Starting phenix.real_space_refine
on Wed Feb  4 16:03:45 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9j62_61159/02_2026/9j62_61159.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9j62_61159/02_2026/9j62_61159.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.76
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9j62_61159/02_2026/9j62_61159.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9j62_61159/02_2026/9j62_61159.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9j62_61159/02_2026/9j62_61159.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9j62_61159/02_2026/9j62_61159.map"
  }
  resolution = 2.76
  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=  -0.002 sd=   0.030
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 6181 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     S      37      5.16       5
     C    4109      2.51       5
     N    1061      2.21       5
     O    1220      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 35 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6428
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4862
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 596, 4862
          Classifications: {'peptide': 596}
          Link IDs: {'PTRANS': 27, 'TRANS': 568}
    Chain: "B"
      Number of atoms: 1509
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 190, 1509
          Classifications: {'peptide': 190}
          Link IDs: {'PTRANS': 11, 'TRANS': 178}
    Chain: "A"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 43
          Unusual residues: {' ZN': 1, 'NAG': 3}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    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: 1.29, per 1000 atoms: 0.20
  Number of scatterers: 6428
  At special positions: 0
  Unit cell: (76.56, 93.28, 124.96, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      1     29.99
     S      37     16.00
     O    1220      8.00
     N    1061      7.00
     C    4109      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 344 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 530 " - pdb=" SG  CYS A 542 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 368 " - pdb=" SG  CYS B 421 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 380 " - pdb=" SG  CYS B 510 " distance=1.93
    Simple disulfide: pdb=" SG  CYS B 465 " - pdb=" SG  CYS B 473 " 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
    NAG-ASN
      " NAG A 701 " - " ASN A  53 "
      " NAG A 702 " - " ASN A  90 "
      " NAG A 704 " - " ASN A 322 "
      " NAG B 601 " - " ASN B 331 "
  Time building additional restraints: 0.61
  Conformation dependent library (CDL) restraints added in 177.1 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 703 "
        pdb="ZN    ZN A 703 " - pdb=" NE2 HIS A 378 "
        pdb="ZN    ZN A 703 " - pdb=" NE2 HIS A 374 "


  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1480

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 6 sheets defined
      55.0% alpha, 5.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 53
      removed outlier: 3.970A  pdb=" N   GLN A  24 " --> pdb=" O   THR A  20 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   PHE A  28 " --> pdb=" O   GLN A  24 " (cutoff:3.500A)
      removed outlier: 4.199A  pdb=" N   ASN A  33 " --> pdb=" O   LEU A  29 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   HIS A  34 " --> pdb=" O   ASP A  30 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   ASP A  38 " --> pdb=" O   HIS A  34 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   LEU A  39 " --> pdb=" O   GLU A  35 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   GLN A  42 " --> pdb=" O   ASP A  38 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   SER A  47 " --> pdb=" O   SER A  43 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   ASN A  49 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 57 through 79
      removed outlier: 3.706A  pdb=" N   ASN A  61 " --> pdb=" O   GLU A  57 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   LYS A  68 " --> pdb=" O   ASN A  64 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   LYS A  74 " --> pdb=" O   SER A  70 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   GLU A  75 " --> pdb=" O   ALA A  71 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   LEU A  79 " --> pdb=" O   GLU A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 84 through 88
      removed outlier: 4.021A  pdb=" N   GLU A  87 " --> pdb=" O   PRO A  84 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   ILE A  88 " --> pdb=" O   LEU A  85 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 84 through 88'
    Processing helix  chain 'A' and resid 90 through 101
      removed outlier: 3.801A  pdb=" N   GLN A  96 " --> pdb=" O   THR A  92 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 103 through 108
      removed outlier: 3.720A  pdb=" N   VAL A 107 " --> pdb=" O   GLY A 104 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   LEU A 108 " --> pdb=" O   SER A 105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 129
      removed outlier: 3.740A  pdb=" N   LYS A 114 " --> pdb=" O   GLU A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 147 through 155
    Processing helix  chain 'A' and resid 157 through 172
      removed outlier: 3.673A  pdb=" N   TRP A 163 " --> pdb=" O   ASN A 159 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   TRP A 168 " --> pdb=" O   ALA A 164 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   ARG A 169 " --> pdb=" O   TRP A 165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 173 through 175
      No H-bonds generated for 'chain 'A' and resid 173 through 175'
    Processing helix  chain 'A' and resid 176 through 194
      removed outlier: 3.521A  pdb=" N   GLU A 181 " --> pdb=" O   ARG A 177 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   GLU A 182 " --> pdb=" O   PRO A 178 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   VAL A 185 " --> pdb=" O   GLU A 181 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   GLU A 189 " --> pdb=" O   VAL A 185 " (cutoff:3.500A)
      removed outlier: 4.220A  pdb=" N   MET A 190 " --> pdb=" O   LEU A 186 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ALA A 191 " --> pdb=" O   LYS A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 205
      removed outlier: 3.661A  pdb=" N   TYR A 202 " --> pdb=" O   ASP A 198 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   TRP A 203 " --> pdb=" O   TYR A 199 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 206 through 208
      No H-bonds generated for 'chain 'A' and resid 206 through 208'
    Processing helix  chain 'A' and resid 220 through 231
      removed outlier: 3.870A  pdb=" N   GLU A 224 " --> pdb=" O   GLY A 220 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 252
      removed outlier: 3.715A  pdb=" N   HIS A 239 " --> pdb=" O   PRO A 235 " (cutoff:3.500A)
      removed outlier: 4.122A  pdb=" N   ASN A 250 " --> pdb=" O   ALA A 246 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   ALA A 251 " --> pdb=" O   LYS A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 279
    Processing helix  chain 'A' and resid 293 through 300
    Processing helix  chain 'A' and resid 303 through 318
      removed outlier: 3.545A  pdb=" N   PHE A 308 " --> pdb=" O   ALA A 304 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   LYS A 313 " --> pdb=" O   LYS A 309 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   PHE A 315 " --> pdb=" O   ALA A 311 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   VAL A 318 " --> pdb=" O   PHE A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 331
      removed outlier: 4.003A  pdb=" N   TRP A 328 " --> pdb=" O   THR A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 385
      removed outlier: 3.865A  pdb=" N   HIS A 373 " --> pdb=" O   PHE A 369 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   TYR A 385 " --> pdb=" O   TYR A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 393
    Processing helix  chain 'A' and resid 399 through 413
      removed outlier: 3.886A  pdb=" N   ALA A 403 " --> pdb=" O   GLY A 399 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   GLY A 405 " --> pdb=" O   HIS A 401 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   MET A 408 " --> pdb=" O   VAL A 404 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   SER A 409 " --> pdb=" O   GLY A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 421
    Processing helix  chain 'A' and resid 431 through 444
    Processing helix  chain 'A' and resid 448 through 466
      removed outlier: 4.450A  pdb=" N   PHE A 452 " --> pdb=" O   GLY A 448 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 469 through 471
      No H-bonds generated for 'chain 'A' and resid 469 through 471'
    Processing helix  chain 'A' and resid 472 through 484
    Processing helix  chain 'A' and resid 498 through 502
    Processing helix  chain 'A' and resid 503 through 508
    Processing helix  chain 'A' and resid 513 through 533
      removed outlier: 3.539A  pdb=" N   THR A 519 " --> pdb=" O   TYR A 515 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   LEU A 520 " --> pdb=" O   TYR A 516 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   PHE A 523 " --> pdb=" O   THR A 519 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 542
      removed outlier: 3.530A  pdb=" N   CYS A 542 " --> pdb=" O   LEU A 539 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 547 through 559
      removed outlier: 3.503A  pdb=" N   GLY A 551 " --> pdb=" O   SER A 547 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   MET A 557 " --> pdb=" O   LYS A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 575
      removed outlier: 3.850A  pdb=" N   VAL A 573 " --> pdb=" O   ALA A 569 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 581 through 588
    Processing helix  chain 'A' and resid 588 through 597
      removed outlier: 3.533A  pdb=" N   ASP A 597 " --> pdb=" O   THR A 593 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 325 through 330
    Processing helix  chain 'B' and resid 354 through 359
      removed outlier: 4.002A  pdb=" N   SER B 359 " --> pdb=" O   VAL B 355 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 395 through 399
    Processing helix  chain 'B' and resid 406 through 411
    Processing helix  chain 'B' and resid 487 through 490
    Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 133
    Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263
      removed outlier: 5.872A  pdb=" N   LEU A 262 " --> pdb=" O   VAL A 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 350
      removed outlier: 3.534A  pdb=" N   ARG A 357 " --> pdb=" O   TRP A 349 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 344 through 346
      removed outlier: 3.738A  pdb=" N   VAL B 384 " --> pdb=" O   ILE B 346 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   GLY B 383 " --> pdb=" O   GLU B 501 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   SER B 499 " --> pdb=" O   TYR B 385 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   THR B 365 " --> pdb=" O   ALA B 424 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 437 through 439
    Processing sheet with id=AA6, first strand: chain 'B' and resid 458 through 459

    262 hydrogen bonds defined for protein.
    738 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: 0.88

  Time building geometry restraints manager: 0.72 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: 1671
        1.33 -     1.45: 1414
        1.45 -     1.58: 3467
        1.58 -     1.70: 0
        1.70 -     1.82: 58
  Bond restraints: 6610
  Sorted by residual:
  bond pdb=" N   LEU A 142 "
       pdb=" CA  LEU A 142 "
    ideal  model  delta    sigma   weight residual
    1.454  1.489 -0.035 1.23e-02 6.61e+03 8.25e+00
  bond pdb=" N   ASN A 322 "
       pdb=" CA  ASN A 322 "
    ideal  model  delta    sigma   weight residual
    1.455  1.486 -0.031 1.25e-02 6.40e+03 6.12e+00
  bond pdb=" N   LEU A 144 "
       pdb=" CA  LEU A 144 "
    ideal  model  delta    sigma   weight residual
    1.459  1.484 -0.025 1.06e-02 8.90e+03 5.41e+00
  bond pdb=" N   LEU A 143 "
       pdb=" CA  LEU A 143 "
    ideal  model  delta    sigma   weight residual
    1.451  1.486 -0.035 1.62e-02 3.81e+03 4.58e+00
  bond pdb=" N   GLU A 145 "
       pdb=" CA  GLU A 145 "
    ideal  model  delta    sigma   weight residual
    1.464  1.488 -0.024 1.14e-02 7.69e+03 4.38e+00
  ... (remaining 6605 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.98: 8793
        1.98 -     3.96: 168
        3.96 -     5.94: 24
        5.94 -     7.93: 4
        7.93 -     9.91: 1
  Bond angle restraints: 8990
  Sorted by residual:
  angle pdb=" C   ASN B 331 "
        pdb=" CA  ASN B 331 "
        pdb=" CB  ASN B 331 "
      ideal   model   delta    sigma   weight residual
     111.70  106.26    5.44 1.31e+00 5.83e-01 1.73e+01
  angle pdb=" CA  PHE B 326 "
        pdb=" C   PHE B 326 "
        pdb=" N   ASP B 327 "
      ideal   model   delta    sigma   weight residual
     117.63  122.53   -4.90 1.25e+00 6.40e-01 1.53e+01
  angle pdb=" C   ASN A 322 "
        pdb=" CA  ASN A 322 "
        pdb=" CB  ASN A 322 "
      ideal   model   delta    sigma   weight residual
     110.36  103.46    6.90 1.78e+00 3.16e-01 1.50e+01
  angle pdb=" N   ILE A 259 "
        pdb=" CA  ILE A 259 "
        pdb=" C   ILE A 259 "
      ideal   model   delta    sigma   weight residual
     113.20  110.00    3.20 9.60e-01 1.09e+00 1.11e+01
  angle pdb=" N   PRO A 146 "
        pdb=" CA  PRO A 146 "
        pdb=" CB  PRO A 146 "
      ideal   model   delta    sigma   weight residual
     103.25   99.86    3.39 1.05e+00 9.07e-01 1.04e+01
  ... (remaining 8985 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.92: 3344
       17.92 -    35.84: 439
       35.84 -    53.76: 132
       53.76 -    71.68: 23
       71.68 -    89.61: 4
  Dihedral angle restraints: 3942
    sinusoidal: 1635
      harmonic: 2307
  Sorted by residual:
  dihedral pdb=" CB  CYS B 380 "
           pdb=" SG  CYS B 380 "
           pdb=" SG  CYS B 510 "
           pdb=" CB  CYS B 510 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   37.69   55.31     1      1.00e+01 1.00e-02 4.14e+01
  dihedral pdb=" CA  GLU A 145 "
           pdb=" C   GLU A 145 "
           pdb=" N   PRO A 146 "
           pdb=" CA  PRO A 146 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.29   27.71     0      5.00e+00 4.00e-02 3.07e+01
  dihedral pdb=" CB  CYS B 465 "
           pdb=" SG  CYS B 465 "
           pdb=" SG  CYS B 473 "
           pdb=" CB  CYS B 473 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -56.83  -29.17     1      1.00e+01 1.00e-02 1.22e+01
  ... (remaining 3939 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 778
       0.052 -    0.103: 150
       0.103 -    0.155: 21
       0.155 -    0.207: 2
       0.207 -    0.259: 3
  Chirality restraints: 954
  Sorted by residual:
  chirality pdb=" C1  NAG B 601 "
            pdb=" ND2 ASN B 331 "
            pdb=" C2  NAG B 601 "
            pdb=" O5  NAG B 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.14   -0.26 2.00e-01 2.50e+01 1.67e+00
  chirality pdb=" CA  ASN B 331 "
            pdb=" N   ASN B 331 "
            pdb=" C   ASN B 331 "
            pdb=" CB  ASN B 331 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.76   -0.25 2.00e-01 2.50e+01 1.54e+00
  chirality pdb=" C1  NAG A 704 "
            pdb=" ND2 ASN A 322 "
            pdb=" C2  NAG A 704 "
            pdb=" O5  NAG A 704 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.17   -0.23 2.00e-01 2.50e+01 1.37e+00
  ... (remaining 951 not shown)

  Planarity restraints: 1164
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A 702 "   -0.266 2.00e-02 2.50e+03   2.20e-01 6.06e+02
        pdb=" C7  NAG A 702 "    0.074 2.00e-02 2.50e+03
        pdb=" C8  NAG A 702 "   -0.182 2.00e-02 2.50e+03
        pdb=" N2  NAG A 702 "    0.364 2.00e-02 2.50e+03
        pdb=" O7  NAG A 702 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A 704 "   -0.254 2.00e-02 2.50e+03   2.11e-01 5.59e+02
        pdb=" C7  NAG A 704 "    0.070 2.00e-02 2.50e+03
        pdb=" C8  NAG A 704 "   -0.175 2.00e-02 2.50e+03
        pdb=" N2  NAG A 704 "    0.351 2.00e-02 2.50e+03
        pdb=" O7  NAG A 704 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS B 324 "   -0.046 5.00e-02 4.00e+02   7.12e-02 8.11e+00
        pdb=" N   PRO B 325 "    0.123 5.00e-02 4.00e+02
        pdb=" CA  PRO B 325 "   -0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO B 325 "   -0.039 5.00e-02 4.00e+02
  ... (remaining 1161 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 446
        2.74 -     3.28: 6093
        3.28 -     3.82: 10017
        3.82 -     4.36: 12142
        4.36 -     4.90: 20976
  Nonbonded interactions: 49674
  Sorted by model distance:
  nonbonded pdb=" O   PHE A 327 "
            pdb=" OG  SER A 331 "
     model   vdw
     2.198 3.040
  nonbonded pdb=" CE  MET A  82 "
            pdb=" CD2 HIS B 471 "
     model   vdw
     2.222 3.680
  nonbonded pdb=" O   SER A 254 "
            pdb=" OG  SER A 254 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" N   GLU A 197 "
            pdb=" OE1 GLU A 197 "
     model   vdw
     2.249 3.120
  nonbonded pdb=" OD1 ASP A 431 "
            pdb=" OG1 THR A 434 "
     model   vdw
     2.255 3.040
  ... (remaining 49669 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.310
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     7.480
  Find NCS groups from input model:        0.010
  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:6.570
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.560
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
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      :  0.004   0.105   6622  Z= 0.179
  Angle     :  0.846  49.781   9014  Z= 0.446
  Chirality :  0.044   0.259    954
  Planarity :  0.010   0.220   1160
  Dihedral  : 17.318  89.606   2444
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 28.61 %
    Favored  : 69.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.12 (0.30), residues: 782
  helix: -0.52 (0.27), residues: 360
  sheet:  1.01 (0.83), residues: 51
  loop : -1.14 (0.33), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 559 
 TYR   0.016   0.001   TYR A 183 
 PHE   0.012   0.001   PHE B 441 
 TRP   0.013   0.001   TRP A 168 
 HIS   0.005   0.001   HIS B 443 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 6610)
  covalent geometry    : angle       0.65238 ( 8990)
  SS BOND              : bond        0.04305 (    6)
  SS BOND              : angle      14.43932 (   12)
  hydrogen bonds       : bond        0.32394 (  262)
  hydrogen bonds       : angle       7.81378 (  738)
  metal coordination   : bond        0.00034 (    2)
  link_NAG-ASN         : bond        0.00768 (    4)
  link_NAG-ASN         : angle       3.15355 (   12)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 104
  time to evaluate  : 0.261 
Fit side-chains
  outliers start: 10
  outliers final: 2
  residues processed: 110
  average time/residue: 0.6748
  time to fit residues: 77.4203
Evaluate side-chains
  62 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 60
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain B residue  403 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.0570
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    4.9990
   chunk 74 optimal weight:    2.9990
   overall best weight:    0.9702

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

Flipped N/Q/H residues before XYZ refinement:
A 103 ASN
A 139 GLN
A 239 HIS
A 330 ASN
A 340 GLN
A 598 GLN
B 411 ASN
B 478 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.076465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.061684 restraints weight = 15965.026|
|-----------------------------------------------------------------------------|
r_work (start): 0.2985 rms_B_bonded: 3.30
r_work: 0.2860 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.2860
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8587
moved from start:          0.2419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   6622  Z= 0.158
  Angle     :  0.661  10.199   9014  Z= 0.335
  Chirality :  0.046   0.258    954
  Planarity :  0.005   0.052   1160
  Dihedral  :  5.656  54.255    943
  Min Nonbonded Distance : 2.306

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  4.48 %
    Allowed  : 26.30 %
    Favored  : 69.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.42 (0.30), residues: 782
  helix:  0.35 (0.27), residues: 377
  sheet:  1.18 (0.88), residues: 49
  loop : -1.14 (0.33), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 345 
 TYR   0.017   0.001   TYR A 183 
 PHE   0.010   0.001   PHE A 230 
 TRP   0.009   0.001   TRP A 610 
 HIS   0.005   0.001   HIS B 443 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 6610)
  covalent geometry    : angle       0.64640 ( 8990)
  SS BOND              : bond        0.00945 (    6)
  SS BOND              : angle       2.26291 (   12)
  hydrogen bonds       : bond        0.05778 (  262)
  hydrogen bonds       : angle       4.73868 (  738)
  metal coordination   : bond        0.00050 (    2)
  link_NAG-ASN         : bond        0.00663 (    4)
  link_NAG-ASN         : angle       3.14313 (   12)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 66
  time to evaluate  : 0.259 
Fit side-chains
   revert: symmetry clash
REVERT: A   81 GLN cc_start: 0.7879 (OUTLIER) cc_final: 0.7621 (mm-40)
REVERT: A  123 MET cc_start: 0.8048 (mmm) cc_final: 0.7824 (mmm)
REVERT: A  145 GLU cc_start: 0.8751 (tp30) cc_final: 0.8543 (tm-30)
REVERT: B  328 GLN cc_start: 0.8912 (mp10) cc_final: 0.8700 (mp10)
REVERT: B  342 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7061 (mp0)
REVERT: B  379 LEU cc_start: 0.8090 (mm) cc_final: 0.7770 (mm)
  outliers start: 31
  outliers final: 8
  residues processed: 88
  average time/residue: 0.5524
  time to fit residues: 51.2939
Evaluate side-chains
  66 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 56
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue   81 GLN
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  267 LEU
Chi-restraints excluded: chain A residue  344 CYS
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain B residue  338 VAL
Chi-restraints excluded: chain B residue  342 GLU
Chi-restraints excluded: chain B residue  510 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 20 optimal weight:    0.9980
   chunk 7 optimal weight:    0.2980
   chunk 53 optimal weight:    0.6980
   chunk 54 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9990
   chunk 5 optimal weight:    0.8980
   chunk 34 optimal weight:    1.9990
   chunk 60 optimal weight:    0.2980
   chunk 73 optimal weight:    4.9990
   chunk 75 optimal weight:    2.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** B 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 478 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.077012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.062293 restraints weight = 15767.247|
|-----------------------------------------------------------------------------|
r_work (start): 0.3000 rms_B_bonded: 3.28
r_work: 0.2875 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.2875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8565
moved from start:          0.2825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6622  Z= 0.120
  Angle     :  0.579   8.430   9014  Z= 0.294
  Chirality :  0.044   0.331    954
  Planarity :  0.004   0.047   1160
  Dihedral  :  5.129  52.513    940
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 4.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 25.58 %
    Favored  : 70.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.05 (0.31), residues: 782
  helix:  0.81 (0.28), residues: 376
  sheet:  0.86 (0.87), residues: 49
  loop : -1.06 (0.33), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 345 
 TYR   0.014   0.001   TYR A 183 
 PHE   0.008   0.001   PHE B 366 
 TRP   0.009   0.001   TRP B 425 
 HIS   0.003   0.001   HIS A 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 6610)
  covalent geometry    : angle       0.56294 ( 8990)
  SS BOND              : bond        0.00640 (    6)
  SS BOND              : angle       1.71091 (   12)
  hydrogen bonds       : bond        0.04711 (  262)
  hydrogen bonds       : angle       4.38424 (  738)
  metal coordination   : bond        0.00058 (    2)
  link_NAG-ASN         : bond        0.01227 (    4)
  link_NAG-ASN         : angle       3.33096 (   12)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 60
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
REVERT: A   68 LYS cc_start: 0.8556 (mmtm) cc_final: 0.8220 (mtpm)
REVERT: A   81 GLN cc_start: 0.7857 (OUTLIER) cc_final: 0.7603 (mm-40)
REVERT: A   87 GLU cc_start: 0.8312 (tp30) cc_final: 0.8070 (tp30)
REVERT: A   98 GLN cc_start: 0.9027 (mm-40) cc_final: 0.8687 (mt0)
REVERT: B  328 GLN cc_start: 0.8930 (mp10) cc_final: 0.8683 (mp10)
REVERT: B  342 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.6945 (mp0)
REVERT: B  417 GLU cc_start: 0.8997 (pm20) cc_final: 0.8750 (mp0)
REVERT: B  451 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.6976 (tpt-90)
  outliers start: 24
  outliers final: 8
  residues processed: 80
  average time/residue: 0.6412
  time to fit residues: 53.8050
Evaluate side-chains
  65 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 54
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 GLN
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  344 CYS
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain B residue  338 VAL
Chi-restraints excluded: chain B residue  342 GLU
Chi-restraints excluded: chain B residue  344 VAL
Chi-restraints excluded: chain B residue  380 CYS
Chi-restraints excluded: chain B residue  451 ARG
Chi-restraints excluded: chain B residue  510 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9980
   chunk 76 optimal weight:    0.9980
   chunk 62 optimal weight:    7.9990
   chunk 68 optimal weight:    2.9990
   chunk 37 optimal weight:    0.8980
   chunk 70 optimal weight:    3.9990
   chunk 50 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9980
   overall best weight:    0.9380

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

Flipped N/Q/H residues before XYZ refinement:
B 478 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.075984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.061096 restraints weight = 16136.372|
|-----------------------------------------------------------------------------|
r_work (start): 0.2978 rms_B_bonded: 3.31
r_work: 0.2851 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.2851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8592
moved from start:          0.3036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6622  Z= 0.134
  Angle     :  0.589   9.165   9014  Z= 0.298
  Chirality :  0.044   0.343    954
  Planarity :  0.004   0.046   1160
  Dihedral  :  5.120  53.475    940
  Min Nonbonded Distance : 2.289

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 25.72 %
    Favored  : 70.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.14 (0.31), residues: 782
  helix:  1.03 (0.28), residues: 376
  sheet:  0.68 (0.84), residues: 49
  loop : -1.01 (0.33), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 343 
 TYR   0.016   0.001   TYR A 183 
 PHE   0.009   0.001   PHE A 230 
 TRP   0.009   0.001   TRP B 425 
 HIS   0.005   0.001   HIS A 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 6610)
  covalent geometry    : angle       0.57294 ( 8990)
  SS BOND              : bond        0.00641 (    6)
  SS BOND              : angle       1.44036 (   12)
  hydrogen bonds       : bond        0.04793 (  262)
  hydrogen bonds       : angle       4.31098 (  738)
  metal coordination   : bond        0.00082 (    2)
  link_NAG-ASN         : bond        0.01187 (    4)
  link_NAG-ASN         : angle       3.55916 (   12)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 53
  time to evaluate  : 0.257 
Fit side-chains
   revert: symmetry clash
REVERT: A   68 LYS cc_start: 0.8560 (mmtm) cc_final: 0.8237 (mtpm)
REVERT: A   81 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.7737 (mm-40)
REVERT: A   98 GLN cc_start: 0.9052 (mm-40) cc_final: 0.8803 (mt0)
REVERT: A  123 MET cc_start: 0.7948 (mmm) cc_final: 0.7689 (mmm)
REVERT: B  342 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.6942 (mp0)
REVERT: B  376 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8333 (pp)
REVERT: B  379 LEU cc_start: 0.8104 (mm) cc_final: 0.7736 (mm)
REVERT: B  417 GLU cc_start: 0.9026 (pm20) cc_final: 0.8727 (mp0)
REVERT: B  451 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.6928 (tpt-90)
  outliers start: 26
  outliers final: 10
  residues processed: 75
  average time/residue: 0.5728
  time to fit residues: 45.2843
Evaluate side-chains
  64 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 50
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 GLN
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain B residue  338 VAL
Chi-restraints excluded: chain B residue  342 GLU
Chi-restraints excluded: chain B residue  344 VAL
Chi-restraints excluded: chain B residue  356 LEU
Chi-restraints excluded: chain B residue  359 SER
Chi-restraints excluded: chain B residue  376 LEU
Chi-restraints excluded: chain B residue  380 CYS
Chi-restraints excluded: chain B residue  430 ILE
Chi-restraints excluded: chain B residue  451 ARG
Chi-restraints excluded: chain B residue  510 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 12 optimal weight:    0.8980
   chunk 41 optimal weight:    0.7980
   chunk 45 optimal weight:    2.9990
   chunk 32 optimal weight:    5.9990
   chunk 22 optimal weight:    4.9990
   chunk 8 optimal weight:    2.9990
   chunk 46 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9990
   chunk 73 optimal weight:    5.9990
   chunk 54 optimal weight:    0.9990
   chunk 30 optimal weight:    4.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
B 478 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.075914 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.061178 restraints weight = 16072.188|
|-----------------------------------------------------------------------------|
r_work (start): 0.2966 rms_B_bonded: 3.29
r_work: 0.2838 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.2838
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8564
moved from start:          0.3190

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6622  Z= 0.128
  Angle     :  0.580   8.874   9014  Z= 0.292
  Chirality :  0.044   0.348    954
  Planarity :  0.004   0.045   1160
  Dihedral  :  5.058  53.741    940
  Min Nonbonded Distance : 2.299

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 25.14 %
    Favored  : 71.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.25 (0.31), residues: 782
  helix:  1.14 (0.28), residues: 376
  sheet:  0.65 (0.86), residues: 49
  loop : -0.95 (0.33), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 343 
 TYR   0.015   0.001   TYR A 183 
 PHE   0.008   0.001   PHE A 230 
 TRP   0.009   0.001   TRP B 425 
 HIS   0.004   0.001   HIS A 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 6610)
  covalent geometry    : angle       0.56513 ( 8990)
  SS BOND              : bond        0.00308 (    6)
  SS BOND              : angle       1.20181 (   12)
  hydrogen bonds       : bond        0.04568 (  262)
  hydrogen bonds       : angle       4.22856 (  738)
  metal coordination   : bond        0.00077 (    2)
  link_NAG-ASN         : bond        0.00851 (    4)
  link_NAG-ASN         : angle       3.42080 (   12)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 51
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
REVERT: A   68 LYS cc_start: 0.8651 (mmtm) cc_final: 0.8378 (mtpm)
REVERT: A   81 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.7774 (mm-40)
REVERT: A   87 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.7944 (tp30)
REVERT: A   98 GLN cc_start: 0.9081 (mm-40) cc_final: 0.8818 (mt0)
REVERT: A  123 MET cc_start: 0.7954 (mmm) cc_final: 0.7692 (mtt)
REVERT: B  342 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.6920 (mp0)
REVERT: B  376 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8235 (pp)
REVERT: B  379 LEU cc_start: 0.8072 (mm) cc_final: 0.7710 (mm)
REVERT: B  417 GLU cc_start: 0.9046 (pm20) cc_final: 0.8795 (pm20)
REVERT: B  451 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.6938 (tpt-90)
  outliers start: 26
  outliers final: 10
  residues processed: 74
  average time/residue: 0.5912
  time to fit residues: 46.1853
Evaluate side-chains
  63 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 48
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 GLN
Chi-restraints excluded: chain A residue   82 MET
Chi-restraints excluded: chain A residue   87 GLU
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain B residue  338 VAL
Chi-restraints excluded: chain B residue  342 GLU
Chi-restraints excluded: chain B residue  344 VAL
Chi-restraints excluded: chain B residue  359 SER
Chi-restraints excluded: chain B residue  376 LEU
Chi-restraints excluded: chain B residue  380 CYS
Chi-restraints excluded: chain B residue  430 ILE
Chi-restraints excluded: chain B residue  451 ARG
Chi-restraints excluded: chain B residue  510 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 0 optimal weight:    6.9990
   chunk 72 optimal weight:    1.9990
   chunk 2 optimal weight:    0.5980
   chunk 77 optimal weight:    0.8980
   chunk 33 optimal weight:    0.0980
   chunk 53 optimal weight:    1.9990
   chunk 60 optimal weight:    0.6980
   chunk 29 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 73 optimal weight:    1.9990
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 = 0.3282 r_free = 0.3282 target = 0.075855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.061236 restraints weight = 16016.760|
|-----------------------------------------------------------------------------|
r_work (start): 0.2978 rms_B_bonded: 3.27
r_work: 0.2851 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.2851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8558
moved from start:          0.3321

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6622  Z= 0.128
  Angle     :  0.579  10.082   9014  Z= 0.291
  Chirality :  0.044   0.373    954
  Planarity :  0.004   0.045   1160
  Dihedral  :  5.061  53.901    940
  Min Nonbonded Distance : 2.310

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 25.14 %
    Favored  : 71.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.30 (0.31), residues: 782
  helix:  1.21 (0.28), residues: 375
  sheet:  0.53 (0.85), residues: 49
  loop : -0.93 (0.33), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 343 
 TYR   0.015   0.001   TYR A 183 
 PHE   0.008   0.001   PHE A 230 
 TRP   0.009   0.001   TRP B 425 
 HIS   0.004   0.001   HIS A 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 6610)
  covalent geometry    : angle       0.56118 ( 8990)
  SS BOND              : bond        0.00287 (    6)
  SS BOND              : angle       1.36188 (   12)
  hydrogen bonds       : bond        0.04511 (  262)
  hydrogen bonds       : angle       4.19055 (  738)
  metal coordination   : bond        0.00079 (    2)
  link_NAG-ASN         : bond        0.01055 (    4)
  link_NAG-ASN         : angle       3.79795 (   12)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 49
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
REVERT: A   68 LYS cc_start: 0.8608 (mmtm) cc_final: 0.8367 (mtpm)
REVERT: A   87 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.7998 (tp30)
REVERT: A   98 GLN cc_start: 0.9078 (mm-40) cc_final: 0.8835 (mt0)
REVERT: A  187 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8152 (ttmt)
REVERT: B  342 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.6830 (mp0)
REVERT: B  376 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8236 (pp)
REVERT: B  379 LEU cc_start: 0.8109 (mm) cc_final: 0.7748 (mm)
REVERT: B  417 GLU cc_start: 0.9059 (pm20) cc_final: 0.8795 (pm20)
REVERT: B  431 ASP cc_start: 0.8627 (m-30) cc_final: 0.8406 (m-30)
REVERT: B  451 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.6917 (tpt-90)
  outliers start: 26
  outliers final: 10
  residues processed: 71
  average time/residue: 0.5853
  time to fit residues: 43.8434
Evaluate side-chains
  63 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 48
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 MET
Chi-restraints excluded: chain A residue   87 GLU
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  187 LYS
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain B residue  338 VAL
Chi-restraints excluded: chain B residue  342 GLU
Chi-restraints excluded: chain B residue  344 VAL
Chi-restraints excluded: chain B residue  359 SER
Chi-restraints excluded: chain B residue  376 LEU
Chi-restraints excluded: chain B residue  380 CYS
Chi-restraints excluded: chain B residue  430 ILE
Chi-restraints excluded: chain B residue  451 ARG
Chi-restraints excluded: chain B residue  510 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 36 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9990
   chunk 59 optimal weight:    2.9990
   chunk 14 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9990
   chunk 48 optimal weight:    0.8980
   chunk 11 optimal weight:    4.9990
   chunk 55 optimal weight:    0.9990
   chunk 43 optimal weight:    0.6980
   chunk 3 optimal weight:    2.9990
   chunk 0 optimal weight:    6.9990
   overall best weight:    0.8984

-------------------------------------------------------------------------------
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 = 0.3278 r_free = 0.3278 target = 0.075721 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.061133 restraints weight = 15976.348|
|-----------------------------------------------------------------------------|
r_work (start): 0.2967 rms_B_bonded: 3.26
r_work: 0.2840 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.2840
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8565
moved from start:          0.3393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6622  Z= 0.132
  Angle     :  0.612  14.722   9014  Z= 0.302
  Chirality :  0.044   0.357    954
  Planarity :  0.004   0.045   1160
  Dihedral  :  5.067  54.195    940
  Min Nonbonded Distance : 2.325

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 26.01 %
    Favored  : 71.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.36 (0.31), residues: 782
  helix:  1.17 (0.28), residues: 381
  sheet:  0.54 (0.85), residues: 49
  loop : -0.82 (0.34), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 343 
 TYR   0.015   0.001   TYR A 183 
 PHE   0.008   0.001   PHE A 230 
 TRP   0.009   0.001   TRP B 425 
 HIS   0.004   0.001   HIS A 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 6610)
  covalent geometry    : angle       0.59630 ( 8990)
  SS BOND              : bond        0.00289 (    6)
  SS BOND              : angle       1.17107 (   12)
  hydrogen bonds       : bond        0.04535 (  262)
  hydrogen bonds       : angle       4.15377 (  738)
  metal coordination   : bond        0.00060 (    2)
  link_NAG-ASN         : bond        0.00874 (    4)
  link_NAG-ASN         : angle       3.69959 (   12)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 49
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
REVERT: A   68 LYS cc_start: 0.8602 (mmtm) cc_final: 0.8374 (mtpm)
REVERT: A   87 GLU cc_start: 0.8541 (tp30) cc_final: 0.8064 (tp30)
REVERT: A   98 GLN cc_start: 0.9079 (mm-40) cc_final: 0.8844 (mt0)
REVERT: A  187 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8088 (ttmt)
REVERT: B  342 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.6847 (mp0)
REVERT: B  379 LEU cc_start: 0.8128 (mm) cc_final: 0.7751 (mm)
REVERT: B  417 GLU cc_start: 0.9073 (pm20) cc_final: 0.8820 (pm20)
REVERT: B  431 ASP cc_start: 0.8648 (m-30) cc_final: 0.8432 (m-30)
REVERT: B  451 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.6866 (tpt-90)
  outliers start: 19
  outliers final: 7
  residues processed: 66
  average time/residue: 0.6086
  time to fit residues: 42.2939
Evaluate side-chains
  58 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 48
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 LYS
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain B residue  338 VAL
Chi-restraints excluded: chain B residue  342 GLU
Chi-restraints excluded: chain B residue  344 VAL
Chi-restraints excluded: chain B residue  359 SER
Chi-restraints excluded: chain B residue  380 CYS
Chi-restraints excluded: chain B residue  430 ILE
Chi-restraints excluded: chain B residue  451 ARG
Chi-restraints excluded: chain B residue  510 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 53 optimal weight:    0.9980
   chunk 37 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9980
   chunk 60 optimal weight:    0.9980
   chunk 47 optimal weight:    0.0070
   chunk 28 optimal weight:    2.9990
   chunk 11 optimal weight:    7.9990
   chunk 36 optimal weight:    0.6980
   chunk 54 optimal weight:    0.6980
   chunk 24 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9990
   overall best weight:    0.6798

-------------------------------------------------------------------------------
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 = 0.3296 r_free = 0.3296 target = 0.076734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.061837 restraints weight = 15945.517|
|-----------------------------------------------------------------------------|
r_work (start): 0.2991 rms_B_bonded: 3.29
r_work: 0.2862 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.2862
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8569
moved from start:          0.3488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6622  Z= 0.118
  Angle     :  0.602  13.770   9014  Z= 0.294
  Chirality :  0.043   0.348    954
  Planarity :  0.004   0.044   1160
  Dihedral  :  4.983  54.001    940
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 4.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 26.88 %
    Favored  : 70.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.46 (0.31), residues: 782
  helix:  1.26 (0.28), residues: 378
  sheet:  0.55 (0.86), residues: 49
  loop : -0.76 (0.34), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 345 
 TYR   0.013   0.001   TYR A  50 
 PHE   0.007   0.001   PHE A 315 
 TRP   0.009   0.001   TRP B 425 
 HIS   0.003   0.001   HIS A 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 6610)
  covalent geometry    : angle       0.58522 ( 8990)
  SS BOND              : bond        0.00334 (    6)
  SS BOND              : angle       1.35507 (   12)
  hydrogen bonds       : bond        0.04145 (  262)
  hydrogen bonds       : angle       4.07800 (  738)
  metal coordination   : bond        0.00065 (    2)
  link_NAG-ASN         : bond        0.00873 (    4)
  link_NAG-ASN         : angle       3.67860 (   12)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 51
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
REVERT: A   68 LYS cc_start: 0.8621 (mmtm) cc_final: 0.8385 (mtpm)
REVERT: A   87 GLU cc_start: 0.8491 (tp30) cc_final: 0.8081 (tp30)
REVERT: A   98 GLN cc_start: 0.9073 (mm-40) cc_final: 0.8837 (mt0)
REVERT: B  379 LEU cc_start: 0.8228 (mm) cc_final: 0.7887 (mm)
REVERT: B  417 GLU cc_start: 0.9049 (pm20) cc_final: 0.8792 (pm20)
REVERT: B  451 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.6943 (tpt-90)
REVERT: B  501 GLU cc_start: 0.8267 (pt0) cc_final: 0.7377 (pm20)
  outliers start: 18
  outliers final: 8
  residues processed: 67
  average time/residue: 0.6206
  time to fit residues: 43.8163
Evaluate side-chains
  56 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 47
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain B residue  338 VAL
Chi-restraints excluded: chain B residue  344 VAL
Chi-restraints excluded: chain B residue  380 CYS
Chi-restraints excluded: chain B residue  430 ILE
Chi-restraints excluded: chain B residue  451 ARG
Chi-restraints excluded: chain B residue  510 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 25 optimal weight:    0.8980
   chunk 74 optimal weight:    0.7980
   chunk 71 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9980
   chunk 12 optimal weight:    0.3980
   chunk 4 optimal weight:    0.5980
   chunk 55 optimal weight:    0.6980
   chunk 11 optimal weight:    6.9990
   chunk 57 optimal weight:    0.6980
   chunk 44 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3302 r_free = 0.3302 target = 0.077033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.062035 restraints weight = 16159.364|
|-----------------------------------------------------------------------------|
r_work (start): 0.2999 rms_B_bonded: 3.33
r_work: 0.2870 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.2870
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8567
moved from start:          0.3570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6622  Z= 0.121
  Angle     :  0.625  13.002   9014  Z= 0.305
  Chirality :  0.044   0.347    954
  Planarity :  0.004   0.044   1160
  Dihedral  :  4.930  53.549    940
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 4.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 27.46 %
    Favored  : 70.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.47 (0.31), residues: 782
  helix:  1.25 (0.28), residues: 385
  sheet:  0.53 (0.85), residues: 49
  loop : -0.77 (0.35), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 343 
 TYR   0.013   0.001   TYR A 183 
 PHE   0.007   0.001   PHE A 315 
 TRP   0.010   0.001   TRP B 425 
 HIS   0.003   0.001   HIS A 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 6610)
  covalent geometry    : angle       0.60969 ( 8990)
  SS BOND              : bond        0.00298 (    6)
  SS BOND              : angle       1.58366 (   12)
  hydrogen bonds       : bond        0.04074 (  262)
  hydrogen bonds       : angle       4.05348 (  738)
  metal coordination   : bond        0.00046 (    2)
  link_NAG-ASN         : bond        0.00887 (    4)
  link_NAG-ASN         : angle       3.58461 (   12)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 49
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 GLU cc_start: 0.8495 (tp30) cc_final: 0.8120 (tp30)
REVERT: A  433 GLU cc_start: 0.8988 (mt-10) cc_final: 0.8691 (mm-30)
REVERT: B  379 LEU cc_start: 0.8258 (mm) cc_final: 0.7929 (mm)
REVERT: B  417 GLU cc_start: 0.9074 (pm20) cc_final: 0.8815 (pm20)
REVERT: B  451 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.6990 (tpt-90)
REVERT: B  501 GLU cc_start: 0.8256 (pt0) cc_final: 0.7385 (pm20)
  outliers start: 12
  outliers final: 7
  residues processed: 59
  average time/residue: 0.6322
  time to fit residues: 39.2959
Evaluate side-chains
  54 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 46
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain B residue  338 VAL
Chi-restraints excluded: chain B residue  344 VAL
Chi-restraints excluded: chain B residue  380 CYS
Chi-restraints excluded: chain B residue  451 ARG
Chi-restraints excluded: chain B residue  510 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 47 optimal weight:    9.9990
   chunk 76 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9990
   chunk 45 optimal weight:    0.4980
   chunk 50 optimal weight:    0.6980
   chunk 18 optimal weight:    0.6980
   chunk 37 optimal weight:    0.4980
   chunk 1 optimal weight:    3.9990
   overall best weight:    0.6782

-------------------------------------------------------------------------------
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 = 0.3300 r_free = 0.3300 target = 0.076947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.062068 restraints weight = 15799.607|
|-----------------------------------------------------------------------------|
r_work (start): 0.2997 rms_B_bonded: 3.28
r_work: 0.2869 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.2869
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8565
moved from start:          0.3612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6622  Z= 0.124
  Angle     :  0.631  13.389   9014  Z= 0.308
  Chirality :  0.043   0.348    954
  Planarity :  0.004   0.044   1160
  Dihedral  :  4.895  53.439    940
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 4.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 27.31 %
    Favored  : 70.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.54 (0.32), residues: 782
  helix:  1.30 (0.28), residues: 388
  sheet:  0.60 (0.85), residues: 49
  loop : -0.75 (0.35), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 343 
 TYR   0.013   0.001   TYR A 183 
 PHE   0.007   0.001   PHE A 315 
 TRP   0.010   0.001   TRP A  69 
 HIS   0.004   0.001   HIS A 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 6610)
  covalent geometry    : angle       0.61435 ( 8990)
  SS BOND              : bond        0.00237 (    6)
  SS BOND              : angle       1.80643 (   12)
  hydrogen bonds       : bond        0.04083 (  262)
  hydrogen bonds       : angle       4.02829 (  738)
  metal coordination   : bond        0.00064 (    2)
  link_NAG-ASN         : bond        0.00872 (    4)
  link_NAG-ASN         : angle       3.59393 (   12)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 49
  time to evaluate  : 0.320 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8105 (tp30)
REVERT: A  433 GLU cc_start: 0.8987 (mt-10) cc_final: 0.8687 (mm-30)
REVERT: B  379 LEU cc_start: 0.8264 (mm) cc_final: 0.7920 (mm)
REVERT: B  417 GLU cc_start: 0.9074 (pm20) cc_final: 0.8818 (pm20)
REVERT: B  451 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.6933 (tpt-90)
REVERT: B  501 GLU cc_start: 0.8272 (pt0) cc_final: 0.7387 (pm20)
  outliers start: 14
  outliers final: 8
  residues processed: 58
  average time/residue: 0.6095
  time to fit residues: 37.2750
Evaluate side-chains
  57 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 47
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 SER
Chi-restraints excluded: chain A residue   87 GLU
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain B residue  338 VAL
Chi-restraints excluded: chain B residue  344 VAL
Chi-restraints excluded: chain B residue  380 CYS
Chi-restraints excluded: chain B residue  451 ARG
Chi-restraints excluded: chain B residue  510 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 71 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9980
   chunk 48 optimal weight:    0.6980
   chunk 0 optimal weight:    5.9990
   chunk 17 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 57 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9990
   chunk 77 optimal weight:    0.8980
   chunk 66 optimal weight:    0.9980
   overall best weight:    0.9182

-------------------------------------------------------------------------------
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 = 0.3288 r_free = 0.3288 target = 0.076150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.061292 restraints weight = 15866.936|
|-----------------------------------------------------------------------------|
r_work (start): 0.2981 rms_B_bonded: 3.29
r_work: 0.2852 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.2852
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8586
moved from start:          0.3573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6622  Z= 0.137
  Angle     :  0.632  13.190   9014  Z= 0.310
  Chirality :  0.044   0.352    954
  Planarity :  0.004   0.044   1160
  Dihedral  :  4.972  53.820    940
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 27.17 %
    Favored  : 70.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.52 (0.32), residues: 782
  helix:  1.34 (0.28), residues: 383
  sheet:  0.60 (0.85), residues: 49
  loop : -0.80 (0.34), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 343 
 TYR   0.016   0.001   TYR A 183 
 PHE   0.008   0.001   PHE A 230 
 TRP   0.009   0.001   TRP A 478 
 HIS   0.005   0.001   HIS A 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 6610)
  covalent geometry    : angle       0.61425 ( 8990)
  SS BOND              : bond        0.00287 (    6)
  SS BOND              : angle       2.08082 (   12)
  hydrogen bonds       : bond        0.04425 (  262)
  hydrogen bonds       : angle       4.08779 (  738)
  metal coordination   : bond        0.00087 (    2)
  link_NAG-ASN         : bond        0.00852 (    4)
  link_NAG-ASN         : angle       3.60034 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2140.35 seconds
wall clock time: 37 minutes 19.28 seconds (2239.28 seconds total)