Starting phenix.real_space_refine
on Fri Aug 22 17:58:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8t23_40979/08_2025/8t23_40979.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8t23_40979/08_2025/8t23_40979.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.87
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8t23_40979/08_2025/8t23_40979.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8t23_40979/08_2025/8t23_40979.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8t23_40979/08_2025/8t23_40979.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8t23_40979/08_2025/8t23_40979.map"
  }
  resolution = 3.87
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.019
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    4121      2.51       5
     N    1075      2.21       5
     O    1218      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 43 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6451
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 4904
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 596, 4904
          Classifications: {'peptide': 596}
          Link IDs: {'PTRANS': 30, 'TRANS': 565}
    Chain: "B"
      Number of atoms: 1467
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 185, 1467
          Classifications: {'peptide': 185}
          Link IDs: {'PTRANS': 11, 'TRANS': 173}
          Chain breaks: 1
    Chain: "G"
      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: "H"
      Number of atoms: 24
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 24
          Unusual residues: {'FUC': 1, 'NAG': 1}
          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: "A"
      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
    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: 1.43, per 1000 atoms: 0.22
  Number of scatterers: 6451
  At special positions: 0
  Unit cell: (103.23, 75.48, 135.42, 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    1218      8.00
     N    1075      7.00
     C    4121      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=2.02
    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=2.04
    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=2.04
    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 G   1 " - " NAG G   2 "
    BETA1-6
      " NAG H   1 " - " FUC H   2 "
       ~> Even though FUC is an alpha isomer, a beta linkage is required...
    NAG-ASN
      " NAG A 801 " - " ASN A  53 "
      " NAG B 601 " - " ASN B 343 "
      " NAG G   1 " - " ASN A 322 "
      " NAG H   1 " - " ASN A 216 "
  Time building additional restraints: 0.51
  Conformation dependent library (CDL) restraints added in 298.3 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1472

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 2 sheets defined
      45.6% alpha, 3.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 53
      removed outlier: 3.534A  pdb=" N   LEU A  24 " --> pdb=" O   THR A  20 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   THR A  27 " --> pdb=" O   ASP A  23 " (cutoff:3.500A)
      removed outlier: 4.814A  pdb=" N   PHE A  28 " --> pdb=" O   LEU A  24 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   LEU A  29 " --> pdb=" O   ALA A  25 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   PHE A  32 " --> pdb=" O   PHE A  28 " (cutoff:3.500A)
      removed outlier: 4.932A  pdb=" N   GLU A  37 " --> pdb=" O   ASN A  33 " (cutoff:3.500A)
      removed outlier: 5.327A  pdb=" N   GLU A  38 " --> pdb=" O   TYR A  34 " (cutoff:3.500A)
      removed outlier: 4.414A  pdb=" N   LEU A  39 " --> pdb=" O   GLU A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 61 through 66
    Processing helix  chain 'A' and resid 66 through 83
      removed outlier: 3.646A  pdb=" N   THR A  82 " --> pdb=" O   GLN A  78 " (cutoff:3.500A)
      removed outlier: 4.085A  pdb=" N   TYR A  83 " --> pdb=" O   HIS A  79 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 90 through 102
      removed outlier: 3.610A  pdb=" N   ALA A  99 " --> pdb=" O   ARG A  95 " (cutoff:3.500A)
      removed outlier: 4.826A  pdb=" N   LEU A 100 " --> pdb=" O   GLN A  96 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 129
      removed outlier: 4.873A  pdb=" N   ARG A 115 " --> pdb=" O   ASP A 111 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   LEU A 116 " --> pdb=" O   LYS A 112 " (cutoff:3.500A)
      removed outlier: 5.139A  pdb=" N   MET A 123 " --> pdb=" O   ILE A 119 " (cutoff:3.500A)
      removed outlier: 5.823A  pdb=" N   SER A 124 " --> pdb=" O   LEU A 120 " (cutoff:3.500A)
      removed outlier: 4.361A  pdb=" N   THR A 125 " --> pdb=" O   ASN A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 144 through 148
      removed outlier: 3.616A  pdb=" N   GLY A 147 " --> pdb=" O   LEU A 144 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 155
    Processing helix  chain 'A' and resid 157 through 163
      removed outlier: 4.367A  pdb=" N   ARG A 161 " --> pdb=" O   ASP A 157 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 163 through 172
    Processing helix  chain 'A' and resid 173 through 177
      removed outlier: 3.577A  pdb=" N   LEU A 176 " --> pdb=" O   GLY A 173 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 187
    Processing helix  chain 'A' and resid 199 through 204
    Processing helix  chain 'A' and resid 219 through 223
    Processing helix  chain 'A' and resid 225 through 231
    Processing helix  chain 'A' and resid 233 through 235
      No H-bonds generated for 'chain 'A' and resid 233 through 235'
    Processing helix  chain 'A' and resid 236 through 248
      removed outlier: 4.855A  pdb=" N   ALA A 242 " --> pdb=" O   GLU A 238 " (cutoff:3.500A)
      removed outlier: 4.894A  pdb=" N   ARG A 245 " --> pdb=" O   HIS A 241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 249 through 252
      removed outlier: 3.973A  pdb=" N   TYR A 252 " --> pdb=" O   MET A 249 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 249 through 252'
    Processing helix  chain 'A' and resid 306 through 317
      removed outlier: 4.388A  pdb=" N   PHE A 315 " --> pdb=" O   ALA A 311 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 331
      removed outlier: 3.956A  pdb=" N   TRP A 328 " --> pdb=" O   THR A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 382
    Processing helix  chain 'A' and resid 383 through 386
    Processing helix  chain 'A' and resid 389 through 393
    Processing helix  chain 'A' and resid 397 through 413
      removed outlier: 3.628A  pdb=" N   HIS A 401 " --> pdb=" O   ASN A 397 " (cutoff:3.500A)
      removed outlier: 5.232A  pdb=" N   GLY A 405 " --> pdb=" O   HIS A 401 " (cutoff:3.500A)
      removed outlier: 5.563A  pdb=" N   GLU A 406 " --> pdb=" O   GLU A 402 " (cutoff:3.500A)
      removed outlier: 4.464A  pdb=" N   ILE A 407 " --> pdb=" O   ALA A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 415 through 422
    Processing helix  chain 'A' and resid 431 through 435
    Processing helix  chain 'A' and resid 446 through 452
      removed outlier: 4.238A  pdb=" N   THR A 449 " --> pdb=" O   ILE A 446 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   LEU A 450 " --> pdb=" O   VAL A 447 " (cutoff:3.500A)
      Proline residue:  A 451  - end of helix
      No H-bonds generated for 'chain 'A' and resid 446 through 452'
    Processing helix  chain 'A' and resid 453 through 464
      removed outlier: 4.725A  pdb=" N   ARG A 460 " --> pdb=" O   LEU A 456 " (cutoff:3.500A)
      removed outlier: 4.485A  pdb=" N   TRP A 461 " --> pdb=" O   GLU A 457 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 475 through 485
      removed outlier: 4.026A  pdb=" N   GLU A 479 " --> pdb=" O   GLN A 475 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 499 through 507
      removed outlier: 6.677A  pdb=" N   PHE A 504 " --> pdb=" O   ALA A 501 " (cutoff:3.500A)
      removed outlier: 6.140A  pdb=" N   HIS A 505 " --> pdb=" O   ALA A 502 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   VAL A 506 " --> pdb=" O   LEU A 503 " (cutoff:3.500A)
      removed outlier: 4.423A  pdb=" N   ALA A 507 " --> pdb=" O   PHE A 504 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 519 through 523
      removed outlier: 3.646A  pdb=" N   GLN A 522 " --> pdb=" O   THR A 519 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 524 through 527
    Processing helix  chain 'A' and resid 528 through 533
    Processing helix  chain 'A' and resid 547 through 555
      removed outlier: 3.946A  pdb=" N   GLY A 551 " --> pdb=" O   SER A 547 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   GLN A 552 " --> pdb=" O   ARG A 548 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 575
      removed outlier: 3.840A  pdb=" N   ALA A 569 " --> pdb=" O   PRO A 565 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   VAL A 573 " --> pdb=" O   ALA A 569 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 585 through 587
      No H-bonds generated for 'chain 'A' and resid 585 through 587'
    Processing helix  chain 'A' and resid 588 through 596
      removed outlier: 4.536A  pdb=" N   TRP A 594 " --> pdb=" O   PRO A 590 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 386 through 390
      removed outlier: 3.588A  pdb=" N   ASP B 389 " --> pdb=" O   LYS B 386 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   LEU B 390 " --> pdb=" O   LEU B 387 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 386 through 390'
    Processing helix  chain 'B' and resid 405 through 410
      removed outlier: 4.008A  pdb=" N   ARG B 408 " --> pdb=" O   ASP B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 416 through 422
    Processing helix  chain 'B' and resid 438 through 443
    Processing sheet with id=AA1, first strand: chain 'A' and resid 349 through 352
      removed outlier: 3.941A  pdb=" N   ARG A 357 " --> pdb=" O   TRP A 349 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   LEU A 351 " --> pdb=" O   ASP A 355 " (cutoff:3.500A)
      removed outlier: 5.751A  pdb=" N   ASP A 355 " --> pdb=" O   LEU A 351 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 396 through 403
      removed outlier: 3.898A  pdb=" N   ILE B 402 " --> pdb=" O   TYR B 508 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   TYR B 508 " --> pdb=" O   ILE B 402 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   LEU B 513 " --> pdb=" O   CYS B 432 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   CYS B 432 " --> pdb=" O   LEU B 513 " (cutoff:3.500A)

    173 hydrogen bonds defined for protein.
    468 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: 0.56

  Time building geometry restraints manager: 0.69 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2064
        1.34 -     1.46: 1660
        1.46 -     1.58: 2852
        1.58 -     1.70: 1
        1.70 -     1.82: 58
  Bond restraints: 6635
  Sorted by residual:
  bond pdb=" C1  NAG G   1 "
       pdb=" O5  NAG G   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.486 -0.080 2.00e-02 2.50e+03 1.59e+01
  bond pdb=" CB  PRO A 389 "
       pdb=" CG  PRO A 389 "
    ideal  model  delta    sigma   weight residual
    1.492  1.641 -0.149 5.00e-02 4.00e+02 8.92e+00
  bond pdb=" CG  PRO A 389 "
       pdb=" CD  PRO A 389 "
    ideal  model  delta    sigma   weight residual
    1.503  1.431  0.072 3.40e-02 8.65e+02 4.45e+00
  bond pdb=" CA  LYS A 441 "
       pdb=" CB  LYS A 441 "
    ideal  model  delta    sigma   weight residual
    1.526  1.559 -0.033 1.70e-02 3.46e+03 3.83e+00
  bond pdb=" N   PRO A 389 "
       pdb=" CA  PRO A 389 "
    ideal  model  delta    sigma   weight residual
    1.469  1.444  0.024 1.28e-02 6.10e+03 3.66e+00
  ... (remaining 6630 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.35: 8877
        3.35 -     6.69: 118
        6.69 -    10.04: 10
       10.04 -    13.38: 4
       13.38 -    16.73: 3
  Bond angle restraints: 9012
  Sorted by residual:
  angle pdb=" CA  PRO A 389 "
        pdb=" N   PRO A 389 "
        pdb=" CD  PRO A 389 "
      ideal   model   delta    sigma   weight residual
     112.00   95.27   16.73 1.40e+00 5.10e-01 1.43e+02
  angle pdb=" C   ALA A 212 "
        pdb=" N   ASP A 213 "
        pdb=" CA  ASP A 213 "
      ideal   model   delta    sigma   weight residual
     122.35  132.59  -10.24 1.46e+00 4.69e-01 4.92e+01
  angle pdb=" N   PRO A 389 "
        pdb=" CD  PRO A 389 "
        pdb=" CG  PRO A 389 "
      ideal   model   delta    sigma   weight residual
     103.20   94.54    8.66 1.50e+00 4.44e-01 3.33e+01
  angle pdb=" N   ILE A 544 "
        pdb=" CA  ILE A 544 "
        pdb=" C   ILE A 544 "
      ideal   model   delta    sigma   weight residual
     113.71  108.86    4.85 9.50e-01 1.11e+00 2.61e+01
  angle pdb=" CA  LEU A  45 "
        pdb=" CB  LEU A  45 "
        pdb=" CG  LEU A  45 "
      ideal   model   delta    sigma   weight residual
     116.30  132.29  -15.99 3.50e+00 8.16e-02 2.09e+01
  ... (remaining 9007 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.55: 3535
       23.55 -    47.09: 388
       47.09 -    70.64: 62
       70.64 -    94.19: 10
       94.19 -   117.74: 6
  Dihedral angle restraints: 4001
    sinusoidal: 1708
      harmonic: 2293
  Sorted by residual:
  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  168.30  -75.30     1      1.00e+01 1.00e-02 7.16e+01
  dihedral pdb=" CB  CYS A 344 "
           pdb=" SG  CYS A 344 "
           pdb=" SG  CYS A 361 "
           pdb=" CB  CYS A 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  167.32  -74.32     1      1.00e+01 1.00e-02 7.01e+01
  dihedral pdb=" CB  CYS B 379 "
           pdb=" SG  CYS B 379 "
           pdb=" SG  CYS B 432 "
           pdb=" CB  CYS B 432 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   44.83   48.17     1      1.00e+01 1.00e-02 3.20e+01
  ... (remaining 3998 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.077: 828
       0.077 -    0.154: 113
       0.154 -    0.231: 3
       0.231 -    0.308: 1
       0.308 -    0.385: 1
  Chirality restraints: 946
  Sorted by residual:
  chirality pdb=" C1  NAG H   1 "
            pdb=" ND2 ASN A 216 "
            pdb=" C2  NAG H   1 "
            pdb=" O5  NAG H   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.01   -0.39 2.00e-01 2.50e+01 3.71e+00
  chirality pdb=" CB  VAL A 318 "
            pdb=" CA  VAL A 318 "
            pdb=" CG1 VAL A 318 "
            pdb=" CG2 VAL A 318 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.40   -0.23 2.00e-01 2.50e+01 1.36e+00
  chirality pdb=" C1  NAG G   1 "
            pdb=" ND2 ASN A 322 "
            pdb=" C2  NAG G   1 "
            pdb=" O5  NAG G   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.21   -0.19 2.00e-01 2.50e+01 9.28e-01
  ... (remaining 943 not shown)

  Planarity restraints: 1168
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 388 "    0.144 5.00e-02 4.00e+02   2.00e-01 6.39e+01
        pdb=" N   PRO A 389 "   -0.344 5.00e-02 4.00e+02
        pdb=" CA  PRO A 389 "    0.113 5.00e-02 4.00e+02
        pdb=" CD  PRO A 389 "    0.087 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 168 "   -0.017 2.00e-02 2.50e+03   1.96e-02 9.57e+00
        pdb=" CG  TRP A 168 "    0.047 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 168 "   -0.033 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 168 "    0.009 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 168 "    0.010 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 168 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 168 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 168 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 168 "   -0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 168 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 564 "    0.047 5.00e-02 4.00e+02   7.12e-02 8.12e+00
        pdb=" N   PRO A 565 "   -0.123 5.00e-02 4.00e+02
        pdb=" CA  PRO A 565 "    0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO A 565 "    0.039 5.00e-02 4.00e+02
  ... (remaining 1165 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 191
        2.69 -     3.24: 6608
        3.24 -     3.79: 9892
        3.79 -     4.35: 12329
        4.35 -     4.90: 18650
  Nonbonded interactions: 47670
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 180 "
            pdb=" O   THR A 496 "
     model   vdw
     2.136 3.040
  nonbonded pdb=" O   ASN B 439 "
            pdb=" OG  SER B 443 "
     model   vdw
     2.226 3.040
  nonbonded pdb=" O   GLU A 166 "
            pdb=" OG  SER A 170 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" O   ARG A 305 "
            pdb=" NZ  LYS A 309 "
     model   vdw
     2.233 3.120
  nonbonded pdb=" NH2 ARG B 355 "
            pdb=" OD2 ASP B 398 "
     model   vdw
     2.239 3.120
  ... (remaining 47665 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'G' and resid 1)
  selection = (chain 'H' and resid 1)
}

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:             9.620
  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:             0.000
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.060
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.980
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4948
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      :  0.005   0.149   6647  Z= 0.209
  Angle     :  1.032  19.045   9042  Z= 0.540
  Chirality :  0.051   0.385    946
  Planarity :  0.009   0.200   1164
  Dihedral  : 19.217 117.737   2511
  Min Nonbonded Distance : 2.136

Molprobity Statistics.
  All-atom Clashscore : 16.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.87 %
    Favored  : 88.13 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  : 31.48 %
    Favored  : 67.94 %
  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 aren not related in a simple way.
  whole: -3.06 (0.28), residues: 775
  helix: -1.63 (0.31), residues: 257
  sheet:  2.48 (1.14), residues: 24
  loop : -2.66 (0.26), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 192 
 TYR   0.015   0.001   TYR A 510 
 PHE   0.020   0.002   PHE B 338 
 TRP   0.047   0.002   TRP A 168 
 HIS   0.008   0.001   HIS A 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00462 ( 6635)
  covalent geometry    : angle       1.00443 ( 9012)
  SS BOND              : bond        0.00539 (    6)
  SS BOND              : angle       1.15684 (   12)
  hydrogen bonds       : bond        0.15776 (  173)
  hydrogen bonds       : angle       6.45848 (  468)
  link_BETA1-4         : bond        0.00233 (    1)
  link_BETA1-4         : angle       1.35764 (    3)
  link_BETA1-6         : bond        0.00809 (    1)
  link_BETA1-6         : angle       1.93647 (    3)
  link_NAG-ASN         : bond        0.01295 (    4)
  link_NAG-ASN         : angle       6.53667 (   12)

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

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

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 126
  time to evaluate  : 0.236 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 LEU cc_start: 0.6107 (mt) cc_final: 0.5497 (mm)
REVERT: A   62 MET cc_start: 0.4429 (mpp) cc_final: 0.4110 (pmm)
REVERT: A  123 MET cc_start: -0.0391 (tpt) cc_final: -0.0686 (tpt)
REVERT: A  202 TYR cc_start: 0.7222 (m-10) cc_final: 0.6389 (t80)
REVERT: A  379 ILE cc_start: 0.8955 (tt) cc_final: 0.8682 (mm)
REVERT: A  382 ASP cc_start: 0.8908 (t70) cc_final: 0.8392 (p0)
REVERT: A  408 MET cc_start: 0.3341 (mmp) cc_final: 0.2562 (mmm)
REVERT: A  474 MET cc_start: -0.1394 (ptt) cc_final: -0.2041 (ptt)
REVERT: A  497 TYR cc_start: 0.6833 (OUTLIER) cc_final: 0.6258 (t80)
REVERT: A  539 LEU cc_start: 0.6118 (tp) cc_final: 0.5861 (mp)
  outliers start: 4
  outliers final: 1
  residues processed: 127
  average time/residue: 0.0754
  time to fit residues: 12.8155
Evaluate side-chains
  81 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 79
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  497 TYR
Chi-restraints excluded: chain B residue  512 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    0.7980
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
A 329 GLN
** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 474 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4529 r_free = 0.4529 target = 0.141411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4336 r_free = 0.4336 target = 0.123228 restraints weight = 42640.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4345 r_free = 0.4345 target = 0.125095 restraints weight = 34068.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4362 r_free = 0.4362 target = 0.126346 restraints weight = 28036.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4371 r_free = 0.4371 target = 0.127359 restraints weight = 23664.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4375 r_free = 0.4375 target = 0.127689 restraints weight = 21652.558|
|-----------------------------------------------------------------------------|
r_work (final): 0.4347
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5335
moved from start:          0.2423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6647  Z= 0.175
  Angle     :  0.853  18.219   9042  Z= 0.419
  Chirality :  0.052   0.529    946
  Planarity :  0.006   0.068   1164
  Dihedral  : 11.890 103.925    982
  Min Nonbonded Distance : 2.365

Molprobity Statistics.
  All-atom Clashscore : 16.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.61 %
    Favored  : 88.39 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 27.09 %
    Favored  : 68.23 %
  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 aren not related in a simple way.
  whole: -2.82 (0.30), residues: 775
  helix: -1.32 (0.32), residues: 264
  sheet:  0.80 (1.07), residues: 28
  loop : -2.49 (0.28), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 115 
 TYR   0.019   0.002   TYR A 180 
 PHE   0.021   0.002   PHE B 490 
 TRP   0.021   0.002   TRP A 168 
 HIS   0.006   0.001   HIS A 417 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 6635)
  covalent geometry    : angle       0.82073 ( 9012)
  SS BOND              : bond        0.00340 (    6)
  SS BOND              : angle       1.53377 (   12)
  hydrogen bonds       : bond        0.04066 (  173)
  hydrogen bonds       : angle       5.94080 (  468)
  link_BETA1-4         : bond        0.00172 (    1)
  link_BETA1-4         : angle       1.67190 (    3)
  link_BETA1-6         : bond        0.01170 (    1)
  link_BETA1-6         : angle       2.70416 (    3)
  link_NAG-ASN         : bond        0.01281 (    4)
  link_NAG-ASN         : angle       6.13940 (   12)

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

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

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 92
  time to evaluate  : 0.252 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.4771 (mpp) cc_final: 0.4545 (pmm)
REVERT: A   92 ILE cc_start: 0.7157 (mm) cc_final: 0.6932 (mt)
REVERT: A  211 TRP cc_start: 0.5647 (p90) cc_final: 0.3274 (m100)
REVERT: A  252 TYR cc_start: 0.3142 (OUTLIER) cc_final: 0.2199 (p90)
REVERT: A  279 TYR cc_start: 0.5712 (OUTLIER) cc_final: 0.5045 (m-10)
REVERT: A  345 HIS cc_start: 0.8305 (OUTLIER) cc_final: 0.7613 (t70)
REVERT: A  376 MET cc_start: 0.8981 (tpt) cc_final: 0.8230 (ptt)
REVERT: A  382 ASP cc_start: 0.9189 (t70) cc_final: 0.8531 (p0)
REVERT: A  417 HIS cc_start: 0.8981 (t-90) cc_final: 0.8714 (t-90)
REVERT: A  462 MET cc_start: 0.7531 (ppp) cc_final: 0.7092 (ppp)
REVERT: A  474 MET cc_start: -0.0906 (ptt) cc_final: -0.1429 (ptt)
REVERT: A  579 MET cc_start: 0.6850 (ppp) cc_final: 0.5583 (ppp)
REVERT: B  410 ILE cc_start: 0.8033 (mm) cc_final: 0.7593 (mm)
  outliers start: 32
  outliers final: 14
  residues processed: 117
  average time/residue: 0.0773
  time to fit residues: 12.1079
Evaluate side-chains
  94 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 77
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 TYR
Chi-restraints excluded: chain A residue  125 THR
Chi-restraints excluded: chain A residue  252 TYR
Chi-restraints excluded: chain A residue  279 TYR
Chi-restraints excluded: chain A residue  345 HIS
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  400 PHE
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain B residue  380 TYR
Chi-restraints excluded: chain B residue  418 ILE
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  456 PHE
Chi-restraints excluded: chain B residue  460 ASN
Chi-restraints excluded: chain B residue  480 CYS
Chi-restraints excluded: chain B residue  486 PHE
Chi-restraints excluded: chain B residue  512 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 42 optimal weight:    0.9990
   chunk 54 optimal weight:    0.4980
   chunk 17 optimal weight:    0.0020
   chunk 64 optimal weight:    2.9990
   chunk 37 optimal weight:    0.6980
   chunk 62 optimal weight:    3.9990
   chunk 31 optimal weight:    0.0870
   chunk 9 optimal weight:    0.0570
   chunk 34 optimal weight:    0.9980
   chunk 18 optimal weight:    2.9990
   chunk 24 optimal weight:    0.0980
   overall best weight:    0.1484

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

Flipped N/Q/H residues before XYZ refinement:
** A 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 598 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4560 r_free = 0.4560 target = 0.144402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4376 r_free = 0.4376 target = 0.126302 restraints weight = 41677.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4380 r_free = 0.4380 target = 0.127691 restraints weight = 34754.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4392 r_free = 0.4392 target = 0.128637 restraints weight = 29336.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4400 r_free = 0.4400 target = 0.129248 restraints weight = 25563.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4406 r_free = 0.4406 target = 0.129850 restraints weight = 23296.454|
|-----------------------------------------------------------------------------|
r_work (final): 0.4370
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5231
moved from start:          0.2836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6647  Z= 0.138
  Angle     :  0.792  18.485   9042  Z= 0.383
  Chirality :  0.050   0.496    946
  Planarity :  0.006   0.066   1164
  Dihedral  : 10.814 100.689    980
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 14.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.32 %
    Favored  : 89.68 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 27.53 %
    Favored  : 68.37 %
  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 aren not related in a simple way.
  whole: -2.51 (0.30), residues: 775
  helix: -0.88 (0.34), residues: 245
  sheet:  1.48 (1.09), residues: 24
  loop : -2.39 (0.28), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 255 
 TYR   0.014   0.001   TYR A 217 
 PHE   0.016   0.002   PHE A  72 
 TRP   0.021   0.001   TRP A 168 
 HIS   0.006   0.001   HIS A 417 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 6635)
  covalent geometry    : angle       0.75749 ( 9012)
  SS BOND              : bond        0.00375 (    6)
  SS BOND              : angle       1.15774 (   12)
  hydrogen bonds       : bond        0.03769 (  173)
  hydrogen bonds       : angle       5.81142 (  468)
  link_BETA1-4         : bond        0.00111 (    1)
  link_BETA1-4         : angle       1.61728 (    3)
  link_BETA1-6         : bond        0.01340 (    1)
  link_BETA1-6         : angle       2.47989 (    3)
  link_NAG-ASN         : bond        0.01368 (    4)
  link_NAG-ASN         : angle       6.20156 (   12)

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

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

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 84
  time to evaluate  : 0.241 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 LYS cc_start: -0.0662 (OUTLIER) cc_final: -0.1319 (pttm)
REVERT: A  150 ASP cc_start: 0.9054 (p0) cc_final: 0.8121 (t0)
REVERT: A  171 GLU cc_start: 0.9033 (pp20) cc_final: 0.8602 (pm20)
REVERT: A  252 TYR cc_start: 0.2599 (OUTLIER) cc_final: 0.1818 (p90)
REVERT: A  279 TYR cc_start: 0.5601 (OUTLIER) cc_final: 0.4869 (m-10)
REVERT: A  345 HIS cc_start: 0.8128 (OUTLIER) cc_final: 0.7520 (t70)
REVERT: A  376 MET cc_start: 0.8994 (tpt) cc_final: 0.8032 (ptp)
REVERT: A  381 TYR cc_start: 0.5851 (OUTLIER) cc_final: 0.4204 (p90)
REVERT: A  382 ASP cc_start: 0.9166 (t70) cc_final: 0.8341 (p0)
REVERT: A  398 GLU cc_start: 0.8251 (pm20) cc_final: 0.8031 (pm20)
REVERT: A  400 PHE cc_start: 0.8310 (OUTLIER) cc_final: 0.7711 (t80)
REVERT: A  462 MET cc_start: 0.7423 (ppp) cc_final: 0.6952 (ppp)
REVERT: A  579 MET cc_start: 0.6834 (ppp) cc_final: 0.6054 (ppp)
  outliers start: 28
  outliers final: 18
  residues processed: 103
  average time/residue: 0.0680
  time to fit residues: 9.3927
Evaluate side-chains
  98 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 74
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LYS
Chi-restraints excluded: chain A residue   83 TYR
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  231 THR
Chi-restraints excluded: chain A residue  252 TYR
Chi-restraints excluded: chain A residue  279 TYR
Chi-restraints excluded: chain A residue  345 HIS
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  381 TYR
Chi-restraints excluded: chain A residue  383 MET
Chi-restraints excluded: chain A residue  400 PHE
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  514 ARG
Chi-restraints excluded: chain A residue  542 CYS
Chi-restraints excluded: chain B residue  380 TYR
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  418 ILE
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  456 PHE
Chi-restraints excluded: chain B residue  460 ASN
Chi-restraints excluded: chain B residue  480 CYS
Chi-restraints excluded: chain B residue  511 VAL
Chi-restraints excluded: chain B residue  512 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 32 optimal weight:    0.9980
   chunk 46 optimal weight:    0.7980
   chunk 15 optimal weight:    2.9990
   chunk 61 optimal weight:    0.8980
   chunk 41 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9980
   chunk 25 optimal weight:    3.9990
   chunk 73 optimal weight:    0.5980
   chunk 28 optimal weight:    2.9990
   chunk 8 optimal weight:    4.9990
   chunk 24 optimal weight:    0.1980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 474 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4529 r_free = 0.4529 target = 0.141302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.122835 restraints weight = 42087.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4340 r_free = 0.4340 target = 0.124906 restraints weight = 33753.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4352 r_free = 0.4352 target = 0.125977 restraints weight = 27623.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4360 r_free = 0.4360 target = 0.126586 restraints weight = 23798.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4364 r_free = 0.4364 target = 0.126977 restraints weight = 22100.067|
|-----------------------------------------------------------------------------|
r_work (final): 0.4343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5354
moved from start:          0.3669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6647  Z= 0.149
  Angle     :  0.785  17.755   9042  Z= 0.382
  Chirality :  0.050   0.517    946
  Planarity :  0.006   0.063   1164
  Dihedral  : 10.232  90.709    980
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 16.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.87 %
    Favored  : 88.13 %
  Rotamer:
    Outliers :  5.27 %
    Allowed  : 27.82 %
    Favored  : 66.91 %
  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 aren not related in a simple way.
  whole: -2.45 (0.30), residues: 775
  helix: -0.98 (0.34), residues: 253
  sheet:  1.52 (1.09), residues: 24
  loop : -2.28 (0.28), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 482 
 TYR   0.016   0.002   TYR A 515 
 PHE   0.026   0.002   PHE A 438 
 TRP   0.023   0.002   TRP A 566 
 HIS   0.007   0.001   HIS A 555 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 6635)
  covalent geometry    : angle       0.74947 ( 9012)
  SS BOND              : bond        0.00294 (    6)
  SS BOND              : angle       0.92226 (   12)
  hydrogen bonds       : bond        0.03622 (  173)
  hydrogen bonds       : angle       5.87166 (  468)
  link_BETA1-4         : bond        0.00238 (    1)
  link_BETA1-4         : angle       1.89252 (    3)
  link_BETA1-6         : bond        0.01148 (    1)
  link_BETA1-6         : angle       3.08136 (    3)
  link_NAG-ASN         : bond        0.01285 (    4)
  link_NAG-ASN         : angle       6.15053 (   12)

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

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

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 79
  time to evaluate  : 0.153 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   79 HIS cc_start: 0.7350 (m-70) cc_final: 0.7056 (t-90)
REVERT: A  171 GLU cc_start: 0.9208 (pp20) cc_final: 0.8835 (pm20)
REVERT: A  211 TRP cc_start: 0.5653 (p90) cc_final: 0.3452 (m100)
REVERT: A  252 TYR cc_start: 0.3067 (OUTLIER) cc_final: 0.2540 (p90)
REVERT: A  279 TYR cc_start: 0.6002 (OUTLIER) cc_final: 0.4920 (m-10)
REVERT: A  345 HIS cc_start: 0.8233 (OUTLIER) cc_final: 0.7745 (t70)
REVERT: A  376 MET cc_start: 0.8999 (tpt) cc_final: 0.8053 (ptp)
REVERT: A  381 TYR cc_start: 0.5810 (OUTLIER) cc_final: 0.4019 (p90)
REVERT: A  382 ASP cc_start: 0.9143 (t70) cc_final: 0.8333 (p0)
REVERT: A  400 PHE cc_start: 0.8298 (OUTLIER) cc_final: 0.7884 (t80)
REVERT: A  462 MET cc_start: 0.7556 (ppp) cc_final: 0.7180 (ppp)
REVERT: A  497 TYR cc_start: 0.7004 (t80) cc_final: 0.6803 (t80)
REVERT: A  579 MET cc_start: 0.7027 (ppp) cc_final: 0.5557 (tpp)
REVERT: B  410 ILE cc_start: 0.7979 (mm) cc_final: 0.7622 (mm)
REVERT: B  486 PHE cc_start: 0.6933 (OUTLIER) cc_final: 0.6437 (t80)
  outliers start: 36
  outliers final: 24
  residues processed: 105
  average time/residue: 0.0758
  time to fit residues: 10.4728
Evaluate side-chains
  101 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 71
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 LEU
Chi-restraints excluded: chain A residue   61 LYS
Chi-restraints excluded: chain A residue   83 TYR
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  231 THR
Chi-restraints excluded: chain A residue  252 TYR
Chi-restraints excluded: chain A residue  279 TYR
Chi-restraints excluded: chain A residue  345 HIS
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  381 TYR
Chi-restraints excluded: chain A residue  383 MET
Chi-restraints excluded: chain A residue  400 PHE
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  503 LEU
Chi-restraints excluded: chain A residue  514 ARG
Chi-restraints excluded: chain A residue  520 ILE
Chi-restraints excluded: chain B residue  380 TYR
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  418 ILE
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  456 PHE
Chi-restraints excluded: chain B residue  460 ASN
Chi-restraints excluded: chain B residue  464 PHE
Chi-restraints excluded: chain B residue  472 ILE
Chi-restraints excluded: chain B residue  480 CYS
Chi-restraints excluded: chain B residue  486 PHE
Chi-restraints excluded: chain B residue  511 VAL
Chi-restraints excluded: chain B residue  512 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 58 optimal weight:    0.8980
   chunk 9 optimal weight:    0.8980
   chunk 56 optimal weight:    0.7980
   chunk 32 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9990
   chunk 35 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 17 optimal weight:    0.0000
   chunk 47 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9990
   overall best weight:    0.6984

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

Flipped N/Q/H residues before XYZ refinement:
** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4527 r_free = 0.4527 target = 0.140488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4367 r_free = 0.4367 target = 0.126048 restraints weight = 41383.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4366 r_free = 0.4366 target = 0.126885 restraints weight = 36462.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4373 r_free = 0.4373 target = 0.127320 restraints weight = 33415.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4379 r_free = 0.4379 target = 0.127764 restraints weight = 30691.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4384 r_free = 0.4384 target = 0.128251 restraints weight = 28211.003|
|-----------------------------------------------------------------------------|
r_work (final): 0.4357
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5428
moved from start:          0.4375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6647  Z= 0.148
  Angle     :  0.798  19.446   9042  Z= 0.386
  Chirality :  0.049   0.498    946
  Planarity :  0.006   0.061   1164
  Dihedral  :  9.103  77.268    980
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 16.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.35 %
    Favored  : 88.65 %
  Rotamer:
    Outliers :  6.00 %
    Allowed  : 27.53 %
    Favored  : 66.47 %
  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 aren not related in a simple way.
  whole: -2.43 (0.30), residues: 775
  helix: -1.01 (0.34), residues: 247
  sheet:  1.49 (1.03), residues: 24
  loop : -2.23 (0.28), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 204 
 TYR   0.016   0.002   TYR A 515 
 PHE   0.042   0.002   PHE A  72 
 TRP   0.025   0.002   TRP A 566 
 HIS   0.007   0.001   HIS A 555 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 6635)
  covalent geometry    : angle       0.76243 ( 9012)
  SS BOND              : bond        0.00300 (    6)
  SS BOND              : angle       0.93782 (   12)
  hydrogen bonds       : bond        0.03613 (  173)
  hydrogen bonds       : angle       5.94631 (  468)
  link_BETA1-4         : bond        0.00199 (    1)
  link_BETA1-4         : angle       1.96340 (    3)
  link_BETA1-6         : bond        0.01364 (    1)
  link_BETA1-6         : angle       2.51418 (    3)
  link_NAG-ASN         : bond        0.01295 (    4)
  link_NAG-ASN         : angle       6.27122 (   12)

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

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

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 74
  time to evaluate  : 0.194 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  171 GLU cc_start: 0.9042 (pp20) cc_final: 0.8751 (pm20)
REVERT: A  252 TYR cc_start: 0.3663 (OUTLIER) cc_final: 0.2940 (p90)
REVERT: A  279 TYR cc_start: 0.6077 (OUTLIER) cc_final: 0.4891 (m-10)
REVERT: A  323 MET cc_start: -0.0570 (mmt) cc_final: -0.1765 (mmt)
REVERT: A  328 TRP cc_start: 0.6736 (m100) cc_final: 0.5770 (m-90)
REVERT: A  345 HIS cc_start: 0.8195 (OUTLIER) cc_final: 0.7704 (t70)
REVERT: A  376 MET cc_start: 0.8869 (tpt) cc_final: 0.7919 (ptp)
REVERT: A  381 TYR cc_start: 0.5638 (OUTLIER) cc_final: 0.3715 (p90)
REVERT: A  382 ASP cc_start: 0.9058 (t70) cc_final: 0.8285 (p0)
REVERT: A  400 PHE cc_start: 0.8186 (OUTLIER) cc_final: 0.7790 (t80)
REVERT: A  462 MET cc_start: 0.7387 (ppp) cc_final: 0.7118 (ppp)
REVERT: A  464 PHE cc_start: 0.2392 (OUTLIER) cc_final: -0.0691 (t80)
REVERT: A  579 MET cc_start: 0.7066 (ppp) cc_final: 0.6496 (ppp)
REVERT: B  484 GLU cc_start: 0.6557 (tm-30) cc_final: 0.6229 (tm-30)
REVERT: B  486 PHE cc_start: 0.6943 (OUTLIER) cc_final: 0.6569 (t80)
  outliers start: 41
  outliers final: 24
  residues processed: 106
  average time/residue: 0.0811
  time to fit residues: 11.4302
Evaluate side-chains
  96 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 65
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 LEU
Chi-restraints excluded: chain A residue   61 LYS
Chi-restraints excluded: chain A residue   83 TYR
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  231 THR
Chi-restraints excluded: chain A residue  252 TYR
Chi-restraints excluded: chain A residue  279 TYR
Chi-restraints excluded: chain A residue  345 HIS
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  381 TYR
Chi-restraints excluded: chain A residue  400 PHE
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  464 PHE
Chi-restraints excluded: chain A residue  487 VAL
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  503 LEU
Chi-restraints excluded: chain A residue  513 ILE
Chi-restraints excluded: chain A residue  520 ILE
Chi-restraints excluded: chain A residue  542 CYS
Chi-restraints excluded: chain B residue  380 TYR
Chi-restraints excluded: chain B residue  418 ILE
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  456 PHE
Chi-restraints excluded: chain B residue  460 ASN
Chi-restraints excluded: chain B residue  464 PHE
Chi-restraints excluded: chain B residue  472 ILE
Chi-restraints excluded: chain B residue  486 PHE
Chi-restraints excluded: chain B residue  511 VAL
Chi-restraints excluded: chain B residue  512 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 14 optimal weight:    0.8980
   chunk 11 optimal weight:    0.0000
   chunk 56 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 55 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 73 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9980
   chunk 51 optimal weight:    0.2980
   overall best weight:    0.6384

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

Flipped N/Q/H residues before XYZ refinement:
** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 526 GLN
** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4522 r_free = 0.4522 target = 0.139803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4311 r_free = 0.4311 target = 0.121334 restraints weight = 42906.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4330 r_free = 0.4330 target = 0.123300 restraints weight = 34026.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4339 r_free = 0.4339 target = 0.124261 restraints weight = 28566.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4349 r_free = 0.4349 target = 0.125021 restraints weight = 24463.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4354 r_free = 0.4354 target = 0.125482 restraints weight = 22324.238|
|-----------------------------------------------------------------------------|
r_work (final): 0.4333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5470
moved from start:          0.4844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6647  Z= 0.143
  Angle     :  0.796  18.109   9042  Z= 0.385
  Chirality :  0.049   0.510    946
  Planarity :  0.006   0.069   1164
  Dihedral  :  8.179  60.689    980
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 16.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.35 %
    Favored  : 88.65 %
  Rotamer:
    Outliers :  5.71 %
    Allowed  : 29.14 %
    Favored  : 65.15 %
  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 aren not related in a simple way.
  whole: -2.45 (0.30), residues: 775
  helix: -0.97 (0.34), residues: 249
  sheet:  1.17 (0.99), residues: 27
  loop : -2.28 (0.28), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B 403 
 TYR   0.016   0.002   TYR A 521 
 PHE   0.011   0.002   PHE B 515 
 TRP   0.027   0.002   TRP A 566 
 HIS   0.006   0.001   HIS A 555 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 6635)
  covalent geometry    : angle       0.75733 ( 9012)
  SS BOND              : bond        0.00481 (    6)
  SS BOND              : angle       1.80532 (   12)
  hydrogen bonds       : bond        0.03457 (  173)
  hydrogen bonds       : angle       5.93876 (  468)
  link_BETA1-4         : bond        0.00514 (    1)
  link_BETA1-4         : angle       1.76493 (    3)
  link_BETA1-6         : bond        0.01066 (    1)
  link_BETA1-6         : angle       3.12385 (    3)
  link_NAG-ASN         : bond        0.01336 (    4)
  link_NAG-ASN         : angle       6.38528 (   12)

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

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

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 72
  time to evaluate  : 0.150 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 MET cc_start: -0.0668 (tpt) cc_final: -0.1229 (tpt)
REVERT: A  171 GLU cc_start: 0.9199 (pp20) cc_final: 0.8916 (pm20)
REVERT: A  252 TYR cc_start: 0.4067 (OUTLIER) cc_final: 0.2991 (p90)
REVERT: A  279 TYR cc_start: 0.6090 (OUTLIER) cc_final: 0.4816 (m-10)
REVERT: A  323 MET cc_start: -0.0615 (mmt) cc_final: -0.2093 (mmt)
REVERT: A  376 MET cc_start: 0.8890 (OUTLIER) cc_final: 0.7928 (ptp)
REVERT: A  378 HIS cc_start: 0.7200 (OUTLIER) cc_final: 0.6611 (t-90)
REVERT: A  381 TYR cc_start: 0.5749 (OUTLIER) cc_final: 0.3923 (p90)
REVERT: A  462 MET cc_start: 0.7457 (ppp) cc_final: 0.7213 (ppp)
REVERT: A  579 MET cc_start: 0.7295 (ppp) cc_final: 0.6754 (ppp)
  outliers start: 39
  outliers final: 25
  residues processed: 101
  average time/residue: 0.0694
  time to fit residues: 9.3913
Evaluate side-chains
  92 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 62
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 LEU
Chi-restraints excluded: chain A residue   61 LYS
Chi-restraints excluded: chain A residue   83 TYR
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  252 TYR
Chi-restraints excluded: chain A residue  279 TYR
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  376 MET
Chi-restraints excluded: chain A residue  378 HIS
Chi-restraints excluded: chain A residue  381 TYR
Chi-restraints excluded: chain A residue  383 MET
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  474 MET
Chi-restraints excluded: chain A residue  487 VAL
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  503 LEU
Chi-restraints excluded: chain A residue  514 ARG
Chi-restraints excluded: chain A residue  573 VAL
Chi-restraints excluded: chain B residue  380 TYR
Chi-restraints excluded: chain B residue  418 ILE
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  456 PHE
Chi-restraints excluded: chain B residue  460 ASN
Chi-restraints excluded: chain B residue  464 PHE
Chi-restraints excluded: chain B residue  472 ILE
Chi-restraints excluded: chain B residue  511 VAL
Chi-restraints excluded: chain B residue  512 VAL
Chi-restraints excluded: chain B residue  528 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 62 optimal weight:    0.6980
   chunk 15 optimal weight:    1.9990
   chunk 64 optimal weight:    2.9990
   chunk 46 optimal weight:    0.7980
   chunk 14 optimal weight:    0.5980
   chunk 40 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9990
   chunk 31 optimal weight:    0.0870
   chunk 16 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9980
   chunk 5 optimal weight:    0.6980
   overall best weight:    0.5758

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

Flipped N/Q/H residues before XYZ refinement:
A 220 ASN
** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4514 r_free = 0.4514 target = 0.139538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4309 r_free = 0.4309 target = 0.121532 restraints weight = 42017.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4328 r_free = 0.4328 target = 0.123628 restraints weight = 33633.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4339 r_free = 0.4339 target = 0.124553 restraints weight = 28314.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4347 r_free = 0.4347 target = 0.125214 restraints weight = 23682.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4352 r_free = 0.4352 target = 0.125610 restraints weight = 21978.607|
|-----------------------------------------------------------------------------|
r_work (final): 0.4334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5486
moved from start:          0.5343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6647  Z= 0.138
  Angle     :  0.779  17.995   9042  Z= 0.377
  Chirality :  0.048   0.490    946
  Planarity :  0.005   0.064   1164
  Dihedral  :  7.158  53.616    980
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 16.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.97 %
    Favored  : 89.03 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 29.28 %
    Favored  : 65.15 %
  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 aren not related in a simple way.
  whole: -2.38 (0.31), residues: 775
  helix: -0.88 (0.35), residues: 249
  sheet:  1.28 (0.97), residues: 27
  loop : -2.25 (0.28), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 403 
 TYR   0.014   0.002   TYR B 423 
 PHE   0.011   0.002   PHE B 515 
 TRP   0.043   0.002   TRP A 328 
 HIS   0.006   0.001   HIS A 555 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 6635)
  covalent geometry    : angle       0.73901 ( 9012)
  SS BOND              : bond        0.00338 (    6)
  SS BOND              : angle       1.39904 (   12)
  hydrogen bonds       : bond        0.03435 (  173)
  hydrogen bonds       : angle       5.92311 (  468)
  link_BETA1-4         : bond        0.01033 (    1)
  link_BETA1-4         : angle       1.80605 (    3)
  link_BETA1-6         : bond        0.01205 (    1)
  link_BETA1-6         : angle       2.77606 (    3)
  link_NAG-ASN         : bond        0.01264 (    4)
  link_NAG-ASN         : angle       6.54589 (   12)

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

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

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 72
  time to evaluate  : 0.180 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  171 GLU cc_start: 0.9128 (pp20) cc_final: 0.8816 (pm20)
REVERT: A  252 TYR cc_start: 0.3977 (OUTLIER) cc_final: 0.3019 (p90)
REVERT: A  279 TYR cc_start: 0.6163 (OUTLIER) cc_final: 0.4918 (m-10)
REVERT: A  332 MET cc_start: 0.7826 (pmm) cc_final: 0.6750 (tpp)
REVERT: A  376 MET cc_start: 0.8898 (tpt) cc_final: 0.7985 (ptp)
REVERT: A  378 HIS cc_start: 0.7262 (OUTLIER) cc_final: 0.6545 (t-90)
REVERT: A  381 TYR cc_start: 0.5680 (OUTLIER) cc_final: 0.3798 (p90)
REVERT: A  382 ASP cc_start: 0.8967 (t70) cc_final: 0.8399 (t0)
REVERT: A  462 MET cc_start: 0.7503 (ppp) cc_final: 0.7216 (ppp)
REVERT: A  579 MET cc_start: 0.7400 (ppp) cc_final: 0.6829 (ppp)
  outliers start: 38
  outliers final: 30
  residues processed: 102
  average time/residue: 0.0636
  time to fit residues: 8.9705
Evaluate side-chains
  97 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 63
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 LEU
Chi-restraints excluded: chain A residue   27 THR
Chi-restraints excluded: chain A residue   61 LYS
Chi-restraints excluded: chain A residue   83 TYR
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  231 THR
Chi-restraints excluded: chain A residue  252 TYR
Chi-restraints excluded: chain A residue  279 TYR
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  378 HIS
Chi-restraints excluded: chain A residue  381 TYR
Chi-restraints excluded: chain A residue  383 MET
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  474 MET
Chi-restraints excluded: chain A residue  487 VAL
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  503 LEU
Chi-restraints excluded: chain A residue  513 ILE
Chi-restraints excluded: chain A residue  514 ARG
Chi-restraints excluded: chain A residue  539 LEU
Chi-restraints excluded: chain A residue  573 VAL
Chi-restraints excluded: chain B residue  380 TYR
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  418 ILE
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  456 PHE
Chi-restraints excluded: chain B residue  460 ASN
Chi-restraints excluded: chain B residue  464 PHE
Chi-restraints excluded: chain B residue  472 ILE
Chi-restraints excluded: chain B residue  511 VAL
Chi-restraints excluded: chain B residue  512 VAL
Chi-restraints excluded: chain B residue  528 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 39 optimal weight:    0.7980
   chunk 17 optimal weight:    0.7980
   chunk 32 optimal weight:    7.9990
   chunk 55 optimal weight:    0.5980
   chunk 0 optimal weight:    3.9990
   chunk 14 optimal weight:    0.1980
   chunk 15 optimal weight:    0.0470
   chunk 38 optimal weight:    0.8980
   chunk 47 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 1 optimal weight:    3.9990
   overall best weight:    0.4878

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

Flipped N/Q/H residues before XYZ refinement:
A 373 HIS
** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4513 r_free = 0.4513 target = 0.139366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4315 r_free = 0.4315 target = 0.121310 restraints weight = 42031.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4332 r_free = 0.4332 target = 0.123241 restraints weight = 33463.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4343 r_free = 0.4343 target = 0.124080 restraints weight = 28602.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4349 r_free = 0.4349 target = 0.124725 restraints weight = 24359.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4355 r_free = 0.4355 target = 0.125170 restraints weight = 22503.455|
|-----------------------------------------------------------------------------|
r_work (final): 0.4334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5595
moved from start:          0.5593

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6647  Z= 0.133
  Angle     :  0.757  17.472   9042  Z= 0.368
  Chirality :  0.048   0.491    946
  Planarity :  0.005   0.065   1164
  Dihedral  :  6.775  53.217    980
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 16.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.35 %
    Favored  : 88.65 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 28.99 %
    Favored  : 65.45 %
  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 aren not related in a simple way.
  whole: -2.37 (0.31), residues: 775
  helix: -0.83 (0.35), residues: 249
  sheet:  1.21 (0.97), residues: 27
  loop : -2.27 (0.28), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 403 
 TYR   0.012   0.001   TYR A 515 
 PHE   0.011   0.001   PHE B 515 
 TRP   0.032   0.002   TRP A 566 
 HIS   0.006   0.001   HIS A 555 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 6635)
  covalent geometry    : angle       0.71750 ( 9012)
  SS BOND              : bond        0.00323 (    6)
  SS BOND              : angle       1.29109 (   12)
  hydrogen bonds       : bond        0.03374 (  173)
  hydrogen bonds       : angle       5.89660 (  468)
  link_BETA1-4         : bond        0.00687 (    1)
  link_BETA1-4         : angle       1.09954 (    3)
  link_BETA1-6         : bond        0.00964 (    1)
  link_BETA1-6         : angle       2.91148 (    3)
  link_NAG-ASN         : bond        0.01267 (    4)
  link_NAG-ASN         : angle       6.38887 (   12)

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

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

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 69
  time to evaluate  : 0.233 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  171 GLU cc_start: 0.9258 (pp20) cc_final: 0.8954 (pm20)
REVERT: A  252 TYR cc_start: 0.4391 (OUTLIER) cc_final: 0.3326 (p90)
REVERT: A  279 TYR cc_start: 0.6264 (OUTLIER) cc_final: 0.4997 (m-10)
REVERT: A  332 MET cc_start: 0.7832 (pmm) cc_final: 0.6556 (tpp)
REVERT: A  376 MET cc_start: 0.8924 (OUTLIER) cc_final: 0.8011 (ptp)
REVERT: A  381 TYR cc_start: 0.5633 (OUTLIER) cc_final: 0.3107 (p90)
REVERT: A  382 ASP cc_start: 0.8941 (t70) cc_final: 0.8405 (t0)
REVERT: A  462 MET cc_start: 0.7528 (ppp) cc_final: 0.7256 (ppp)
REVERT: A  464 PHE cc_start: 0.2009 (OUTLIER) cc_final: -0.1533 (t80)
REVERT: A  579 MET cc_start: 0.7472 (ppp) cc_final: 0.6896 (ppp)
  outliers start: 38
  outliers final: 32
  residues processed: 98
  average time/residue: 0.0602
  time to fit residues: 8.0478
Evaluate side-chains
  101 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 64
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 LEU
Chi-restraints excluded: chain A residue   27 THR
Chi-restraints excluded: chain A residue   61 LYS
Chi-restraints excluded: chain A residue   83 TYR
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  231 THR
Chi-restraints excluded: chain A residue  252 TYR
Chi-restraints excluded: chain A residue  256 ILE
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  279 TYR
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  376 MET
Chi-restraints excluded: chain A residue  381 TYR
Chi-restraints excluded: chain A residue  383 MET
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  464 PHE
Chi-restraints excluded: chain A residue  474 MET
Chi-restraints excluded: chain A residue  487 VAL
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  503 LEU
Chi-restraints excluded: chain A residue  513 ILE
Chi-restraints excluded: chain A residue  514 ARG
Chi-restraints excluded: chain A residue  539 LEU
Chi-restraints excluded: chain A residue  573 VAL
Chi-restraints excluded: chain B residue  380 TYR
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  418 ILE
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  456 PHE
Chi-restraints excluded: chain B residue  460 ASN
Chi-restraints excluded: chain B residue  464 PHE
Chi-restraints excluded: chain B residue  511 VAL
Chi-restraints excluded: chain B residue  512 VAL
Chi-restraints excluded: chain B residue  528 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 9 optimal weight:    5.9990
   chunk 29 optimal weight:    0.5980
   chunk 76 optimal weight:    0.9990
   chunk 47 optimal weight:    4.9990
   chunk 41 optimal weight:    0.0050
   chunk 16 optimal weight:    2.9990
   chunk 65 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 62 optimal weight:    0.6980
   chunk 73 optimal weight:    0.7980
   chunk 39 optimal weight:    4.9990
   overall best weight:    0.6196

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

Flipped N/Q/H residues before XYZ refinement:
** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4504 r_free = 0.4504 target = 0.138349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.120275 restraints weight = 42943.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.122409 restraints weight = 33800.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4335 r_free = 0.4335 target = 0.123395 restraints weight = 28125.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4341 r_free = 0.4341 target = 0.124033 restraints weight = 23894.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4347 r_free = 0.4347 target = 0.124529 restraints weight = 21833.386|
|-----------------------------------------------------------------------------|
r_work (final): 0.4329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5574
moved from start:          0.5927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6647  Z= 0.138
  Angle     :  0.770  17.869   9042  Z= 0.375
  Chirality :  0.049   0.493    946
  Planarity :  0.006   0.066   1164
  Dihedral  :  6.797  53.672    980
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 17.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.35 %
    Favored  : 88.65 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 29.87 %
    Favored  : 64.57 %
  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 aren not related in a simple way.
  whole: -2.42 (0.30), residues: 775
  helix: -0.86 (0.34), residues: 249
  sheet:  1.02 (0.98), residues: 27
  loop : -2.30 (0.28), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 403 
 TYR   0.013   0.002   TYR A 515 
 PHE   0.011   0.002   PHE A 452 
 TRP   0.043   0.002   TRP A 328 
 HIS   0.007   0.001   HIS A 555 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 6635)
  covalent geometry    : angle       0.73433 ( 9012)
  SS BOND              : bond        0.00387 (    6)
  SS BOND              : angle       1.22212 (   12)
  hydrogen bonds       : bond        0.03553 (  173)
  hydrogen bonds       : angle       5.93800 (  468)
  link_BETA1-4         : bond        0.00429 (    1)
  link_BETA1-4         : angle       0.93251 (    3)
  link_BETA1-6         : bond        0.00565 (    1)
  link_BETA1-6         : angle       2.81453 (    3)
  link_NAG-ASN         : bond        0.01267 (    4)
  link_NAG-ASN         : angle       6.18126 (   12)

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

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

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 66
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  155 SER cc_start: 0.6279 (t) cc_final: 0.5946 (m)
REVERT: A  171 GLU cc_start: 0.9101 (pp20) cc_final: 0.8816 (pm20)
REVERT: A  172 VAL cc_start: 0.8610 (t) cc_final: 0.7948 (t)
REVERT: A  252 TYR cc_start: 0.4408 (OUTLIER) cc_final: 0.3488 (p90)
REVERT: A  279 TYR cc_start: 0.6337 (OUTLIER) cc_final: 0.4945 (m-10)
REVERT: A  332 MET cc_start: 0.7736 (pmm) cc_final: 0.6419 (tpp)
REVERT: A  376 MET cc_start: 0.8934 (OUTLIER) cc_final: 0.8083 (ptp)
REVERT: A  462 MET cc_start: 0.7547 (ppp) cc_final: 0.7310 (ppp)
REVERT: A  464 PHE cc_start: 0.2124 (OUTLIER) cc_final: -0.1467 (t80)
REVERT: A  579 MET cc_start: 0.7523 (ppp) cc_final: 0.6903 (ppp)
  outliers start: 38
  outliers final: 29
  residues processed: 93
  average time/residue: 0.0707
  time to fit residues: 8.8550
Evaluate side-chains
  95 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 62
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 LEU
Chi-restraints excluded: chain A residue   61 LYS
Chi-restraints excluded: chain A residue   83 TYR
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  181 GLU
Chi-restraints excluded: chain A residue  231 THR
Chi-restraints excluded: chain A residue  252 TYR
Chi-restraints excluded: chain A residue  279 TYR
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  376 MET
Chi-restraints excluded: chain A residue  378 HIS
Chi-restraints excluded: chain A residue  381 TYR
Chi-restraints excluded: chain A residue  383 MET
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  464 PHE
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  503 LEU
Chi-restraints excluded: chain A residue  513 ILE
Chi-restraints excluded: chain A residue  514 ARG
Chi-restraints excluded: chain A residue  539 LEU
Chi-restraints excluded: chain A residue  573 VAL
Chi-restraints excluded: chain B residue  380 TYR
Chi-restraints excluded: chain B residue  418 ILE
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  456 PHE
Chi-restraints excluded: chain B residue  460 ASN
Chi-restraints excluded: chain B residue  464 PHE
Chi-restraints excluded: chain B residue  511 VAL
Chi-restraints excluded: chain B residue  512 VAL
Chi-restraints excluded: chain B residue  528 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 25 optimal weight:    0.0770
   chunk 4 optimal weight:    4.9990
   chunk 59 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 60 optimal weight:    0.9980
   chunk 68 optimal weight:    2.9990
   chunk 13 optimal weight:    3.9990
   chunk 22 optimal weight:    0.8980
   chunk 41 optimal weight:    0.0270
   overall best weight:    0.7998

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

Flipped N/Q/H residues before XYZ refinement:
** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4500 r_free = 0.4500 target = 0.137253 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4291 r_free = 0.4291 target = 0.119140 restraints weight = 42038.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4314 r_free = 0.4314 target = 0.121262 restraints weight = 33527.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4318 r_free = 0.4318 target = 0.121774 restraints weight = 28123.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4330 r_free = 0.4330 target = 0.122596 restraints weight = 25118.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4340 r_free = 0.4340 target = 0.123548 restraints weight = 22676.550|
|-----------------------------------------------------------------------------|
r_work (final): 0.4318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5646
moved from start:          0.6360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6647  Z= 0.154
  Angle     :  0.808  17.881   9042  Z= 0.395
  Chirality :  0.051   0.514    946
  Planarity :  0.006   0.067   1164
  Dihedral  :  6.918  54.096    980
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 19.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.00 %
    Favored  : 88.00 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 31.33 %
    Favored  : 63.98 %
  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 aren not related in a simple way.
  whole: -2.54 (0.30), residues: 775
  helix: -1.01 (0.34), residues: 243
  sheet:  0.82 (1.02), residues: 27
  loop : -2.32 (0.28), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 454 
 TYR   0.017   0.002   TYR A 158 
 PHE   0.015   0.002   PHE B 497 
 TRP   0.044   0.002   TRP A 328 
 HIS   0.005   0.002   HIS A 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 6635)
  covalent geometry    : angle       0.77454 ( 9012)
  SS BOND              : bond        0.00362 (    6)
  SS BOND              : angle       1.07296 (   12)
  hydrogen bonds       : bond        0.03744 (  173)
  hydrogen bonds       : angle       6.05581 (  468)
  link_BETA1-4         : bond        0.00683 (    1)
  link_BETA1-4         : angle       0.90514 (    3)
  link_BETA1-6         : bond        0.01067 (    1)
  link_BETA1-6         : angle       2.72829 (    3)
  link_NAG-ASN         : bond        0.01330 (    4)
  link_NAG-ASN         : angle       6.16713 (   12)

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

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

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1550 Ramachandran restraints generated.
    775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 65
  time to evaluate  : 0.163 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  171 GLU cc_start: 0.9152 (pp20) cc_final: 0.8872 (pm20)
REVERT: A  172 VAL cc_start: 0.8541 (t) cc_final: 0.7865 (t)
REVERT: A  252 TYR cc_start: 0.4867 (OUTLIER) cc_final: 0.3877 (p90)
REVERT: A  279 TYR cc_start: 0.6472 (OUTLIER) cc_final: 0.4988 (m-10)
REVERT: A  332 MET cc_start: 0.7247 (pmm) cc_final: 0.5700 (tpp)
REVERT: A  366 MET cc_start: 0.7285 (ppp) cc_final: 0.6769 (mtt)
REVERT: A  381 TYR cc_start: 0.5679 (OUTLIER) cc_final: 0.3150 (p90)
REVERT: A  464 PHE cc_start: 0.2322 (OUTLIER) cc_final: -0.1260 (t80)
REVERT: A  579 MET cc_start: 0.7564 (ppp) cc_final: 0.6894 (ppp)
  outliers start: 32
  outliers final: 25
  residues processed: 91
  average time/residue: 0.0638
  time to fit residues: 7.9517
Evaluate side-chains
  92 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 63
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 LEU
Chi-restraints excluded: chain A residue   61 LYS
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  181 GLU
Chi-restraints excluded: chain A residue  231 THR
Chi-restraints excluded: chain A residue  252 TYR
Chi-restraints excluded: chain A residue  279 TYR
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  381 TYR
Chi-restraints excluded: chain A residue  383 MET
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  464 PHE
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  503 LEU
Chi-restraints excluded: chain A residue  514 ARG
Chi-restraints excluded: chain A residue  539 LEU
Chi-restraints excluded: chain A residue  573 VAL
Chi-restraints excluded: chain B residue  380 TYR
Chi-restraints excluded: chain B residue  418 ILE
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  456 PHE
Chi-restraints excluded: chain B residue  460 ASN
Chi-restraints excluded: chain B residue  464 PHE
Chi-restraints excluded: chain B residue  511 VAL
Chi-restraints excluded: chain B residue  512 VAL
Chi-restraints excluded: chain B residue  528 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 49 optimal weight:    4.9990
   chunk 18 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 50 optimal weight:    3.9990
   chunk 5 optimal weight:    0.4980
   chunk 44 optimal weight:    0.3980
   chunk 61 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9980
   chunk 25 optimal weight:    0.0970
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4484 r_free = 0.4484 target = 0.136155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.117947 restraints weight = 42776.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4296 r_free = 0.4296 target = 0.120029 restraints weight = 34255.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.120714 restraints weight = 28140.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4314 r_free = 0.4314 target = 0.121630 restraints weight = 24669.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4320 r_free = 0.4320 target = 0.122171 restraints weight = 22157.632|
|-----------------------------------------------------------------------------|
r_work (final): 0.4308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5728
moved from start:          0.6758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   6647  Z= 0.155
  Angle     :  0.813  17.342   9042  Z= 0.399
  Chirality :  0.051   0.509    946
  Planarity :  0.006   0.065   1164
  Dihedral  :  6.998  54.153    980
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 19.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.39 %
    Favored  : 87.61 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 31.04 %
    Favored  : 64.28 %
  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 aren not related in a simple way.
  whole: -2.58 (0.30), residues: 775
  helix: -0.95 (0.34), residues: 237
  sheet:  0.67 (1.24), residues: 23
  loop : -2.37 (0.27), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 403 
 TYR   0.017   0.002   TYR A 158 
 PHE   0.046   0.002   PHE A 452 
 TRP   0.039   0.002   TRP A 328 
 HIS   0.009   0.002   HIS A 555 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 6635)
  covalent geometry    : angle       0.78032 ( 9012)
  SS BOND              : bond        0.00388 (    6)
  SS BOND              : angle       1.16742 (   12)
  hydrogen bonds       : bond        0.03756 (  173)
  hydrogen bonds       : angle       6.19818 (  468)
  link_BETA1-4         : bond        0.00526 (    1)
  link_BETA1-4         : angle       0.88658 (    3)
  link_BETA1-6         : bond        0.01093 (    1)
  link_BETA1-6         : angle       2.67402 (    3)
  link_NAG-ASN         : bond        0.01292 (    4)
  link_NAG-ASN         : angle       6.14235 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1491.57 seconds
wall clock time: 26 minutes 28.25 seconds (1588.25 seconds total)