Starting phenix.real_space_refine
on Thu Jul 24 16:44:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8aqt_15589/07_2025/8aqt_15589.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8aqt_15589/07_2025/8aqt_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_2025/8aqt_15589.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8aqt_15589/07_2025/8aqt_15589.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8aqt_15589/07_2025/8aqt_15589.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8aqt_15589/07_2025/8aqt_15589.cif"
  }
  resolution = 4.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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 dihedrals: 6
          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 dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 7.07, per 1000 atoms: 1.12
  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: 2.65
  Conformation dependent library (CDL) restraints added in 1.9 seconds
  

  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: 3.68
  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: 2.69

  Time building geometry restraints manager: 3.05 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 -    24.45: 3664
       24.45 -    48.90: 187
       48.90 -    73.36: 28
       73.36 -    97.81: 3
       97.81 -   122.26: 3
  Dihedral angle restraints: 3885
    sinusoidal: 1600
      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 3882 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:             91.810
  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:             0.040
  Extract box with map and model:          0.420
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     33.270
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:4.510
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  130.290
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5934
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  : 14.457 122.259   2401
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.80 (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
 TRP   0.016   0.002   TRP A  48 
 HIS   0.006   0.001   HIS A 374 
 PHE   0.016   0.001   PHE A 390 
 TYR   0.009   0.001   TYR A 215 
 ARG   0.005   0.000   ARG A 161 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00396 (    2)
  link_NAG-ASN         : angle       2.98636 (    6)
  link_BETA1-4         : bond        0.00013 (    1)
  link_BETA1-4         : angle       4.42955 (    3)
  hydrogen bonds       : bond        0.16052 (  191)
  hydrogen bonds       : angle       6.77141 (  564)
  SS BOND              : bond        0.00345 (    6)
  SS BOND              : angle       1.09912 (   12)
  covalent geometry    : bond        0.00314 ( 6494)
  covalent geometry    : angle       0.69510 ( 8819)

*********************** 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  : 0.927 
Fit side-chains
   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: 0.8254 (mt0)
REVERT: A   74 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7629 (tm-30)
REVERT: A  461 TRP cc_start: 0.7929 (m-10) cc_final: 0.7554 (m-10)
REVERT: A  539 LEU cc_start: 0.7599 (mt) cc_final: 0.7331 (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: 0.7391 (mmm160)
  outliers start: 3
  outliers final: 3
  residues processed: 173
  average time/residue: 0.4521
  time to fit residues: 100.0395
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  : 1.654 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 65 optimal weight:    6.9990
   chunk 58 optimal weight:    1.9990
   chunk 32 optimal weight:    0.0170
   chunk 19 optimal weight:    6.9990
   chunk 39 optimal weight:    5.9990
   chunk 31 optimal weight:    0.0770
   chunk 60 optimal weight:    5.9990
   chunk 23 optimal weight:    9.9990
   chunk 36 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9990
   chunk 69 optimal weight:    4.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A  76 GLN
A 188 ASN
A 508 ASN
B 422 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4397 r_free = 0.4397 target = 0.142437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.126942 restraints weight = 31122.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.129136 restraints weight = 22379.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4232 r_free = 0.4232 target = 0.130752 restraints weight = 17105.793|
|-----------------------------------------------------------------------------|
r_work (final): 0.4200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6159
moved from start:          0.2670

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= 0.141
  Angle     :  0.680  10.046   8840  Z= 0.340
  Chirality :  0.047   0.339    929
  Planarity :  0.006   0.121   1142
  Dihedral  :  8.966 109.917    913
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 9.97
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  5.43 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  :  4.45 %
    Favored  : 95.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.56 (0.29), residues: 773
  helix: -0.21 (0.31), residues: 284
  sheet:  1.44 (1.06), residues: 25
  loop : -1.79 (0.28), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 459 
 HIS   0.003   0.001   HIS A 374 
 PHE   0.030   0.002   PHE A 592 
 TYR   0.012   0.001   TYR A 215 
 ARG   0.005   0.001   ARG A 273 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00198 (    2)
  link_NAG-ASN         : angle       2.90278 (    6)
  link_BETA1-4         : bond        0.00712 (    1)
  link_BETA1-4         : angle       2.89790 (    3)
  hydrogen bonds       : bond        0.04043 (  191)
  hydrogen bonds       : angle       5.50675 (  564)
  SS BOND              : bond        0.00623 (    6)
  SS BOND              : angle       2.52946 (   12)
  covalent geometry    : bond        0.00334 ( 6494)
  covalent geometry    : angle       0.66808 ( 8819)

*********************** 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
  124 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 122
  time to evaluate  : 1.811 
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: 0.8114 (m-30) cc_final: 0.7696 (m-30)
REVERT: A   74 GLU cc_start: 0.8307 (tm-30) cc_final: 0.7828 (tm-30)
REVERT: A  539 LEU cc_start: 0.8061 (mt) cc_final: 0.7393 (tp)
REVERT: A  579 MET cc_start: 0.1366 (ttp) cc_final: 0.1135 (ttt)
REVERT: B  386 LYS cc_start: 0.9007 (pttm) cc_final: 0.8584 (tttm)
  outliers start: 2
  outliers final: 1
  residues processed: 124
  average time/residue: 0.4142
  time to fit residues: 70.2400
Evaluate side-chains
  92 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 91
  time to evaluate  : 1.983 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 62 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9990
   chunk 7 optimal weight:    0.1980
   chunk 15 optimal weight:   10.0000
   chunk 24 optimal weight:    0.0030
   chunk 46 optimal weight:    1.9990
   chunk 59 optimal weight:    4.9990
   chunk 36 optimal weight:    0.2980
   chunk 41 optimal weight:    0.1980
   chunk 61 optimal weight:    0.9990
   overall best weight:    0.3392

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

Flipped N/Q/H residues before XYZ refinement:
A 508 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4405 r_free = 0.4405 target = 0.143087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.128185 restraints weight = 31851.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.130326 restraints weight = 23208.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.131867 restraints weight = 17744.099|
|-----------------------------------------------------------------------------|
r_work (final): 0.4215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6139
moved from start:          0.3299

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= 0.117
  Angle     :  0.632   9.362   8840  Z= 0.313
  Chirality :  0.047   0.338    929
  Planarity :  0.005   0.119   1142
  Dihedral  :  8.509 106.594    913
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 8.18
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  :  4.53 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  3.26 %
    Favored  : 96.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.55 (0.29), residues: 773
  helix: -0.21 (0.31), residues: 291
  sheet:  1.29 (1.02), residues: 25
  loop : -1.79 (0.28), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 459 
 HIS   0.004   0.001   HIS A 374 
 PHE   0.021   0.001   PHE A 452 
 TYR   0.016   0.001   TYR B 421 
 ARG   0.004   0.000   ARG B 466 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00230 (    2)
  link_NAG-ASN         : angle       2.47441 (    6)
  link_BETA1-4         : bond        0.00101 (    1)
  link_BETA1-4         : angle       3.39418 (    3)
  hydrogen bonds       : bond        0.03475 (  191)
  hydrogen bonds       : angle       5.14348 (  564)
  SS BOND              : bond        0.00420 (    6)
  SS BOND              : angle       1.36949 (   12)
  covalent geometry    : bond        0.00270 ( 6494)
  covalent geometry    : angle       0.62475 ( 8819)

*********************** 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
  125 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 124
  time to evaluate  : 0.770 
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: 0.8195 (m-30) cc_final: 0.7906 (m-30)
REVERT: A   74 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7999 (tm-30)
REVERT: A  539 LEU cc_start: 0.7980 (mt) cc_final: 0.7449 (tp)
REVERT: B  390 LEU cc_start: 0.9131 (mp) cc_final: 0.8518 (tp)
  outliers start: 1
  outliers final: 1
  residues processed: 125
  average time/residue: 0.2363
  time to fit residues: 38.8621
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  : 0.751 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 46 optimal weight:   10.0000
   chunk 43 optimal weight:    6.9990
   chunk 68 optimal weight:    0.9980
   chunk 24 optimal weight:    2.9990
   chunk 19 optimal weight:    0.0570
   chunk 58 optimal weight:    0.4980
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.5980
   chunk 2 optimal weight:    1.9990
   chunk 67 optimal weight:    2.9990
   chunk 55 optimal weight:    6.9990
   overall best weight:    0.6098

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

Flipped N/Q/H residues before XYZ refinement:
A 368 ASN
A 508 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4389 r_free = 0.4389 target = 0.142001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.126741 restraints weight = 31656.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.128822 restraints weight = 22589.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.130489 restraints weight = 17318.156|
|-----------------------------------------------------------------------------|
r_work (final): 0.4196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6165
moved from start:          0.3753

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= 0.115
  Angle     :  0.644  10.004   8840  Z= 0.313
  Chirality :  0.046   0.338    929
  Planarity :  0.005   0.116   1142
  Dihedral  :  8.282 105.231    913
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  5.17 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  3.12 %
    Favored  : 96.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.47 (0.29), residues: 773
  helix: -0.19 (0.31), residues: 288
  sheet:  1.01 (1.00), residues: 25
  loop : -1.67 (0.28), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 459 
 HIS   0.004   0.001   HIS A 374 
 PHE   0.025   0.001   PHE A 452 
 TYR   0.013   0.001   TYR A 497 
 ARG   0.006   0.000   ARG B 466 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00218 (    2)
  link_NAG-ASN         : angle       2.31239 (    6)
  link_BETA1-4         : bond        0.00113 (    1)
  link_BETA1-4         : angle       3.43451 (    3)
  hydrogen bonds       : bond        0.03274 (  191)
  hydrogen bonds       : angle       5.01396 (  564)
  SS BOND              : bond        0.00406 (    6)
  SS BOND              : angle       1.55031 (   12)
  covalent geometry    : bond        0.00272 ( 6494)
  covalent geometry    : angle       0.63639 ( 8819)

*********************** 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
  115 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 114
  time to evaluate  : 0.761 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 ASP cc_start: 0.8134 (m-30) cc_final: 0.7801 (m-30)
REVERT: A   74 GLU cc_start: 0.8285 (tm-30) cc_final: 0.8074 (tm-30)
REVERT: A  383 MET cc_start: 0.8153 (ptp) cc_final: 0.7552 (tpt)
REVERT: A  539 LEU cc_start: 0.7931 (mt) cc_final: 0.7330 (tp)
REVERT: B  356 LYS cc_start: 0.7422 (mmtt) cc_final: 0.7106 (mmtt)
REVERT: B  466 ARG cc_start: 0.8090 (mmm160) cc_final: 0.7859 (mmm160)
REVERT: B  518 LEU cc_start: 0.8427 (tp) cc_final: 0.8095 (tt)
  outliers start: 1
  outliers final: 1
  residues processed: 115
  average time/residue: 0.2173
  time to fit residues: 31.9881
Evaluate side-chains
  90 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 89
  time to evaluate  : 0.925 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 45 optimal weight:    0.7980
   chunk 17 optimal weight:    6.9990
   chunk 62 optimal weight:    4.9990
   chunk 20 optimal weight:    6.9990
   chunk 65 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9980
   chunk 68 optimal weight:    0.9990
   chunk 60 optimal weight:    3.9990
   chunk 51 optimal weight:    0.8980
   chunk 55 optimal weight:    1.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
A 508 ASN
A 572 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4339 r_free = 0.4339 target = 0.138191 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.122987 restraints weight = 30979.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.125248 restraints weight = 21643.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.126914 restraints weight = 16282.312|
|-----------------------------------------------------------------------------|
r_work (final): 0.4154
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6234
moved from start:          0.4114

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= 0.132
  Angle     :  0.647   9.641   8840  Z= 0.315
  Chirality :  0.046   0.354    929
  Planarity :  0.005   0.115   1142
  Dihedral  :  8.265 107.132    913
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 9.80
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  5.30 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  2.37 %
    Favored  : 97.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.50 (0.29), residues: 773
  helix: -0.31 (0.31), residues: 298
  sheet:  0.83 (1.05), residues: 23
  loop : -1.62 (0.28), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 459 
 HIS   0.006   0.001   HIS A 374 
 PHE   0.023   0.001   PHE A 452 
 TYR   0.008   0.001   TYR B 421 
 ARG   0.004   0.000   ARG B 466 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00232 (    2)
  link_NAG-ASN         : angle       2.31855 (    6)
  link_BETA1-4         : bond        0.00029 (    1)
  link_BETA1-4         : angle       3.49143 (    3)
  hydrogen bonds       : bond        0.03397 (  191)
  hydrogen bonds       : angle       4.97496 (  564)
  SS BOND              : bond        0.00369 (    6)
  SS BOND              : angle       1.57382 (   12)
  covalent geometry    : bond        0.00305 ( 6494)
  covalent geometry    : angle       0.63952 ( 8819)

*********************** 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
  109 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 108
  time to evaluate  : 0.747 
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: 0.8200 (m-30) cc_final: 0.7858 (m-30)
REVERT: A   74 GLU cc_start: 0.8482 (tm-30) cc_final: 0.7964 (tm-30)
REVERT: A  383 MET cc_start: 0.8139 (ptp) cc_final: 0.7402 (tpt)
REVERT: A  534 LYS cc_start: 0.5877 (mtmm) cc_final: 0.5666 (ttpp)
REVERT: A  539 LEU cc_start: 0.7657 (mt) cc_final: 0.7215 (tp)
REVERT: B  390 LEU cc_start: 0.9135 (mt) cc_final: 0.8485 (tp)
  outliers start: 1
  outliers final: 1
  residues processed: 109
  average time/residue: 0.2245
  time to fit residues: 31.1781
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  : 0.766 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 18 optimal weight:    3.9990
   chunk 28 optimal weight:    3.9990
   chunk 45 optimal weight:    0.0970
   chunk 43 optimal weight:    0.9990
   chunk 37 optimal weight:    0.0020
   chunk 51 optimal weight:    0.4980
   chunk 44 optimal weight:    0.8980
   chunk 6 optimal weight:    0.0870
   chunk 71 optimal weight:    3.9990
   chunk 33 optimal weight:    7.9990
   chunk 4 optimal weight:    1.9990
   overall best weight:    0.3164

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

Flipped N/Q/H residues before XYZ refinement:
A 417 HIS
A 508 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4373 r_free = 0.4373 target = 0.140138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.125750 restraints weight = 32448.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.127907 restraints weight = 22407.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.129449 restraints weight = 16665.197|
|-----------------------------------------------------------------------------|
r_work (final): 0.4183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6158
moved from start:          0.4413

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= 0.111
  Angle     :  0.649   9.375   8840  Z= 0.316
  Chirality :  0.046   0.314    929
  Planarity :  0.005   0.113   1142
  Dihedral  :  8.061 105.401    913
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.92 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  2.37 %
    Favored  : 97.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.41 (0.29), residues: 773
  helix: -0.19 (0.31), residues: 291
  sheet:  0.64 (1.06), residues: 23
  loop : -1.57 (0.28), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 459 
 HIS   0.002   0.001   HIS A 505 
 PHE   0.043   0.002   PHE A 592 
 TYR   0.009   0.001   TYR A 535 
 ARG   0.010   0.000   ARG B 466 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00243 (    2)
  link_NAG-ASN         : angle       2.18768 (    6)
  link_BETA1-4         : bond        0.00356 (    1)
  link_BETA1-4         : angle       3.44763 (    3)
  hydrogen bonds       : bond        0.03058 (  191)
  hydrogen bonds       : angle       4.81705 (  564)
  SS BOND              : bond        0.00207 (    6)
  SS BOND              : angle       1.94751 (   12)
  covalent geometry    : bond        0.00268 ( 6494)
  covalent geometry    : angle       0.64020 ( 8819)

*********************** 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
  111 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 110
  time to evaluate  : 0.695 
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: 0.8146 (m-30) cc_final: 0.7810 (m-30)
REVERT: A   74 GLU cc_start: 0.8289 (tm-30) cc_final: 0.7752 (tm-30)
REVERT: A  383 MET cc_start: 0.7906 (ptp) cc_final: 0.7361 (tpt)
REVERT: A  539 LEU cc_start: 0.7915 (mt) cc_final: 0.7283 (tp)
REVERT: B  390 LEU cc_start: 0.9142 (mt) cc_final: 0.8483 (tp)
  outliers start: 1
  outliers final: 1
  residues processed: 111
  average time/residue: 0.1975
  time to fit residues: 28.4530
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  : 0.682 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 47 optimal weight:    0.0970
   chunk 40 optimal weight:    7.9990
   chunk 39 optimal weight:    3.9990
   chunk 33 optimal weight:    4.9990
   chunk 6 optimal weight:    8.9990
   chunk 32 optimal weight:    0.0970
   chunk 38 optimal weight:    0.9980
   chunk 49 optimal weight:    0.6980
   chunk 73 optimal weight:    0.4980
   chunk 17 optimal weight:    0.9990
   chunk 8 optimal weight:    7.9990
   overall best weight:    0.4776

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

Flipped N/Q/H residues before XYZ refinement:
A 373 HIS
A 508 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4357 r_free = 0.4357 target = 0.139782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.125070 restraints weight = 32100.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.127381 restraints weight = 21887.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.129040 restraints weight = 16122.030|
|-----------------------------------------------------------------------------|
r_work (final): 0.4173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6164
moved from start:          0.4589

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= 0.113
  Angle     :  0.642   9.354   8840  Z= 0.314
  Chirality :  0.046   0.280    929
  Planarity :  0.005   0.111   1142
  Dihedral  :  7.953 104.137    913
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  5.05 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  0.89 %
    Favored  : 98.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.30 (0.30), residues: 773
  helix: -0.11 (0.31), residues: 291
  sheet:  0.60 (1.05), residues: 23
  loop : -1.49 (0.28), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 459 
 HIS   0.003   0.001   HIS A 374 
 PHE   0.028   0.002   PHE A 592 
 TYR   0.008   0.001   TYR B 421 
 ARG   0.012   0.001   ARG A 169 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00231 (    2)
  link_NAG-ASN         : angle       2.20504 (    6)
  link_BETA1-4         : bond        0.00373 (    1)
  link_BETA1-4         : angle       3.37831 (    3)
  hydrogen bonds       : bond        0.03150 (  191)
  hydrogen bonds       : angle       4.96931 (  564)
  SS BOND              : bond        0.00201 (    6)
  SS BOND              : angle       0.79919 (   12)
  covalent geometry    : bond        0.00269 ( 6494)
  covalent geometry    : angle       0.63608 ( 8819)

*********************** 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
  106 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 105
  time to evaluate  : 0.727 
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   38 ASP cc_start: 0.8151 (m-30) cc_final: 0.7834 (m-30)
REVERT: A   74 GLU cc_start: 0.8315 (tm-30) cc_final: 0.7789 (tm-30)
REVERT: A  539 LEU cc_start: 0.7717 (mt) cc_final: 0.7190 (tp)
REVERT: B  390 LEU cc_start: 0.9116 (mt) cc_final: 0.8439 (tp)
  outliers start: 1
  outliers final: 1
  residues processed: 106
  average time/residue: 0.1853
  time to fit residues: 26.0074
Evaluate side-chains
  80 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 79
  time to evaluate  : 0.759 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 2 optimal weight:    0.7980
   chunk 48 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 11 optimal weight:    3.9990
   chunk 12 optimal weight:    0.0020
   chunk 59 optimal weight:    0.0870
   chunk 40 optimal weight:    8.9990
   chunk 19 optimal weight:    0.0270
   chunk 41 optimal weight:    4.9990
   chunk 60 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9990
   overall best weight:    0.3826

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

Flipped N/Q/H residues before XYZ refinement:
A 508 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4368 r_free = 0.4368 target = 0.140074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.125108 restraints weight = 31725.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.127415 restraints weight = 22056.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.129135 restraints weight = 16359.460|
|-----------------------------------------------------------------------------|
r_work (final): 0.4182
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6173
moved from start:          0.4762

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= 0.111
  Angle     :  0.658  12.483   8840  Z= 0.320
  Chirality :  0.046   0.275    929
  Planarity :  0.005   0.110   1142
  Dihedral  :  7.841 103.161    913
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.66 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  0.74 %
    Favored  : 99.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.30 (0.30), residues: 773
  helix: -0.21 (0.30), residues: 298
  sheet:  0.50 (1.03), residues: 23
  loop : -1.42 (0.29), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 459 
 HIS   0.002   0.001   HIS A 505 
 PHE   0.024   0.001   PHE A 592 
 TYR   0.008   0.001   TYR A 510 
 ARG   0.006   0.001   ARG A 169 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00221 (    2)
  link_NAG-ASN         : angle       2.18358 (    6)
  link_BETA1-4         : bond        0.00424 (    1)
  link_BETA1-4         : angle       3.30910 (    3)
  hydrogen bonds       : bond        0.03038 (  191)
  hydrogen bonds       : angle       4.95457 (  564)
  SS BOND              : bond        0.00334 (    6)
  SS BOND              : angle       1.83334 (   12)
  covalent geometry    : bond        0.00268 ( 6494)
  covalent geometry    : angle       0.64973 ( 8819)

*********************** 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
  104 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 103
  time to evaluate  : 0.752 
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   38 ASP cc_start: 0.8231 (m-30) cc_final: 0.7869 (m-30)
REVERT: A   74 GLU cc_start: 0.8306 (tm-30) cc_final: 0.7846 (tm-30)
REVERT: A  356 PHE cc_start: 0.7655 (m-10) cc_final: 0.7443 (m-10)
REVERT: A  379 ILE cc_start: 0.8836 (tp) cc_final: 0.8443 (tp)
REVERT: A  383 MET cc_start: 0.8037 (ptp) cc_final: 0.7456 (tpt)
REVERT: A  539 LEU cc_start: 0.7931 (mt) cc_final: 0.7269 (tp)
REVERT: A  557 MET cc_start: 0.5955 (mmt) cc_final: 0.5741 (mmt)
REVERT: B  390 LEU cc_start: 0.9110 (mt) cc_final: 0.8428 (tp)
REVERT: B  466 ARG cc_start: 0.8231 (mmm160) cc_final: 0.8018 (mmm160)
  outliers start: 1
  outliers final: 1
  residues processed: 104
  average time/residue: 0.1925
  time to fit residues: 27.1352
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  : 0.648 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 50 optimal weight:    0.0870
   chunk 45 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9990
   chunk 62 optimal weight:    5.9990
   chunk 1 optimal weight:    0.6980
   chunk 10 optimal weight:    2.9990
   chunk 44 optimal weight:    0.0050
   chunk 52 optimal weight:    5.9990
   chunk 68 optimal weight:    4.9990
   chunk 55 optimal weight:    0.3980
   chunk 40 optimal weight:    0.6980
   overall best weight:    0.3772

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

Flipped N/Q/H residues before XYZ refinement:
A 508 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4363 r_free = 0.4363 target = 0.139913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.125501 restraints weight = 32303.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.127628 restraints weight = 22893.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4205 r_free = 0.4205 target = 0.129168 restraints weight = 17322.401|
|-----------------------------------------------------------------------------|
r_work (final): 0.4178
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6180
moved from start:          0.4870

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= 0.113
  Angle     :  0.658   9.408   8840  Z= 0.322
  Chirality :  0.046   0.299    929
  Planarity :  0.005   0.109   1142
  Dihedral  :  7.725 102.205    913
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.05 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  0.45 %
    Favored  : 99.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.26 (0.30), residues: 773
  helix: -0.20 (0.30), residues: 304
  sheet:  1.06 (1.00), residues: 25
  loop : -1.44 (0.29), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 459 
 HIS   0.002   0.001   HIS A 374 
 PHE   0.020   0.001   PHE A 592 
 TYR   0.008   0.001   TYR A 510 
 ARG   0.005   0.001   ARG A 577 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00250 (    2)
  link_NAG-ASN         : angle       2.23450 (    6)
  link_BETA1-4         : bond        0.00353 (    1)
  link_BETA1-4         : angle       3.28534 (    3)
  hydrogen bonds       : bond        0.03046 (  191)
  hydrogen bonds       : angle       4.90011 (  564)
  SS BOND              : bond        0.00174 (    6)
  SS BOND              : angle       1.58301 (   12)
  covalent geometry    : bond        0.00271 ( 6494)
  covalent geometry    : angle       0.65102 ( 8819)

*********************** 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
  105 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 104
  time to evaluate  : 0.683 
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: 0.8086 (m-30) cc_final: 0.7795 (m-30)
REVERT: A   74 GLU cc_start: 0.8352 (tm-30) cc_final: 0.7897 (tm-30)
REVERT: A  347 THR cc_start: 0.4836 (p) cc_final: 0.4586 (p)
REVERT: A  360 MET cc_start: 0.5593 (mmp) cc_final: 0.5309 (mmp)
REVERT: A  379 ILE cc_start: 0.8782 (tp) cc_final: 0.8371 (tp)
REVERT: A  383 MET cc_start: 0.8010 (ptp) cc_final: 0.7282 (tpt)
REVERT: A  517 THR cc_start: 0.9151 (p) cc_final: 0.8383 (p)
REVERT: A  539 LEU cc_start: 0.7752 (mt) cc_final: 0.7191 (tp)
REVERT: A  557 MET cc_start: 0.5745 (mmt) cc_final: 0.5436 (mmt)
REVERT: B  390 LEU cc_start: 0.9046 (mt) cc_final: 0.8405 (tp)
REVERT: B  466 ARG cc_start: 0.8224 (mmm160) cc_final: 0.7955 (mmm160)
REVERT: B  518 LEU cc_start: 0.8391 (tp) cc_final: 0.8073 (tt)
  outliers start: 1
  outliers final: 1
  residues processed: 105
  average time/residue: 0.1785
  time to fit residues: 25.0443
Evaluate side-chains
  85 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 84
  time to evaluate  : 0.755 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 10 optimal weight:    7.9990
   chunk 42 optimal weight:    0.0870
   chunk 65 optimal weight:    4.9990
   chunk 66 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9990
   chunk 55 optimal weight:    4.9990
   chunk 5 optimal weight:    5.9990
   chunk 54 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 23 optimal weight:    3.9990
   overall best weight:    1.8166

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

Flipped N/Q/H residues before XYZ refinement:
A 239 HIS
A 442 GLN
A 508 ASN
B 448 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4360 r_free = 0.4360 target = 0.141417 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.128321 restraints weight = 33948.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.130086 restraints weight = 24177.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4240 r_free = 0.4240 target = 0.131369 restraints weight = 18406.745|
|-----------------------------------------------------------------------------|
r_work (final): 0.4112
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6357
moved from start:          0.5509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.076   6503  Z= 0.175
  Angle     :  0.788  10.830   8840  Z= 0.400
  Chirality :  0.048   0.291    929
  Planarity :  0.006   0.109   1142
  Dihedral  :  8.562 108.718    913
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 13.37
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.60 %
    Favored  : 93.27 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  0.59 %
    Favored  : 99.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.52 (0.30), residues: 773
  helix: -0.35 (0.30), residues: 295
  sheet:  0.79 (1.09), residues: 23
  loop : -1.60 (0.29), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.093   0.004   TRP A 461 
 HIS   0.006   0.002   HIS A 374 
 PHE   0.016   0.002   PHE B 374 
 TYR   0.018   0.002   TYR A 207 
 ARG   0.006   0.001   ARG A 577 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00267 (    2)
  link_NAG-ASN         : angle       2.53065 (    6)
  link_BETA1-4         : bond        0.00784 (    1)
  link_BETA1-4         : angle       3.10418 (    3)
  hydrogen bonds       : bond        0.03837 (  191)
  hydrogen bonds       : angle       5.38218 (  564)
  SS BOND              : bond        0.00167 (    6)
  SS BOND              : angle       2.16839 (   12)
  covalent geometry    : bond        0.00397 ( 6494)
  covalent geometry    : angle       0.78017 ( 8819)

********************** 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
  94 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 93
  time to evaluate  : 0.748 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 ASP cc_start: 0.8214 (m-30) cc_final: 0.7904 (m-30)
REVERT: A  108 LEU cc_start: 0.7633 (tt) cc_final: 0.6738 (mp)
REVERT: A  517 THR cc_start: 0.9173 (p) cc_final: 0.8542 (t)
REVERT: A  557 MET cc_start: 0.5760 (mmt) cc_final: 0.5469 (mmt)
REVERT: B  440 ASN cc_start: 0.8520 (t0) cc_final: 0.8301 (t0)
  outliers start: 1
  outliers final: 1
  residues processed: 94
  average time/residue: 0.1724
  time to fit residues: 22.1472
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  : 0.754 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 42 optimal weight:    4.9990
   chunk 34 optimal weight:    8.9990
   chunk 58 optimal weight:    0.9990
   chunk 70 optimal weight:    0.0980
   chunk 39 optimal weight:    3.9990
   chunk 69 optimal weight:    2.9990
   chunk 5 optimal weight:    4.9990
   chunk 8 optimal weight:    7.9990
   chunk 38 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9990
   chunk 57 optimal weight:    0.6980
   overall best weight:    0.7584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4381 r_free = 0.4381 target = 0.143424 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.130448 restraints weight = 34223.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.132251 restraints weight = 24059.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4265 r_free = 0.4265 target = 0.133576 restraints weight = 18129.751|
|-----------------------------------------------------------------------------|
r_work (final): 0.4142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6295
moved from start:          0.5633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.077   6503  Z= 0.122
  Angle     :  0.694   9.348   8840  Z= 0.342
  Chirality :  0.047   0.293    929
  Planarity :  0.005   0.109   1142
  Dihedral  :  8.248 106.143    913
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 10.05
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.05 %
    Favored  : 94.83 %
  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 : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.46 (0.30), residues: 773
  helix: -0.18 (0.30), residues: 302
  sheet:  1.22 (1.04), residues: 25
  loop : -1.73 (0.28), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.081   0.002   TRP A 461 
 HIS   0.004   0.001   HIS A 540 
 PHE   0.020   0.002   PHE A 452 
 TYR   0.009   0.001   TYR A 510 
 ARG   0.008   0.001   ARG B 466 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00197 (    2)
  link_NAG-ASN         : angle       2.25775 (    6)
  link_BETA1-4         : bond        0.00263 (    1)
  link_BETA1-4         : angle       3.11680 (    3)
  hydrogen bonds       : bond        0.03132 (  191)
  hydrogen bonds       : angle       5.10999 (  564)
  SS BOND              : bond        0.00241 (    6)
  SS BOND              : angle       1.26282 (   12)
  covalent geometry    : bond        0.00290 ( 6494)
  covalent geometry    : angle       0.68862 ( 8819)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3156.92 seconds
wall clock time: 58 minutes 2.41 seconds (3482.41 seconds total)