07707 /  1.12 (   12)
  hydrogen bonds       : bond        0.04150 /  2.63 (  191)
  hydrogen bonds       : angle       5.45449 /  4.04 (  564)
  link_BETA1-4         : bond        0.00061 /  0.03 (    1)
  link_BETA1-4         : angle       3.09674 /  1.68 (    3)
  link_NAG-ASN         : bond        0.00282 /  0.14 (    2)
  link_NAG-ASN         : angle       2.35808 /  0.95 (    6)

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 95
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 LEU cc_start: 0.8883 (mm) cc_final: 0.8660 (mm)
REVERT: A   60 GLN cc_start: 0.8913 (mt0) cc_final: 0.8706 (mt0)
  outliers start: 2
  outliers final: 1
  residues processed: 96
  average time/residue: 0.0782
  time to fit residues: 9.9548
Evaluate side-chains
  76 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 75
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 72 optimal weight:    3.9990
   chunk 60 optimal weight:    0.2980
   chunk 4 optimal weight:    3.9990
   chunk 27 optimal weight:    7.9990
   chunk 71 optimal weight:    0.9990
   chunk 35 optimal weight:    5.9990
   chunk 52 optimal weight:    5.9990
   chunk 55 optimal weight:    5.9990
   chunk 49 optimal weight:    0.9990
   chunk 50 optimal weight:    0.8980
   chunk 59 optimal weight:    2.9990
   overall best weight:    1.2386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.133877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.118284 restraints weight = 31312.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.120560 restraints weight = 21587.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.122294 restraints weight = 15950.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.123487 restraints weight = 12406.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.124271 restraints weight = 10121.168|
|-----------------------------------------------------------------------------|
r_work (final): 0.4111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6341
moved from start:          0.5508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.082   6503  Z= 0.133
  Angle     :  0.675   9.138   8840  Z= 0.335
  Chirality :  0.047   0.289    929
  Planarity :  0.005   0.118   1142
  Dihedral  :  5.045  36.133    850
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 10.62
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  6.08 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  1.93 %
    Favored  : 97.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.77 (0.30), residues: 773
  helix: -0.58 (0.30), residues: 302
  sheet:  1.34 (0.97), residues: 25
  loop : -1.81 (0.29), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 466 
 TYR   0.009   0.001   TYR A 217 
 PHE   0.023   0.002   PHE A 452 
 TRP   0.015   0.001   TRP A 461 
 HIS   0.003   0.001   HIS A 505 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00313 /  0.13 ( 6494)
  covalent geometry    : angle       0.66738 /  0.33 ( 8819)
  SS BOND              : bond        0.00305 /  0.16 (    6)
  SS BOND              : angle       2.05501 /  0.92 (   12)
  hydrogen bonds       : bond        0.03403 /  2.13 (  191)
  hydrogen bonds       : angle       5.23753 /  3.87 (  564)
  link_BETA1-4         : bond        0.00388 /  0.20 (    1)
  link_BETA1-4         : angle       3.14058 /  1.69 (    3)
  link_NAG-ASN         : bond        0.00210 /  0.10 (    2)
  link_NAG-ASN         : angle       1.80341 /  0.81 (    6)

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 94
  time to evaluate  : 0.177 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 LEU cc_start: 0.8771 (mm) cc_final: 0.8557 (mm)
REVERT: A  108 LEU cc_start: 0.7658 (tt) cc_final: 0.6834 (mp)
REVERT: B  390 LEU cc_start: 0.9011 (mt) cc_final: 0.8481 (tp)
  outliers start: 1
  outliers final: 1
  residues processed: 95
  average time/residue: 0.0786
  time to fit residues: 9.9314
Evaluate side-chains
  73 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 72
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 34 optimal weight:    0.3980
   chunk 63 optimal weight:    9.9990
   chunk 22 optimal weight:    7.9990
   chunk 17 optimal weight:    1.9990
   chunk 65 optimal weight:    4.9990
   chunk 61 optimal weight:    5.9990
   chunk 14 optimal weight:    4.9990
   chunk 64 optimal weight:    0.7980
   chunk 12 optimal weight:    6.9990
   chunk 6 optimal weight:    0.6980
   chunk 42 optimal weight:    0.0570
   overall best weight:    0.7900

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 508 ASN
** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4370 r_free = 0.4370 target = 0.139331 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.127320 restraints weight = 32445.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.129245 restraints weight = 22371.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.130584 restraints weight = 16364.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.131521 restraints weight = 12640.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.4257 r_free = 0.4257 target = 0.132242 restraints weight = 10262.089|
|-----------------------------------------------------------------------------|
r_work (final): 0.4144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6296
moved from start:          0.5665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.082   6503  Z= 0.116
  Angle     :  0.657  12.303   8840  Z= 0.323
  Chirality :  0.047   0.291    929
  Planarity :  0.005   0.117   1142
  Dihedral  :  4.848  35.058    850
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 11.26
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  6.34 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  1.63 %
    Favored  : 98.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.70 (0.30), residues: 773
  helix: -0.52 (0.30), residues: 300
  sheet:  0.99 (1.06), residues: 23
  loop : -1.72 (0.29), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 192 
 TYR   0.011   0.001   TYR B 508 
 PHE   0.018   0.001   PHE A 452 
 TRP   0.016   0.001   TRP A 461 
 HIS   0.003   0.001   HIS A 505 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00278 /  0.12 ( 6494)
  covalent geometry    : angle       0.65299 /  0.32 ( 8819)
  SS BOND              : bond        0.00317 /  0.16 (    6)
  SS BOND              : angle       1.13502 /  0.51 (   12)
  hydrogen bonds       : bond        0.03235 /  2.04 (  191)
  hydrogen bonds       : angle       5.08228 /  3.75 (  564)
  link_BETA1-4         : bond        0.00532 /  0.28 (    1)
  link_BETA1-4         : angle       3.21426 /  1.73 (    3)
  link_NAG-ASN         : bond        0.00355 /  0.18 (    2)
  link_NAG-ASN         : angle       1.52964 /  0.72 (    6)

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 93
  time to evaluate  : 0.146 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 LEU cc_start: 0.8781 (mm) cc_final: 0.8539 (mm)
REVERT: A   74 GLU cc_start: 0.8435 (tm-30) cc_final: 0.8129 (tm-30)
REVERT: A  108 LEU cc_start: 0.7717 (tt) cc_final: 0.7348 (mp)
REVERT: A  591 LEU cc_start: 0.8297 (tt) cc_final: 0.8030 (mm)
  outliers start: 1
  outliers final: 1
  residues processed: 94
  average time/residue: 0.0648
  time to fit residues: 8.2428
Evaluate side-chains
  74 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 73
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 58 optimal weight:    0.0970
   chunk 12 optimal weight:    8.9990
   chunk 64 optimal weight:    4.9990
   chunk 9 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9990
   chunk 5 optimal weight:    0.3980
   chunk 1 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 56 optimal weight:    5.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 508 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4374 r_free = 0.4374 target = 0.141339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.128608 restraints weight = 33719.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.130428 restraints weight = 23515.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.131699 restraints weight = 17380.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.132617 restraints weight = 13612.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4272 r_free = 0.4272 target = 0.133200 restraints weight = 11161.471|
|-----------------------------------------------------------------------------|
r_work (final): 0.4146
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6275
moved from start:          0.5871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.083   6503  Z= 0.115
  Angle     :  0.662   9.299   8840  Z= 0.326
  Chirality :  0.047   0.313    929
  Planarity :  0.005   0.116   1142
  Dihedral  :  4.685  31.894    850
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 10.05
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  5.56 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  1.04 %
    Favored  : 98.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.67 (0.30), residues: 773
  helix: -0.58 (0.29), residues: 302
  sheet:  2.05 (1.07), residues: 21
  loop : -1.69 (0.29), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 466 
 TYR   0.011   0.001   TYR B 508 
 PHE   0.018   0.001   PHE A 452 
 TRP   0.018   0.001   TRP A 461 
 HIS   0.002   0.001   HIS A 505 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00277 /  0.12 ( 6494)
  covalent geometry    : angle       0.65321 /  0.32 ( 8819)
  SS BOND              : bond        0.00251 /  0.13 (    6)
  SS BOND              : angle       2.38265 /  1.17 (   12)
  hydrogen bonds       : bond        0.03211 /  2.09 (  191)
  hydrogen bonds       : angle       5.04163 /  3.71 (  564)
  link_BETA1-4         : bond        0.00428 /  0.23 (    1)
  link_BETA1-4         : angle       3.20702 /  1.72 (    3)
  link_NAG-ASN         : bond        0.00321 /  0.16 (    2)
  link_NAG-ASN         : angle       1.43536 /  0.71 (    6)

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 94
  time to evaluate  : 0.158 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 LEU cc_start: 0.8766 (mm) cc_final: 0.8556 (mm)
REVERT: A   74 GLU cc_start: 0.8402 (tm-30) cc_final: 0.8187 (tm-30)
REVERT: A  108 LEU cc_start: 0.7803 (tt) cc_final: 0.7543 (mp)
REVERT: A  379 ILE cc_start: 0.8749 (tp) cc_final: 0.8470 (tp)
REVERT: A  557 MET cc_start: 0.6465 (mtt) cc_final: 0.6110 (tpp)
REVERT: A  591 LEU cc_start: 0.8300 (tt) cc_final: 0.7991 (mm)
  outliers start: 1
  outliers final: 1
  residues processed: 95
  average time/residue: 0.0625
  time to fit residues: 8.1306
Evaluate side-chains
  79 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 78
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 16 optimal weight:    0.5980
   chunk 55 optimal weight:    5.9990
   chunk 5 optimal weight:    0.6980
   chunk 76 optimal weight:    4.9990
   chunk 44 optimal weight:    0.0670
   chunk 31 optimal weight:    0.0570
   chunk 53 optimal weight:    0.7980
   chunk 8 optimal weight:    8.9990
   chunk 35 optimal weight:    3.9990
   chunk 71 optimal weight:    0.8980
   chunk 39 optimal weight:    2.9990
   overall best weight:    0.4436

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 508 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4387 r_free = 0.4387 target = 0.140412 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.128523 restraints weight = 32758.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.130481 restraints weight = 22316.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.131853 restraints weight = 16203.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.132819 restraints weight = 12394.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.133526 restraints weight = 9979.516|
|-----------------------------------------------------------------------------|
r_work (final): 0.4156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6260
moved from start:          0.5956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.082   6503  Z= 0.112
  Angle     :  0.653   9.333   8840  Z= 0.321
  Chirality :  0.047   0.305    929
  Planarity :  0.005   0.113   1142
  Dihedral  :  4.524  30.392    850
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 9.48
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.21 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  1.04 %
    Favored  : 98.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.72 (0.29), residues: 773
  helix: -0.53 (0.29), residues: 308
  sheet:  1.14 (1.05), residues: 23
  loop : -1.77 (0.29), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 466 
 TYR   0.010   0.001   TYR B 508 
 PHE   0.017   0.001   PHE A 452 
 TRP   0.023   0.001   TRP A 473 
 HIS   0.002   0.001   HIS A 505 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00269 /  0.11 ( 6494)
  covalent geometry    : angle       0.64825 /  0.32 ( 8819)
  SS BOND              : bond        0.00250 /  0.13 (    6)
  SS BOND              : angle       1.48548 /  0.82 (   12)
  hydrogen bonds       : bond        0.03134 /  2.03 (  191)
  hydrogen bonds       : angle       4.88476 /  3.58 (  564)
  link_BETA1-4         : bond        0.00455 /  0.24 (    1)
  link_BETA1-4         : angle       3.19583 /  1.72 (    3)
  link_NAG-ASN         : bond        0.00372 /  0.19 (    2)
  link_NAG-ASN         : angle       1.38717 /  0.67 (    6)

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 99
  time to evaluate  : 0.164 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 ASP cc_start: 0.8034 (m-30) cc_final: 0.7639 (m-30)
REVERT: A   45 LEU cc_start: 0.8793 (mm) cc_final: 0.8582 (mm)
REVERT: A   74 GLU cc_start: 0.8459 (tm-30) cc_final: 0.8200 (tm-30)
REVERT: A  108 LEU cc_start: 0.7779 (tt) cc_final: 0.7503 (mp)
REVERT: A  190 MET cc_start: 0.8171 (tpp) cc_final: 0.7767 (tpt)
REVERT: A  557 MET cc_start: 0.6530 (mtt) cc_final: 0.6138 (tpp)
REVERT: A  591 LEU cc_start: 0.8278 (tt) cc_final: 0.7960 (mm)
  outliers start: 1
  outliers final: 1
  residues processed: 100
  average time/residue: 0.0559
  time to fit residues: 7.6607
Evaluate side-chains
  79 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 78
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 17 optimal weight:    0.8980
   chunk 40 optimal weight:    0.7980
   chunk 56 optimal weight:    1.9990
   chunk 22 optimal weight:    0.0170
   chunk 6 optimal weight:    0.0570
   chunk 49 optimal weight:    0.6980
   chunk 25 optimal weight:    0.0770
   chunk 72 optimal weight:    3.9990
   chunk 74 optimal weight:    0.4980
   chunk 39 optimal weight:    2.9990
   chunk 52 optimal weight:    0.6980
   overall best weight:    0.2694

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 508 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4382 r_free = 0.4382 target = 0.142795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.130044 restraints weight = 33732.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.131854 restraints weight = 23355.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4265 r_free = 0.4265 target = 0.133182 restraints weight = 17216.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.134132 restraints weight = 13340.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4288 r_free = 0.4288 target = 0.134776 restraints weight = 10824.805|
|-----------------------------------------------------------------------------|
r_work (final): 0.4170
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6233
moved from start:          0.6071

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.083   6503  Z= 0.113
  Angle     :  0.667   9.322   8840  Z= 0.327
  Chirality :  0.047   0.276    929
  Planarity :  0.005   0.112   1142
  Dihedral  :  4.499  30.084    850
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.69 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  0.15 %
    Favored  : 99.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.62 (0.29), residues: 773
  helix: -0.50 (0.30), residues: 302
  sheet:  1.16 (1.04), residues: 23
  loop : -1.66 (0.29), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 466 
 TYR   0.010   0.001   TYR B 508 
 PHE   0.017   0.001   PHE A 452 
 TRP   0.022   0.001   TRP A 473 
 HIS   0.002   0.000   HIS A 505 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00273 /  0.11 ( 6494)
  covalent geometry    : angle       0.65855 /  0.32 ( 8819)
  SS BOND              : bond        0.00508 /  0.25 (    6)
  SS BOND              : angle       2.40942 /  1.00 (   12)
  hydrogen bonds       : bond        0.03060 /  1.96 (  191)
  hydrogen bonds       : angle       4.84944 /  3.56 (  564)
  link_BETA1-4         : bond        0.00394 /  0.21 (    1)
  link_BETA1-4         : angle       3.17809 /  1.70 (    3)
  link_NAG-ASN         : bond        0.00354 /  0.17 (    2)
  link_NAG-ASN         : angle       1.42249 /  0.69 (    6)

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 99
  time to evaluate  : 0.193 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 ASP cc_start: 0.7959 (m-30) cc_final: 0.7614 (m-30)
REVERT: A   45 LEU cc_start: 0.8693 (mm) cc_final: 0.8475 (mm)
REVERT: A   74 GLU cc_start: 0.8438 (tm-30) cc_final: 0.8191 (tm-30)
REVERT: A  190 MET cc_start: 0.8160 (tpp) cc_final: 0.7749 (tpt)
REVERT: A  360 MET cc_start: 0.4589 (mmp) cc_final: 0.4374 (mmp)
REVERT: A  557 MET cc_start: 0.6717 (mtt) cc_final: 0.6038 (tpt)
REVERT: A  591 LEU cc_start: 0.8271 (tt) cc_final: 0.8025 (mm)
  outliers start: 1
  outliers final: 1
  residues processed: 100
  average time/residue: 0.0602
  time to fit residues: 8.1466
Evaluate side-chains
  76 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 75
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 19 optimal weight:    0.6980
   chunk 20 optimal weight:    0.7980
   chunk 45 optimal weight:    0.7980
   chunk 66 optimal weight:    0.9990
   chunk 64 optimal weight:    4.9990
   chunk 32 optimal weight:    0.0470
   chunk 68 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 51 optimal weight:    8.9990
   chunk 59 optimal weight:    1.9990
   overall best weight:    0.6680

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 508 ASN
B 448 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4369 r_free = 0.4369 target = 0.142040 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.4205 r_free = 0.4205 target = 0.129185 restraints weight = 33809.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4232 r_free = 0.4232 target = 0.131018 restraints weight = 23303.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.132370 restraints weight = 17168.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.133202 restraints weight = 13297.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4276 r_free = 0.4276 target = 0.133936 restraints weight = 10940.802|
|-----------------------------------------------------------------------------|
r_work (final): 0.4157
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6261
moved from start:          0.6237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.080   6503  Z= 0.114
  Angle     :  0.664   9.359   8840  Z= 0.328
  Chirality :  0.047   0.272    929
  Planarity :  0.005   0.111   1142
  Dihedral  :  4.454  30.353    850
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.69 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  0.30 %
    Favored  : 99.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.66 (0.29), residues: 773
  helix: -0.47 (0.29), residues: 314
  sheet:  1.05 (1.02), residues: 23
  loop : -1.75 (0.29), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 169 
 TYR   0.012   0.001   TYR A 497 
 PHE   0.017   0.001   PHE A 452 
 TRP   0.020   0.001   TRP A 461 
 HIS   0.002   0.001   HIS A 374 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00271 /  0.11 ( 6494)
  covalent geometry    : angle       0.66038 /  0.33 ( 8819)
  SS BOND              : bond        0.00392 /  0.19 (    6)
  SS BOND              : angle       1.15480 /  0.65 (   12)
  hydrogen bonds       : bond        0.03089 /  2.01 (  191)
  hydrogen bonds       : angle       4.84674 /  3.54 (  564)
  link_BETA1-4         : bond        0.00458 /  0.24 (    1)
  link_BETA1-4         : angle       3.09134 /  1.65 (    3)
  link_NAG-ASN         : bond        0.00345 /  0.18 (    2)
  link_NAG-ASN         : angle       1.33003 /  0.67 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1040.34 seconds
wall clock time: 18 minutes 41.16 seconds (1121.16 seconds total)