Starting phenix.real_space_refine
on Wed Mar  4 22:30:03 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8a6l_15210/03_2026/8a6l_15210_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8a6l_15210/03_2026/8a6l_15210.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.18
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8a6l_15210/03_2026/8a6l_15210.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8a6l_15210/03_2026/8a6l_15210.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8a6l_15210/03_2026/8a6l_15210_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8a6l_15210/03_2026/8a6l_15210_trim.cif"
  }
  resolution = 3.18
  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=   0.003 sd=   0.038
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      32      5.16       5
     C    5531      2.51       5
     N    1387      2.21       5
     O    1527      1.98       5
     H    8495      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 16972
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 7066
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 454, 7066
          Classifications: {'peptide': 454}
          Link IDs: {'PTRANS': 21, 'TRANS': 432}
    Chain: "B"
      Number of atoms: 7125
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 452, 7125
          Classifications: {'peptide': 452}
          Link IDs: {'PTRANS': 24, 'TRANS': 427}
    Chain: "C"
      Number of atoms: 2722
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 173, 2722
          Classifications: {'peptide': 173}
          Link IDs: {'PTRANS': 11, 'TRANS': 161}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "A"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "B"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Classifications: {'water': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 2.52, per 1000 atoms: 0.15
  Number of scatterers: 16972
  At special positions: 0
  Unit cell: (97.818, 89.598, 141.384, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      32     16.00
     O    1527      8.00
     N    1387      7.00
     C    5531      6.00
     H    8495      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 210 " - pdb=" SG  CYS B 154 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  76 " - pdb=" SG  CYS C 175 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 701 " - " ASN A 424 "
      " NAG A 702 " - " ASN A 506 "
      " NAG A 703 " - " ASN A 365 "
      " NAG A 704 " - " ASN A 381 "
  Time building additional restraints: 1.42
  Conformation dependent library (CDL) restraints added in 641.3 milliseconds
  

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1978

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 5 sheets defined
      53.8% alpha, 12.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.37
  Creating SS restraints...
    Processing helix  chain 'A' and resid 179 through 207
    Processing helix  chain 'A' and resid 217 through 221
      removed outlier: 3.536A  pdb=" N   THR A 221 " --> pdb=" O   TRP A 218 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 229 through 235
    Processing helix  chain 'A' and resid 240 through 245
      removed outlier: 3.837A  pdb=" N   LYS A 245 " --> pdb=" O   LEU A 241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 247 through 255
    Processing helix  chain 'A' and resid 286 through 301
    Processing helix  chain 'A' and resid 323 through 341
    Processing helix  chain 'A' and resid 349 through 353
    Processing helix  chain 'A' and resid 355 through 371
      removed outlier: 3.572A  pdb=" N   PHE A 359 " --> pdb=" O   ASP A 355 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 394
      removed outlier: 4.635A  pdb=" N   SER A 394 " --> pdb=" O   SER A 390 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 426
    Processing helix  chain 'A' and resid 440 through 445
      removed outlier: 4.341A  pdb=" N   PHE A 444 " --> pdb=" O   LEU A 440 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 446 through 448
      No H-bonds generated for 'chain 'A' and resid 446 through 448'
    Processing helix  chain 'A' and resid 449 through 460
    Processing helix  chain 'A' and resid 504 through 507
    Processing helix  chain 'A' and resid 508 through 514
      removed outlier: 3.898A  pdb=" N   GLU A 514 " --> pdb=" O   LYS A 510 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 518 through 533
    Processing helix  chain 'A' and resid 533 through 538
      removed outlier: 3.808A  pdb=" N   HIS A 538 " --> pdb=" O   ARG A 534 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 584 through 588
    Processing helix  chain 'B' and resid 43 through 54
    Processing helix  chain 'B' and resid 56 through 70
      removed outlier: 3.661A  pdb=" N   VAL B  60 " --> pdb=" O   SER B  56 " (cutoff:3.500A)
      Proline residue:  B  62  - end of helix
    Processing helix  chain 'B' and resid 71 through 100
    Processing helix  chain 'B' and resid 107 through 113
    Processing helix  chain 'B' and resid 118 through 129
    Processing helix  chain 'B' and resid 129 through 148
    Processing helix  chain 'B' and resid 157 through 179
      removed outlier: 3.535A  pdb=" N   SER B 179 " --> pdb=" O   VAL B 175 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 179 through 212
      removed outlier: 3.794A  pdb=" N   ALA B 183 " --> pdb=" O   SER B 179 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   GLN B 187 " --> pdb=" O   ALA B 183 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   ASP B 188 " --> pdb=" O   THR B 184 " (cutoff:3.500A)
      removed outlier: 4.235A  pdb=" N   ILE B 189 " --> pdb=" O   ARG B 185 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   GLN B 208 " --> pdb=" O   MET B 204 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   CYS B 210 " --> pdb=" O   ILE B 206 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   LYS B 211 " --> pdb=" O   VAL B 207 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 230 through 243
      removed outlier: 3.557A  pdb=" N   LEU B 236 " --> pdb=" O   GLY B 232 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   PHE B 243 " --> pdb=" O   LEU B 239 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 250 through 255
      removed outlier: 3.539A  pdb=" N   VAL B 254 " --> pdb=" O   PHE B 250 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   THR B 255 " --> pdb=" O   LEU B 251 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 250 through 255'
    Processing helix  chain 'B' and resid 260 through 291
      Proline residue:  B 266  - end of helix
      removed outlier: 3.752A  pdb=" N   ILE B 273 " --> pdb=" O   ILE B 269 " (cutoff:3.500A)
      Proline residue:  B 274  - end of helix
    Processing helix  chain 'B' and resid 292 through 297
    Processing helix  chain 'B' and resid 301 through 311
    Processing helix  chain 'B' and resid 317 through 347
      removed outlier: 3.559A  pdb=" N   ALA B 343 " --> pdb=" O   ARG B 339 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 364 through 379
      removed outlier: 3.627A  pdb=" N   PHE B 370 " --> pdb=" O   PRO B 366 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   THR B 371 " --> pdb=" O   ALA B 367 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 383 through 412
      removed outlier: 3.651A  pdb=" N   LEU B 387 " --> pdb=" O   ASP B 383 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   ILE B 388 " --> pdb=" O   MET B 384 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   ILE B 394 " --> pdb=" O   TYR B 390 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   VAL B 401 " --> pdb=" O   LEU B 397 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 424 through 445
      removed outlier: 3.650A  pdb=" N   ILE B 428 " --> pdb=" O   LEU B 424 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 447 through 468
      Proline residue:  B 461  - end of helix
      removed outlier: 3.787A  pdb=" N   PHE B 464 " --> pdb=" O   VAL B 460 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 476 through 492
    Processing helix  chain 'C' and resid 23 through 28
    Processing helix  chain 'C' and resid 145 through 159
      removed outlier: 3.549A  pdb=" N   LYS C 149 " --> pdb=" O   THR C 145 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 399 through 402
      removed outlier: 6.403A  pdb=" N   LEU A 376 " --> pdb=" O   LEU A 399 " (cutoff:3.500A)
      removed outlier: 7.673A  pdb=" N   THR A 401 " --> pdb=" O   LEU A 376 " (cutoff:3.500A)
      removed outlier: 6.083A  pdb=" N   ALA A 378 " --> pdb=" O   THR A 401 " (cutoff:3.500A)
      removed outlier: 6.567A  pdb=" N   PHE A 345 " --> pdb=" O   ILE A 377 " (cutoff:3.500A)
      removed outlier: 8.391A  pdb=" N   GLY A 379 " --> pdb=" O   PHE A 345 " (cutoff:3.500A)
      removed outlier: 6.852A  pdb=" N   VAL A 347 " --> pdb=" O   GLY A 379 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   GLY A 344 " --> pdb=" O   VAL A 304 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   LEU A 306 " --> pdb=" O   GLY A 344 " (cutoff:3.500A)
      removed outlier: 7.123A  pdb=" N   TYR A 225 " --> pdb=" O   VAL A 260 " (cutoff:3.500A)
      removed outlier: 6.045A  pdb=" N   LEU A 224 " --> pdb=" O   PHE A 466 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 540 through 544
      removed outlier: 4.498A  pdb=" N   SER A 552 " --> pdb=" O   PHE A 544 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   ARG A 625 " --> pdb=" O   LEU A 595 " (cutoff:3.500A)
      removed outlier: 5.517A  pdb=" N   LEU A 595 " --> pdb=" O   ARG A 625 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   ALA A 593 " --> pdb=" O   LEU A 609 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 574 through 575
    Processing sheet with id=AA4, first strand: chain 'C' and resid 92 through 94
      removed outlier: 6.280A  pdb=" N   LEU C 137 " --> pdb=" O   VAL C  34 " (cutoff:3.500A)
      removed outlier: 4.468A  pdb=" N   ARG C  36 " --> pdb=" O   ILE C 135 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   ILE C 135 " --> pdb=" O   ARG C  36 " (cutoff:3.500A)
      removed outlier: 7.546A  pdb=" N   HIS C 118 " --> pdb=" O   THR C 113 " (cutoff:3.500A)
      removed outlier: 5.134A  pdb=" N   THR C 113 " --> pdb=" O   HIS C 118 " (cutoff:3.500A)
      removed outlier: 6.753A  pdb=" N   MET C 120 " --> pdb=" O   VAL C 111 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 92 through 94

    463 hydrogen bonds defined for protein.
    1338 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: 4.07

  Time building geometry restraints manager: 2.02 seconds

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

  Histogram of bond lengths:
        0.83 -     1.04: 8484
        1.04 -     1.24: 1093
        1.24 -     1.44: 2651
        1.44 -     1.64: 4910
        1.64 -     1.84: 49
  Bond restraints: 17187
  Sorted by residual:
  bond pdb=" CA  LEU B 437 "
       pdb=" C   LEU B 437 "
    ideal  model  delta    sigma   weight residual
    1.524  1.504  0.020 1.27e-02 6.20e+03 2.39e+00
  bond pdb=" CB  VAL A 565 "
       pdb=" CG2 VAL A 565 "
    ideal  model  delta    sigma   weight residual
    1.521  1.477  0.044 3.30e-02 9.18e+02 1.75e+00
  bond pdb=" CG  LEU A 375 "
       pdb=" CD1 LEU A 375 "
    ideal  model  delta    sigma   weight residual
    1.521  1.480  0.041 3.30e-02 9.18e+02 1.55e+00
  bond pdb=" C1  NAG A 701 "
       pdb=" O5  NAG A 701 "
    ideal  model  delta    sigma   weight residual
    1.406  1.430 -0.024 2.00e-02 2.50e+03 1.45e+00
  bond pdb=" CB  GLN A 559 "
       pdb=" CG  GLN A 559 "
    ideal  model  delta    sigma   weight residual
    1.520  1.484  0.036 3.00e-02 1.11e+03 1.43e+00
  ... (remaining 17182 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.50: 30307
        1.50 -     3.01: 738
        3.01 -     4.51: 60
        4.51 -     6.01: 9
        6.01 -     7.52: 2
  Bond angle restraints: 31116
  Sorted by residual:
  angle pdb=" CA  CYS A 210 "
        pdb=" CB  CYS A 210 "
        pdb=" SG  CYS A 210 "
      ideal   model   delta    sigma   weight residual
     114.40  121.92   -7.52 2.30e+00 1.89e-01 1.07e+01
  angle pdb=" N   GLY A 547 "
        pdb=" CA  GLY A 547 "
        pdb=" C   GLY A 547 "
      ideal   model   delta    sigma   weight residual
     112.34  106.03    6.31 2.04e+00 2.40e-01 9.57e+00
  angle pdb=" N   CYS C  76 "
        pdb=" CA  CYS C  76 "
        pdb=" C   CYS C  76 "
      ideal   model   delta    sigma   weight residual
     109.59  105.65    3.94 1.47e+00 4.63e-01 7.18e+00
  angle pdb=" N   TYR C  32 "
        pdb=" CA  TYR C  32 "
        pdb=" C   TYR C  32 "
      ideal   model   delta    sigma   weight residual
     110.42  106.76    3.66 1.55e+00 4.16e-01 5.58e+00
  angle pdb=" C   ILE B 429 "
        pdb=" N   TYR B 430 "
        pdb=" CA  TYR B 430 "
      ideal   model   delta    sigma   weight residual
     120.28  117.13    3.15 1.34e+00 5.57e-01 5.53e+00
  ... (remaining 31111 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.71: 7575
       17.71 -    35.43: 349
       35.43 -    53.14: 160
       53.14 -    70.86: 63
       70.86 -    88.57: 8
  Dihedral angle restraints: 8155
    sinusoidal: 4412
      harmonic: 3743
  Sorted by residual:
  dihedral pdb=" CA  GLY A 547 "
           pdb=" C   GLY A 547 "
           pdb=" N   PRO A 548 "
           pdb=" CA  PRO A 548 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.54  -17.46     0      5.00e+00 4.00e-02 1.22e+01
  dihedral pdb=" CA  VAL B 129 "
           pdb=" C   VAL B 129 "
           pdb=" N   ILE B 130 "
           pdb=" CA  ILE B 130 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.94  -17.06     0      5.00e+00 4.00e-02 1.16e+01
  dihedral pdb=" CB  CYS A 210 "
           pdb=" SG  CYS A 210 "
           pdb=" SG  CYS B 154 "
           pdb=" CB  CYS B 154 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -114.16   28.16     1      1.00e+01 1.00e-02 1.14e+01
  ... (remaining 8152 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 1087
       0.050 -    0.101: 231
       0.101 -    0.151: 33
       0.151 -    0.202: 1
       0.202 -    0.252: 3
  Chirality restraints: 1355
  Sorted by residual:
  chirality pdb=" C1  NAG A 702 "
            pdb=" ND2 ASN A 506 "
            pdb=" C2  NAG A 702 "
            pdb=" O5  NAG A 702 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.15   -0.25 2.00e-01 2.50e+01 1.59e+00
  chirality pdb=" C1  NAG A 703 "
            pdb=" ND2 ASN A 365 "
            pdb=" C2  NAG A 703 "
            pdb=" O5  NAG A 703 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.19   -0.21 2.00e-01 2.50e+01 1.06e+00
  chirality pdb=" C1  NAG A 704 "
            pdb=" ND2 ASN A 381 "
            pdb=" C2  NAG A 704 "
            pdb=" O5  NAG A 704 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.20   -0.20 2.00e-01 2.50e+01 1.03e+00
  ... (remaining 1352 not shown)

  Planarity restraints: 2507
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B 437 "    0.020 2.00e-02 2.50e+03   4.02e-02 1.62e+01
        pdb=" C   LEU B 437 "   -0.070 2.00e-02 2.50e+03
        pdb=" O   LEU B 437 "    0.026 2.00e-02 2.50e+03
        pdb=" N   LEU B 438 "    0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE B 393 "   -0.014 2.00e-02 2.50e+03   2.75e-02 7.56e+00
        pdb=" C   PHE B 393 "    0.048 2.00e-02 2.50e+03
        pdb=" O   PHE B 393 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   ILE B 394 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 439 "   -0.013 2.00e-02 2.50e+03   2.57e-02 6.58e+00
        pdb=" C   VAL B 439 "    0.044 2.00e-02 2.50e+03
        pdb=" O   VAL B 439 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   PHE B 440 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 2504 not shown)

  Histogram of nonbonded interaction distances:
        1.50 -     2.12: 447
        2.12 -     2.74: 31670
        2.74 -     3.36: 49063
        3.36 -     3.98: 62067
        3.98 -     4.60: 99955
  Nonbonded interactions: 243202
  Sorted by model distance:
  nonbonded pdb=" HG  SER A 494 "
            pdb=" OG  SER C 125 "
     model   vdw
     1.499 2.450
  nonbonded pdb=" O   LYS A 300 "
            pdb=" HG  SER A 301 "
     model   vdw
     1.543 2.450
  nonbonded pdb=" O   GLY A 409 "
            pdb=" HG  SER A 410 "
     model   vdw
     1.549 2.450
  nonbonded pdb=" O   LEU B 251 "
            pdb=" HG1 THR B 255 "
     model   vdw
     1.586 2.450
  nonbonded pdb=" OD1 ASP A 498 "
            pdb=" HG1 THR C 136 "
     model   vdw
     1.588 2.450
  ... (remaining 243197 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.600
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.090
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     15.900
  Find NCS groups from input model:        0.050
  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:             0.010
  Load rotamer database and sin/cos tables:1.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.230
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8073
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   0.044   8698  Z= 0.229
  Angle     :  0.627   7.515  11848  Z= 0.345
  Chirality :  0.042   0.252   1355
  Planarity :  0.005   0.040   1483
  Dihedral  : 10.515  88.573   3155
  Min Nonbonded Distance : 2.188

Molprobity Statistics.
  All-atom Clashscore : 4.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.80 (0.26), residues: 1073
  helix:  1.67 (0.22), residues: 516
  sheet: -1.25 (0.42), residues: 133
  loop : -0.18 (0.32), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 162 
 TYR   0.014   0.002   TYR A 312 
 PHE   0.025   0.002   PHE A 444 
 TRP   0.020   0.001   TRP A 557 
 HIS   0.002   0.001   HIS A 619 

Details of bonding type rmsd
  covalent geometry    : bond        0.00506 ( 8692)
  covalent geometry    : angle       0.61821 (11832)
  SS BOND              : bond        0.00459 (    2)
  SS BOND              : angle       4.70440 (    4)
  hydrogen bonds       : bond        0.12626 (  443)
  hydrogen bonds       : angle       6.09323 ( 1338)
  link_NAG-ASN         : bond        0.00282 (    4)
  link_NAG-ASN         : angle       2.05924 (   12)

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

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

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   74 is missing expected H atoms. Skipping.
Evaluate side-chains
  231 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 231
  time to evaluate  : 0.382 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  406 SER cc_start: 0.8923 (p) cc_final: 0.8673 (m)
REVERT: B   95 GLU cc_start: 0.7678 (tm-30) cc_final: 0.7225 (tm-30)
REVERT: B  406 GLN cc_start: 0.7435 (tt0) cc_final: 0.7121 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 231
  average time/residue: 0.2268
  time to fit residues: 69.0230
Evaluate side-chains
  157 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 157
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 97 optimal weight:    0.1980
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.4980
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    0.9980
   chunk 100 optimal weight:    5.9990
   chunk 106 optimal weight:    0.6980
   chunk 38 optimal weight:    1.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 295 GLN
** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  23 GLN
C  39 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.164078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.121005 restraints weight = 32148.835|
|-----------------------------------------------------------------------------|
r_work (start): 0.3216 rms_B_bonded: 2.54
r_work: 0.3067 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.2916 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.2916
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8442
moved from start:          0.2145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066   8698  Z= 0.135
  Angle     :  0.556   7.173  11848  Z= 0.288
  Chirality :  0.040   0.218   1355
  Planarity :  0.004   0.034   1483
  Dihedral  :  5.297  53.481   1234
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 4.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  :  8.90 %
    Favored  : 90.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.90 (0.26), residues: 1073
  helix:  1.85 (0.23), residues: 535
  sheet: -1.23 (0.45), residues: 123
  loop : -0.42 (0.31), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 226 
 TYR   0.010   0.001   TYR B 145 
 PHE   0.016   0.001   PHE A 444 
 TRP   0.009   0.001   TRP A 557 
 HIS   0.002   0.001   HIS B 358 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 8692)
  covalent geometry    : angle       0.54770 (11832)
  SS BOND              : bond        0.01180 (    2)
  SS BOND              : angle       4.45520 (    4)
  hydrogen bonds       : bond        0.04490 (  443)
  hydrogen bonds       : angle       4.88449 ( 1338)
  link_NAG-ASN         : bond        0.00296 (    4)
  link_NAG-ASN         : angle       1.62352 (   12)

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

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

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   74 is missing expected H atoms. Skipping.
Evaluate side-chains
  180 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 177
  time to evaluate  : 0.429 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  252 SER cc_start: 0.9217 (t) cc_final: 0.8872 (p)
REVERT: A  315 GLU cc_start: 0.7754 (pm20) cc_final: 0.7536 (pm20)
REVERT: A  406 SER cc_start: 0.9215 (p) cc_final: 0.8962 (m)
REVERT: B   95 GLU cc_start: 0.7943 (tm-30) cc_final: 0.7411 (tm-30)
REVERT: B  406 GLN cc_start: 0.7746 (tt0) cc_final: 0.7514 (tt0)
REVERT: C  103 ARG cc_start: 0.7403 (ptt90) cc_final: 0.7057 (mtp-110)
  outliers start: 3
  outliers final: 1
  residues processed: 180
  average time/residue: 0.2279
  time to fit residues: 54.5197
Evaluate side-chains
  158 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 157
  time to evaluate  : 0.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  455 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 95 optimal weight:    1.9990
   chunk 83 optimal weight:    1.9990
   chunk 92 optimal weight:    2.9990
   chunk 73 optimal weight:    2.9990
   chunk 81 optimal weight:    0.9980
   chunk 88 optimal weight:   10.0000
   chunk 82 optimal weight:    4.9990
   chunk 1 optimal weight:    5.9990
   chunk 68 optimal weight:    0.0470
   chunk 78 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   overall best weight:    1.6084

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

Flipped N/Q/H residues before XYZ refinement:
A 387 GLN
C  23 GLN
C 128 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.162361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.118969 restraints weight = 32417.538|
|-----------------------------------------------------------------------------|
r_work (start): 0.3169 rms_B_bonded: 2.54
r_work: 0.3022 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.2872 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.2872
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8468
moved from start:          0.2444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8698  Z= 0.174
  Angle     :  0.539   4.571  11848  Z= 0.278
  Chirality :  0.040   0.210   1355
  Planarity :  0.004   0.049   1483
  Dihedral  :  5.115  47.512   1234
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 3.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  : 10.22 %
    Favored  : 89.23 %
  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 are not related in a simple way.
  whole:  0.80 (0.26), residues: 1073
  helix:  1.87 (0.23), residues: 536
  sheet: -1.30 (0.45), residues: 125
  loop : -0.63 (0.31), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 154 
 TYR   0.009   0.001   TYR A 312 
 PHE   0.012   0.001   PHE B 398 
 TRP   0.008   0.001   TRP B 124 
 HIS   0.002   0.001   HIS B 358 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 ( 8692)
  covalent geometry    : angle       0.53468 (11832)
  SS BOND              : bond        0.00076 (    2)
  SS BOND              : angle       2.67187 (    4)
  hydrogen bonds       : bond        0.04248 (  443)
  hydrogen bonds       : angle       4.63970 ( 1338)
  link_NAG-ASN         : bond        0.00238 (    4)
  link_NAG-ASN         : angle       1.70387 (   12)

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

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

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   74 is missing expected H atoms. Skipping.
Evaluate side-chains
  159 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 154
  time to evaluate  : 0.439 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  252 SER cc_start: 0.9229 (t) cc_final: 0.8874 (p)
REVERT: B   95 GLU cc_start: 0.8013 (tm-30) cc_final: 0.7373 (tm-30)
REVERT: B  406 GLN cc_start: 0.7774 (tt0) cc_final: 0.7470 (tt0)
REVERT: C   23 GLN cc_start: 0.8457 (mm-40) cc_final: 0.8209 (mm-40)
REVERT: C  103 ARG cc_start: 0.7349 (ptt90) cc_final: 0.6955 (mtp-110)
  outliers start: 5
  outliers final: 3
  residues processed: 157
  average time/residue: 0.2236
  time to fit residues: 46.5850
Evaluate side-chains
  148 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 145
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  334 LEU
Chi-restraints excluded: chain B residue   46 CYS
Chi-restraints excluded: chain B residue  455 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 46 optimal weight:    3.9990
   chunk 2 optimal weight:    2.9990
   chunk 83 optimal weight:    0.9980
   chunk 3 optimal weight:    3.9990
   chunk 42 optimal weight:    0.0770
   chunk 77 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 14 optimal weight:    5.9990
   chunk 45 optimal weight:    0.9980
   chunk 27 optimal weight:    0.7980
   chunk 47 optimal weight:    2.9990
   overall best weight:    0.7740

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

Flipped N/Q/H residues before XYZ refinement:
B 264 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.161312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.117426 restraints weight = 32376.788|
|-----------------------------------------------------------------------------|
r_work (start): 0.3272 rms_B_bonded: 2.58
r_work: 0.3127 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.2974 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.2974
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8476
moved from start:          0.2619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8698  Z= 0.115
  Angle     :  0.505   5.420  11848  Z= 0.258
  Chirality :  0.039   0.209   1355
  Planarity :  0.003   0.028   1483
  Dihedral  :  4.839  44.851   1234
  Min Nonbonded Distance : 2.350

Molprobity Statistics.
  All-atom Clashscore : 3.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  : 10.11 %
    Favored  : 89.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.93 (0.26), residues: 1073
  helix:  2.05 (0.23), residues: 532
  sheet: -1.14 (0.46), residues: 119
  loop : -0.69 (0.30), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 339 
 TYR   0.008   0.001   TYR B 145 
 PHE   0.012   0.001   PHE B 398 
 TRP   0.007   0.001   TRP A 318 
 HIS   0.002   0.000   HIS B 358 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 8692)
  covalent geometry    : angle       0.50165 (11832)
  SS BOND              : bond        0.00114 (    2)
  SS BOND              : angle       1.87422 (    4)
  hydrogen bonds       : bond        0.03732 (  443)
  hydrogen bonds       : angle       4.40567 ( 1338)
  link_NAG-ASN         : bond        0.00355 (    4)
  link_NAG-ASN         : angle       1.57855 (   12)

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

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

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   74 is missing expected H atoms. Skipping.
Evaluate side-chains
  165 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 160
  time to evaluate  : 0.402 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  252 SER cc_start: 0.9190 (t) cc_final: 0.8861 (p)
REVERT: A  406 SER cc_start: 0.9251 (p) cc_final: 0.8955 (m)
REVERT: B   95 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7451 (tm-30)
REVERT: B  406 GLN cc_start: 0.7717 (tt0) cc_final: 0.7445 (tt0)
REVERT: C   23 GLN cc_start: 0.8443 (mm-40) cc_final: 0.8200 (mm-40)
  outliers start: 5
  outliers final: 5
  residues processed: 163
  average time/residue: 0.2186
  time to fit residues: 47.5560
Evaluate side-chains
  159 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 154
  time to evaluate  : 0.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  334 LEU
Chi-restraints excluded: chain B residue   46 CYS
Chi-restraints excluded: chain B residue  168 CYS
Chi-restraints excluded: chain B residue  407 ILE
Chi-restraints excluded: chain B residue  455 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 64 optimal weight:    4.9990
   chunk 71 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 93 optimal weight:    1.9990
   chunk 104 optimal weight:    4.9990
   chunk 43 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 54 optimal weight:    0.8980
   chunk 85 optimal weight:    0.9980
   chunk 40 optimal weight:    2.9990
   overall best weight:    1.7786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.161651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.118108 restraints weight = 32168.344|
|-----------------------------------------------------------------------------|
r_work (start): 0.3142 rms_B_bonded: 2.53
r_work: 0.2995 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2843 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.2843
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8477
moved from start:          0.2708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8698  Z= 0.184
  Angle     :  0.533   4.688  11848  Z= 0.273
  Chirality :  0.040   0.214   1355
  Planarity :  0.004   0.025   1483
  Dihedral  :  4.727  45.141   1234
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 4.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 10.55 %
    Favored  : 88.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.87 (0.26), residues: 1073
  helix:  1.96 (0.23), residues: 536
  sheet: -1.27 (0.44), residues: 129
  loop : -0.63 (0.31), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 226 
 TYR   0.007   0.001   TYR A 312 
 PHE   0.014   0.001   PHE B 398 
 TRP   0.008   0.001   TRP A 318 
 HIS   0.002   0.001   HIS B 358 

Details of bonding type rmsd
  covalent geometry    : bond        0.00441 ( 8692)
  covalent geometry    : angle       0.52943 (11832)
  SS BOND              : bond        0.00194 (    2)
  SS BOND              : angle       1.87298 (    4)
  hydrogen bonds       : bond        0.03975 (  443)
  hydrogen bonds       : angle       4.39681 ( 1338)
  link_NAG-ASN         : bond        0.00180 (    4)
  link_NAG-ASN         : angle       1.72445 (   12)

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

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

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   74 is missing expected H atoms. Skipping.
Evaluate side-chains
  156 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 146
  time to evaluate  : 0.379 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  252 SER cc_start: 0.9243 (t) cc_final: 0.8896 (p)
REVERT: A  307 ASP cc_start: 0.9111 (OUTLIER) cc_final: 0.8833 (p0)
REVERT: B   84 PHE cc_start: 0.8335 (t80) cc_final: 0.7970 (t80)
REVERT: B   95 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7314 (tm-30)
REVERT: B  406 GLN cc_start: 0.7756 (tt0) cc_final: 0.7421 (tt0)
REVERT: C   23 GLN cc_start: 0.8425 (mm-40) cc_final: 0.8219 (mm-40)
  outliers start: 10
  outliers final: 6
  residues processed: 154
  average time/residue: 0.2293
  time to fit residues: 47.2431
Evaluate side-chains
  151 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 144
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  307 ASP
Chi-restraints excluded: chain A residue  334 LEU
Chi-restraints excluded: chain B residue   46 CYS
Chi-restraints excluded: chain B residue  168 CYS
Chi-restraints excluded: chain B residue  407 ILE
Chi-restraints excluded: chain B residue  445 GLU
Chi-restraints excluded: chain B residue  455 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 103 optimal weight:    5.9990
   chunk 81 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   chunk 48 optimal weight:    3.9990
   chunk 105 optimal weight:    3.9990
   chunk 63 optimal weight:    5.9990
   chunk 102 optimal weight:    0.9990
   chunk 66 optimal weight:    5.9990
   chunk 25 optimal weight:    0.7980
   chunk 39 optimal weight:    2.9990
   chunk 93 optimal weight:    1.9990
   overall best weight:    1.9588

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.163024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.122499 restraints weight = 31980.846|
|-----------------------------------------------------------------------------|
r_work (start): 0.3167 rms_B_bonded: 2.36
r_work: 0.3017 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2870 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.2870
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8479
moved from start:          0.2805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   8698  Z= 0.192
  Angle     :  0.542   4.284  11848  Z= 0.278
  Chirality :  0.041   0.218   1355
  Planarity :  0.004   0.071   1483
  Dihedral  :  4.767  46.372   1234
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 4.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  : 12.20 %
    Favored  : 86.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.80 (0.26), residues: 1073
  helix:  1.90 (0.23), residues: 537
  sheet: -1.24 (0.44), residues: 124
  loop : -0.70 (0.31), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 313 
 TYR   0.009   0.001   TYR B 390 
 PHE   0.014   0.001   PHE B 398 
 TRP   0.008   0.001   TRP A 318 
 HIS   0.003   0.001   HIS B 358 

Details of bonding type rmsd
  covalent geometry    : bond        0.00461 ( 8692)
  covalent geometry    : angle       0.53664 (11832)
  SS BOND              : bond        0.00204 (    2)
  SS BOND              : angle       2.61679 (    4)
  hydrogen bonds       : bond        0.03991 (  443)
  hydrogen bonds       : angle       4.39149 ( 1338)
  link_NAG-ASN         : bond        0.00186 (    4)
  link_NAG-ASN         : angle       1.80867 (   12)

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

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

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   74 is missing expected H atoms. Skipping.
Evaluate side-chains
  156 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 148
  time to evaluate  : 0.430 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  252 SER cc_start: 0.9237 (t) cc_final: 0.8890 (p)
REVERT: A  307 ASP cc_start: 0.9100 (OUTLIER) cc_final: 0.8830 (p0)
REVERT: B   95 GLU cc_start: 0.8037 (tm-30) cc_final: 0.7358 (tm-30)
REVERT: B  227 GLN cc_start: 0.7833 (tp40) cc_final: 0.7600 (tp-100)
  outliers start: 8
  outliers final: 5
  residues processed: 154
  average time/residue: 0.2194
  time to fit residues: 45.6254
Evaluate side-chains
  150 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 144
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  307 ASP
Chi-restraints excluded: chain A residue  334 LEU
Chi-restraints excluded: chain B residue   46 CYS
Chi-restraints excluded: chain B residue  168 CYS
Chi-restraints excluded: chain B residue  407 ILE
Chi-restraints excluded: chain B residue  455 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 83 optimal weight:    0.9990
   chunk 2 optimal weight:    2.9990
   chunk 25 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9980
   chunk 49 optimal weight:    0.6980
   chunk 57 optimal weight:    0.8980
   chunk 22 optimal weight:    1.9990
   chunk 104 optimal weight:    3.9990
   chunk 88 optimal weight:    0.3980
   chunk 8 optimal weight:    1.9990
   chunk 91 optimal weight:    4.9990
   overall best weight:    0.7982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.165039 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.124918 restraints weight = 31859.279|
|-----------------------------------------------------------------------------|
r_work (start): 0.3183 rms_B_bonded: 2.34
r_work: 0.3032 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.2883 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.2883
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8439
moved from start:          0.2907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8698  Z= 0.115
  Angle     :  0.504   4.281  11848  Z= 0.257
  Chirality :  0.039   0.210   1355
  Planarity :  0.004   0.040   1483
  Dihedral  :  4.523  45.339   1234
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 3.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  : 12.64 %
    Favored  : 86.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.01 (0.26), residues: 1073
  helix:  2.11 (0.23), residues: 532
  sheet: -1.21 (0.44), residues: 129
  loop : -0.59 (0.31), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 313 
 TYR   0.009   0.001   TYR B 390 
 PHE   0.012   0.001   PHE B 398 
 TRP   0.008   0.001   TRP A 318 
 HIS   0.001   0.000   HIS A 538 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 8692)
  covalent geometry    : angle       0.49976 (11832)
  SS BOND              : bond        0.00219 (    2)
  SS BOND              : angle       2.42564 (    4)
  hydrogen bonds       : bond        0.03554 (  443)
  hydrogen bonds       : angle       4.24030 ( 1338)
  link_NAG-ASN         : bond        0.00228 (    4)
  link_NAG-ASN         : angle       1.53073 (   12)

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

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

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   74 is missing expected H atoms. Skipping.
Evaluate side-chains
  153 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 148
  time to evaluate  : 0.445 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  252 SER cc_start: 0.9196 (t) cc_final: 0.8872 (p)
REVERT: A  313 ARG cc_start: 0.8585 (mtt-85) cc_final: 0.8276 (mtt-85)
REVERT: A  406 SER cc_start: 0.9234 (p) cc_final: 0.8888 (m)
REVERT: B   84 PHE cc_start: 0.8326 (t80) cc_final: 0.7969 (t80)
REVERT: B   95 GLU cc_start: 0.8069 (tm-30) cc_final: 0.7598 (tm-30)
REVERT: B  227 GLN cc_start: 0.7848 (tp40) cc_final: 0.7642 (tp-100)
  outliers start: 5
  outliers final: 5
  residues processed: 151
  average time/residue: 0.2111
  time to fit residues: 43.0491
Evaluate side-chains
  147 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 142
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  334 LEU
Chi-restraints excluded: chain B residue   46 CYS
Chi-restraints excluded: chain B residue  168 CYS
Chi-restraints excluded: chain B residue  407 ILE
Chi-restraints excluded: chain B residue  455 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 90 optimal weight:    1.9990
   chunk 70 optimal weight:    0.6980
   chunk 37 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 44 optimal weight:    0.7980
   chunk 4 optimal weight:    2.9990
   chunk 79 optimal weight:    1.9990
   chunk 59 optimal weight:    3.9990
   chunk 86 optimal weight:    4.9990
   chunk 85 optimal weight:    0.9980
   overall best weight:    1.2984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.162324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.118766 restraints weight = 32196.615|
|-----------------------------------------------------------------------------|
r_work (start): 0.3144 rms_B_bonded: 2.57
r_work: 0.2998 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.2848 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.2848
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8467
moved from start:          0.2971

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8698  Z= 0.146
  Angle     :  0.511   4.198  11848  Z= 0.261
  Chirality :  0.039   0.209   1355
  Planarity :  0.004   0.043   1483
  Dihedral  :  4.535  45.461   1234
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 3.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  : 12.64 %
    Favored  : 86.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.00 (0.26), residues: 1073
  helix:  2.09 (0.23), residues: 532
  sheet: -1.15 (0.43), residues: 135
  loop : -0.57 (0.31), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 625 
 TYR   0.006   0.001   TYR C 115 
 PHE   0.013   0.001   PHE B 398 
 TRP   0.008   0.001   TRP A 318 
 HIS   0.002   0.001   HIS B 358 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 8692)
  covalent geometry    : angle       0.50655 (11832)
  SS BOND              : bond        0.00092 (    2)
  SS BOND              : angle       2.42998 (    4)
  hydrogen bonds       : bond        0.03660 (  443)
  hydrogen bonds       : angle       4.26235 ( 1338)
  link_NAG-ASN         : bond        0.00213 (    4)
  link_NAG-ASN         : angle       1.58557 (   12)

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

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

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   74 is missing expected H atoms. Skipping.
Evaluate side-chains
  147 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 141
  time to evaluate  : 0.411 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  252 SER cc_start: 0.9211 (t) cc_final: 0.8887 (p)
REVERT: A  307 ASP cc_start: 0.9074 (OUTLIER) cc_final: 0.8747 (p0)
REVERT: B   95 GLU cc_start: 0.8054 (tm-30) cc_final: 0.7561 (tm-30)
  outliers start: 6
  outliers final: 5
  residues processed: 145
  average time/residue: 0.1928
  time to fit residues: 38.7433
Evaluate side-chains
  146 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 140
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  307 ASP
Chi-restraints excluded: chain A residue  334 LEU
Chi-restraints excluded: chain B residue   46 CYS
Chi-restraints excluded: chain B residue  168 CYS
Chi-restraints excluded: chain B residue  407 ILE
Chi-restraints excluded: chain B residue  455 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 61 optimal weight:    4.9990
   chunk 57 optimal weight:    2.9990
   chunk 33 optimal weight:    0.6980
   chunk 62 optimal weight:    0.7980
   chunk 17 optimal weight:    0.7980
   chunk 52 optimal weight:    0.6980
   chunk 34 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9980
   chunk 70 optimal weight:    3.9990
   overall best weight:    0.7980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.163661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.123756 restraints weight = 32140.959|
|-----------------------------------------------------------------------------|
r_work (start): 0.3236 rms_B_bonded: 2.51
r_work: 0.3055 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.2906 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.2906
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8442
moved from start:          0.3032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8698  Z= 0.113
  Angle     :  0.492   4.068  11848  Z= 0.251
  Chirality :  0.039   0.204   1355
  Planarity :  0.004   0.036   1483
  Dihedral  :  4.379  44.223   1234
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 3.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  : 12.86 %
    Favored  : 86.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.09 (0.27), residues: 1073
  helix:  2.17 (0.23), residues: 532
  sheet: -1.09 (0.44), residues: 130
  loop : -0.56 (0.31), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 339 
 TYR   0.008   0.001   TYR C 115 
 PHE   0.013   0.001   PHE B 398 
 TRP   0.009   0.001   TRP A 190 
 HIS   0.001   0.000   HIS B 358 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 8692)
  covalent geometry    : angle       0.48892 (11832)
  SS BOND              : bond        0.00117 (    2)
  SS BOND              : angle       2.07744 (    4)
  hydrogen bonds       : bond        0.03393 (  443)
  hydrogen bonds       : angle       4.15299 ( 1338)
  link_NAG-ASN         : bond        0.00235 (    4)
  link_NAG-ASN         : angle       1.43392 (   12)

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

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

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   74 is missing expected H atoms. Skipping.
Evaluate side-chains
  157 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 152
  time to evaluate  : 0.407 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  252 SER cc_start: 0.9176 (t) cc_final: 0.8868 (p)
REVERT: A  279 GLN cc_start: 0.8555 (mt0) cc_final: 0.8317 (mt0)
REVERT: A  307 ASP cc_start: 0.8970 (p0) cc_final: 0.8660 (p0)
REVERT: B   84 PHE cc_start: 0.8327 (t80) cc_final: 0.8008 (t80)
REVERT: B   95 GLU cc_start: 0.8054 (tm-30) cc_final: 0.7553 (tm-30)
  outliers start: 5
  outliers final: 5
  residues processed: 155
  average time/residue: 0.1828
  time to fit residues: 39.5181
Evaluate side-chains
  151 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 146
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  334 LEU
Chi-restraints excluded: chain B residue   46 CYS
Chi-restraints excluded: chain B residue  168 CYS
Chi-restraints excluded: chain B residue  407 ILE
Chi-restraints excluded: chain B residue  455 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 18 optimal weight:    0.6980
   chunk 102 optimal weight:    3.9990
   chunk 19 optimal weight:    0.6980
   chunk 32 optimal weight:    0.3980
   chunk 70 optimal weight:    5.9990
   chunk 45 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 97 optimal weight:    0.9990
   chunk 83 optimal weight:    0.4980
   chunk 28 optimal weight:    0.9980
   chunk 8 optimal weight:    0.6980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 386 GLN
** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.165775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.125670 restraints weight = 31645.339|
|-----------------------------------------------------------------------------|
r_work (start): 0.3209 rms_B_bonded: 2.35
r_work: 0.3060 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2913 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.2913
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8432
moved from start:          0.3177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   8698  Z= 0.104
  Angle     :  0.487   4.061  11848  Z= 0.248
  Chirality :  0.038   0.200   1355
  Planarity :  0.004   0.036   1483
  Dihedral  :  4.269  42.324   1234
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 3.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  0.44 %
    Allowed  : 13.19 %
    Favored  : 86.37 %
  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 are not related in a simple way.
  whole:  1.15 (0.27), residues: 1073
  helix:  2.19 (0.23), residues: 532
  sheet: -1.06 (0.45), residues: 130
  loop : -0.50 (0.31), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 339 
 TYR   0.008   0.001   TYR B 385 
 PHE   0.013   0.001   PHE B 398 
 TRP   0.009   0.001   TRP A 190 
 HIS   0.001   0.000   HIS A 538 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 8692)
  covalent geometry    : angle       0.48437 (11832)
  SS BOND              : bond        0.00063 (    2)
  SS BOND              : angle       2.01641 (    4)
  hydrogen bonds       : bond        0.03305 (  443)
  hydrogen bonds       : angle       4.12220 ( 1338)
  link_NAG-ASN         : bond        0.00228 (    4)
  link_NAG-ASN         : angle       1.37470 (   12)

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

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

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   74 is missing expected H atoms. Skipping.
Evaluate side-chains
  156 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 152
  time to evaluate  : 0.397 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  252 SER cc_start: 0.9158 (t) cc_final: 0.8844 (p)
REVERT: A  279 GLN cc_start: 0.8542 (mt0) cc_final: 0.8322 (mt0)
REVERT: A  307 ASP cc_start: 0.8987 (p0) cc_final: 0.8688 (p0)
REVERT: B   84 PHE cc_start: 0.8332 (t80) cc_final: 0.7999 (t80)
REVERT: B   95 GLU cc_start: 0.8049 (tm-30) cc_final: 0.7541 (tm-30)
REVERT: B  447 VAL cc_start: 0.7626 (t) cc_final: 0.7403 (m)
REVERT: B  463 TYR cc_start: 0.6714 (t80) cc_final: 0.6459 (t80)
  outliers start: 4
  outliers final: 4
  residues processed: 154
  average time/residue: 0.1969
  time to fit residues: 41.6643
Evaluate side-chains
  156 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 152
  time to evaluate  : 0.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  334 LEU
Chi-restraints excluded: chain B residue   46 CYS
Chi-restraints excluded: chain B residue  168 CYS
Chi-restraints excluded: chain B residue  407 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 75 optimal weight:    7.9990
   chunk 10 optimal weight:    0.0570
   chunk 2 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 91 optimal weight:    3.9990
   chunk 35 optimal weight:    0.0980
   chunk 67 optimal weight:    4.9990
   chunk 22 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9980
   overall best weight:    0.8300

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

Flipped N/Q/H residues before XYZ refinement:
** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.164050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.120806 restraints weight = 31972.757|
|-----------------------------------------------------------------------------|
r_work (start): 0.3176 rms_B_bonded: 2.53
r_work: 0.3029 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.2879 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.2879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8444
moved from start:          0.3156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   8698  Z= 0.113
  Angle     :  0.490   4.108  11848  Z= 0.250
  Chirality :  0.039   0.200   1355
  Planarity :  0.004   0.075   1483
  Dihedral  :  4.252  41.236   1234
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 3.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  0.44 %
    Allowed  : 13.08 %
    Favored  : 86.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.20 (0.27), residues: 1073
  helix:  2.21 (0.23), residues: 530
  sheet: -1.02 (0.45), residues: 130
  loop : -0.43 (0.31), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 206 
 TYR   0.007   0.001   TYR B 390 
 PHE   0.012   0.001   PHE B 398 
 TRP   0.009   0.001   TRP A 190 
 HIS   0.001   0.000   HIS B 358 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 8692)
  covalent geometry    : angle       0.48688 (11832)
  SS BOND              : bond        0.00069 (    2)
  SS BOND              : angle       1.98888 (    4)
  hydrogen bonds       : bond        0.03307 (  443)
  hydrogen bonds       : angle       4.10257 ( 1338)
  link_NAG-ASN         : bond        0.00220 (    4)
  link_NAG-ASN         : angle       1.38854 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4813.74 seconds
wall clock time: 82 minutes 3.15 seconds (4923.15 seconds total)