Starting phenix.real_space_refine
on Tue Mar  3 14:02:19 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7rtw_24691/03_2026/7rtw_24691.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7rtw_24691/03_2026/7rtw_24691.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.23
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7rtw_24691/03_2026/7rtw_24691.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7rtw_24691/03_2026/7rtw_24691.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7rtw_24691/03_2026/7rtw_24691.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7rtw_24691/03_2026/7rtw_24691.cif"
  }
  resolution = 3.23
  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=   0.000 sd=   1.000
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
     Ca      2      9.91       5
     S      24      5.16       5
     C    3625      2.51       5
     N     931      2.21       5
     O    1062      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  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: 5644
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 3027
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 388, 3027
          Classifications: {'peptide': 388}
          Link IDs: {'PTRANS': 14, 'TRANS': 373}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "B"
      Number of atoms: 2418
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 313, 2418
          Classifications: {'peptide': 313}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 10, 'TRANS': 302}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "C"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "D"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "E"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "F"
      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: "G"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 38
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 11
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 16
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 16
          Unusual residues: {' CA': 2, 'NAG': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 1.30, per 1000 atoms: 0.23
  Number of scatterers: 5644
  At special positions: 0
  Unit cell: (68.22, 92.097, 131.892, 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)
     Ca      2     19.99
     S      24     16.00
     O    1062      8.00
     N     931      7.00
     C    3625      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 271 " - pdb=" SG  CYS A 381 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 299 " - pdb=" SG  CYS A 366 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 271 " - pdb=" SG  CYS B 381 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 299 " - pdb=" SG  CYS B 366 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG C   2 " - " BMA C   3 "
      " NAG D   1 " - " NAG D   2 "
      " NAG D   2 " - " BMA D   3 "
      " NAG E   1 " - " NAG E   2 "
      " NAG E   2 " - " BMA E   3 "
      " NAG F   1 " - " NAG F   2 "
      " NAG G   1 " - " NAG G   2 "
      " NAG G   2 " - " BMA G   3 "
    NAG-ASN
      " NAG A 601 " - " ASN A 144 "
      " NAG C   1 " - " ASN A 126 "
      " NAG D   1 " - " ASN A 351 "
      " NAG E   1 " - " ASN B 126 "
      " NAG F   1 " - " ASN B 144 "
      " NAG G   1 " - " ASN B 351 "
  Time building additional restraints: 0.62
  Conformation dependent library (CDL) restraints added in 450.0 milliseconds
  

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1304

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 0 sheets defined
      85.3% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 17
      removed outlier: 4.122A  pdb=" N   LEU A  15 " --> pdb=" O   TRP A  11 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 36 through 41
    Processing helix  chain 'A' and resid 41 through 48
      removed outlier: 3.674A  pdb=" N   LEU A  46 " --> pdb=" O   ALA A  42 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 48 through 63
      removed outlier: 3.687A  pdb=" N   ALA A  55 " --> pdb=" O   LEU A  51 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 147
      removed outlier: 3.621A  pdb=" N   ALA A  99 " --> pdb=" O   LEU A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 152
    Processing helix  chain 'A' and resid 161 through 183
      removed outlier: 3.722A  pdb=" N   LEU A 165 " --> pdb=" O   ARG A 161 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   ALA A 167 " --> pdb=" O   GLU A 163 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 233
      removed outlier: 4.295A  pdb=" N   ILE A 232 " --> pdb=" O   LEU A 228 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   ARG A 233 " --> pdb=" O   VAL A 229 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 240 through 273
      removed outlier: 4.467A  pdb=" N   ASP A 273 " --> pdb=" O   ASP A 269 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 273 through 286
      removed outlier: 4.001A  pdb=" N   PHE A 277 " --> pdb=" O   ASP A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 289 through 297
    Processing helix  chain 'A' and resid 306 through 329
      removed outlier: 4.157A  pdb=" N   LYS A 310 " --> pdb=" O   PRO A 306 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   GLY A 313 " --> pdb=" O   GLN A 309 " (cutoff:3.500A)
      removed outlier: 4.842A  pdb=" N   SER A 314 " --> pdb=" O   LYS A 310 " (cutoff:3.500A)
      removed outlier: 4.683A  pdb=" N   GLU A 327 " --> pdb=" O   ASP A 323 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 336
      removed outlier: 4.300A  pdb=" N   GLU A 335 " --> pdb=" O   ASN A 331 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 339 through 364
      removed outlier: 4.146A  pdb=" N   LEU A 343 " --> pdb=" O   THR A 339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 409
      removed outlier: 4.471A  pdb=" N   LEU A 369 " --> pdb=" O   ASP A 365 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 87 through 147
    Processing helix  chain 'B' and resid 147 through 157
      removed outlier: 3.721A  pdb=" N   GLN B 152 " --> pdb=" O   GLU B 148 " (cutoff:3.500A)
      removed outlier: 4.178A  pdb=" N   SER B 153 " --> pdb=" O   PRO B 149 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   GLN B 157 " --> pdb=" O   SER B 153 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 162 through 183
      removed outlier: 4.147A  pdb=" N   ARG B 166 " --> pdb=" O   GLN B 162 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   LEU B 171 " --> pdb=" O   ALA B 167 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 194 through 234
    Processing helix  chain 'B' and resid 243 through 270
      removed outlier: 4.492A  pdb=" N   VAL B 247 " --> pdb=" O   CYS B 243 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   LEU B 248 " --> pdb=" O   LEU B 244 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   ALA B 249 " --> pdb=" O   LEU B 245 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   LEU B 250 " --> pdb=" O   GLY B 246 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   SER B 253 " --> pdb=" O   ALA B 249 " (cutoff:3.500A)
      removed outlier: 4.498A  pdb=" N   GLY B 255 " --> pdb=" O   VAL B 251 " (cutoff:3.500A)
      removed outlier: 4.433A  pdb=" N   ALA B 256 " --> pdb=" O   ILE B 252 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   LEU B 261 " --> pdb=" O   LEU B 257 " (cutoff:3.500A)
      removed outlier: 4.136A  pdb=" N   ALA B 262 " --> pdb=" O   GLY B 258 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   PHE B 270 " --> pdb=" O   GLY B 266 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 273 through 286
      removed outlier: 4.051A  pdb=" N   PHE B 277 " --> pdb=" O   ASP B 273 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 290 through 298
    Processing helix  chain 'B' and resid 307 through 323
      removed outlier: 3.631A  pdb=" N   SER B 312 " --> pdb=" O   GLN B 308 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   GLY B 313 " --> pdb=" O   GLN B 309 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 326 through 332
      removed outlier: 3.698A  pdb=" N   ARG B 330 " --> pdb=" O   ALA B 326 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 342 through 364
      removed outlier: 4.121A  pdb=" N   GLU B 348 " --> pdb=" O   LEU B 344 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 365 through 381
      removed outlier: 4.324A  pdb=" N   LEU B 369 " --> pdb=" O   ASP B 365 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   LEU B 371 " --> pdb=" O   ARG B 367 " (cutoff:3.500A)
      removed outlier: 4.293A  pdb=" N   ASP B 372 " --> pdb=" O   SER B 368 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   GLY B 379 " --> pdb=" O   GLN B 375 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 383 through 393
      removed outlier: 4.011A  pdb=" N   TYR B 390 " --> pdb=" O   GLU B 386 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   LEU B 391 " --> pdb=" O   GLY B 387 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 395 through 405
      removed outlier: 3.649A  pdb=" N   ALA B 399 " --> pdb=" O   SER B 395 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   PHE B 402 " --> pdb=" O   THR B 398 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   SER B 403 " --> pdb=" O   ALA B 399 " (cutoff:3.500A)

    441 hydrogen bonds defined for protein.
    1317 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: 0.70

  Time building geometry restraints manager: 0.73 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: 1790
        1.34 -     1.46: 1317
        1.46 -     1.58: 2622
        1.58 -     1.70: 0
        1.70 -     1.82: 30
  Bond restraints: 5759
  Sorted by residual:
  bond pdb=" C1  NAG F   1 "
       pdb=" O5  NAG F   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.482 -0.076 2.00e-02 2.50e+03 1.43e+01
  bond pdb=" C1  NAG F   2 "
       pdb=" O5  NAG F   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.440 -0.034 2.00e-02 2.50e+03 2.81e+00
  bond pdb=" C1  BMA C   3 "
       pdb=" C2  BMA C   3 "
    ideal  model  delta    sigma   weight residual
    1.519  1.551 -0.032 2.00e-02 2.50e+03 2.57e+00
  bond pdb=" C1  BMA D   3 "
       pdb=" C2  BMA D   3 "
    ideal  model  delta    sigma   weight residual
    1.519  1.549 -0.030 2.00e-02 2.50e+03 2.25e+00
  bond pdb=" C1  NAG C   2 "
       pdb=" O5  NAG C   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.436 -0.030 2.00e-02 2.50e+03 2.19e+00
  ... (remaining 5754 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.47: 7559
        1.47 -     2.93: 223
        2.93 -     4.40: 47
        4.40 -     5.86: 21
        5.86 -     7.33: 13
  Bond angle restraints: 7863
  Sorted by residual:
  angle pdb=" N   ARG A 156 "
        pdb=" CA  ARG A 156 "
        pdb=" C   ARG A 156 "
      ideal   model   delta    sigma   weight residual
     111.30  106.71    4.59 1.43e+00 4.89e-01 1.03e+01
  angle pdb=" C   ARG A 145 "
        pdb=" N   THR A 146 "
        pdb=" CA  THR A 146 "
      ideal   model   delta    sigma   weight residual
     122.79  117.90    4.89 1.78e+00 3.16e-01 7.55e+00
  angle pdb=" CA  ARG A 156 "
        pdb=" CB  ARG A 156 "
        pdb=" CG  ARG A 156 "
      ideal   model   delta    sigma   weight residual
     114.10  119.13   -5.03 2.00e+00 2.50e-01 6.33e+00
  angle pdb=" N   VAL A 332 "
        pdb=" CA  VAL A 332 "
        pdb=" C   VAL A 332 "
      ideal   model   delta    sigma   weight residual
     108.88  113.95   -5.07 2.16e+00 2.14e-01 5.51e+00
  angle pdb=" N   ILE A 238 "
        pdb=" CA  ILE A 238 "
        pdb=" C   ILE A 238 "
      ideal   model   delta    sigma   weight residual
     111.91  109.96    1.95 8.90e-01 1.26e+00 4.80e+00
  ... (remaining 7858 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.99: 3224
       22.99 -    45.98: 255
       45.98 -    68.96: 30
       68.96 -    91.95: 39
       91.95 -   114.94: 23
  Dihedral angle restraints: 3571
    sinusoidal: 1545
      harmonic: 2026
  Sorted by residual:
  dihedral pdb=" CB  CYS B 271 "
           pdb=" SG  CYS B 271 "
           pdb=" SG  CYS B 381 "
           pdb=" CB  CYS B 381 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  146.25  -53.25     1      1.00e+01 1.00e-02 3.86e+01
  dihedral pdb=" CB  CYS A 271 "
           pdb=" SG  CYS A 271 "
           pdb=" SG  CYS A 381 "
           pdb=" CB  CYS A 381 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  143.40  -50.40     1      1.00e+01 1.00e-02 3.48e+01
  dihedral pdb=" CA  GLU A 155 "
           pdb=" C   GLU A 155 "
           pdb=" N   ARG A 156 "
           pdb=" CA  ARG A 156 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.73   24.27     0      5.00e+00 4.00e-02 2.36e+01
  ... (remaining 3568 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.083: 923
       0.083 -    0.165: 51
       0.165 -    0.248: 1
       0.248 -    0.331: 6
       0.331 -    0.413: 1
  Chirality restraints: 982
  Sorted by residual:
  chirality pdb=" C1  NAG G   1 "
            pdb=" ND2 ASN B 351 "
            pdb=" C2  NAG G   1 "
            pdb=" O5  NAG G   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.99   -0.41 2.00e-01 2.50e+01 4.27e+00
  chirality pdb=" C1  NAG E   1 "
            pdb=" ND2 ASN B 126 "
            pdb=" C2  NAG E   1 "
            pdb=" O5  NAG E   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.10   -0.30 2.00e-01 2.50e+01 2.30e+00
  chirality pdb=" C5  BMA C   3 "
            pdb=" C4  BMA C   3 "
            pdb=" C6  BMA C   3 "
            pdb=" O5  BMA C   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.55    0.27 2.00e-01 2.50e+01 1.89e+00
  ... (remaining 979 not shown)

  Planarity restraints: 969
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B 341 "   -0.050 5.00e-02 4.00e+02   7.54e-02 9.09e+00
        pdb=" N   PRO B 342 "    0.130 5.00e-02 4.00e+02
        pdb=" CA  PRO B 342 "   -0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO B 342 "   -0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 346 "    0.010 2.00e-02 2.50e+03   2.09e-02 4.35e+00
        pdb=" C   VAL B 346 "   -0.036 2.00e-02 2.50e+03
        pdb=" O   VAL B 346 "    0.014 2.00e-02 2.50e+03
        pdb=" N   GLN B 347 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN B 347 "   -0.008 2.00e-02 2.50e+03   1.68e-02 2.81e+00
        pdb=" C   GLN B 347 "    0.029 2.00e-02 2.50e+03
        pdb=" O   GLN B 347 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   GLU B 348 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 966 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 776
        2.75 -     3.29: 5852
        3.29 -     3.83: 9409
        3.83 -     4.36: 9783
        4.36 -     4.90: 17338
  Nonbonded interactions: 43158
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A  39 "
            pdb=" OD2 ASP A 269 "
     model   vdw
     2.213 3.040
  nonbonded pdb=" OD1 ASN B 126 "
            pdb=" N2  NAG E   1 "
     model   vdw
     2.316 3.120
  nonbonded pdb=" OD2 ASP A 113 "
            pdb="CA    CA A 603 "
     model   vdw
     2.346 2.510
  nonbonded pdb=" O3  NAG C   1 "
            pdb=" O5  NAG C   2 "
     model   vdw
     2.353 3.040
  nonbonded pdb=" OE2 GLU A 110 "
            pdb="CA    CA A 602 "
     model   vdw
     2.355 2.510
  ... (remaining 43153 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 'C' and (resid 1 through 2 or (resid 3 and (name C1 or name C2 or name C3 \ 
 or name C4 or name C5 or name C6 or name O2 or name O3 or name O4 or name O5 )) \ 
))
  selection = (chain 'D' and (resid 1 through 2 or (resid 3 and (name C1 or name C2 or name C3 \ 
 or name C4 or name C5 or name C6 or name O2 or name O3 or name O4 or name O5 )) \ 
))
  selection = (chain 'E' and (resid 1 through 2 or (resid 3 and (name C1 or name C2 or name C3 \ 
 or name C4 or name C5 or name C6 or name O2 or name O3 or name O4 or name O5 )) \ 
))
  selection = chain 'G'
}

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:             4.170
  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:         0.020
  Set scattering table:                    0.010
  Process input model:                     6.670
  Find NCS groups from input model:        0.030
  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:1.100
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.090
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6816
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.076   5778  Z= 0.186
  Angle     :  0.702   7.329   7916  Z= 0.326
  Chirality :  0.046   0.413    982
  Planarity :  0.004   0.075    963
  Dihedral  : 20.750 114.940   2255
  Min Nonbonded Distance : 2.213

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.51 %
    Favored  : 99.49 %
  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:  2.01 (0.34), residues: 693
  helix:  1.98 (0.23), residues: 546
  sheet:  None (None), residues: 0
  loop : -1.19 (0.53), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 117 
 TYR   0.019   0.001   TYR A 296 
 PHE   0.015   0.001   PHE A 402 
 TRP   0.008   0.001   TRP A  88 
 HIS   0.008   0.001   HIS A 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 5759)
  covalent geometry    : angle       0.67649 ( 7863)
  SS BOND              : bond        0.00265 (    4)
  SS BOND              : angle       1.81908 (    8)
  hydrogen bonds       : bond        0.14995 (  441)
  hydrogen bonds       : angle       5.85006 ( 1317)
  link_BETA1-4         : bond        0.00467 (    9)
  link_BETA1-4         : angle       2.24020 (   27)
  link_NAG-ASN         : bond        0.00765 (    6)
  link_NAG-ASN         : angle       2.78048 (   18)

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

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

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.202 
Fit side-chains
REVERT: A  405 ILE cc_start: 0.8137 (mp) cc_final: 0.7908 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 0.0867
  time to fit residues: 8.9835
Evaluate side-chains
  60 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    3.9990
   chunk 27 optimal weight:    3.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
** A  41 GLN ** 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 = 0.4381 r_free = 0.4381 target = 0.162171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.144024 restraints weight = 11019.910|
|-----------------------------------------------------------------------------|
r_work (start): 0.4175 rms_B_bonded: 2.62
r_work: 0.4076 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.4076
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7019
moved from start:          0.1219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5778  Z= 0.157
  Angle     :  0.723   9.104   7916  Z= 0.332
  Chirality :  0.045   0.333    982
  Planarity :  0.004   0.059    963
  Dihedral  : 15.336  93.742   1064
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 10.71 %
    Favored  : 87.59 %
  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:  2.14 (0.33), residues: 693
  helix:  2.12 (0.23), residues: 550
  sheet:  None (None), residues: 0
  loop : -1.45 (0.52), residues: 143

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 334 
 TYR   0.011   0.001   TYR A 373 
 PHE   0.024   0.002   PHE A 380 
 TRP   0.012   0.001   TRP A  11 
 HIS   0.003   0.001   HIS B 336 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 5759)
  covalent geometry    : angle       0.68988 ( 7863)
  SS BOND              : bond        0.00237 (    4)
  SS BOND              : angle       1.16411 (    8)
  hydrogen bonds       : bond        0.05554 (  441)
  hydrogen bonds       : angle       4.60906 ( 1317)
  link_BETA1-4         : bond        0.00700 (    9)
  link_BETA1-4         : angle       3.01467 (   27)
  link_NAG-ASN         : bond        0.00669 (    6)
  link_NAG-ASN         : angle       2.75336 (   18)

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

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

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 66
  time to evaluate  : 0.210 
Fit side-chains
REVERT: A   53 CYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8677 (t)
REVERT: A  348 GLU cc_start: 0.7899 (tp30) cc_final: 0.7646 (tp30)
REVERT: A  405 ILE cc_start: 0.8087 (mp) cc_final: 0.7868 (mt)
  outliers start: 10
  outliers final: 6
  residues processed: 72
  average time/residue: 0.0801
  time to fit residues: 7.5049
Evaluate side-chains
  72 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 65
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 CYS
Chi-restraints excluded: chain A residue  224 CYS
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  273 ASP
Chi-restraints excluded: chain A residue  295 TYR
Chi-restraints excluded: chain B residue  197 VAL
Chi-restraints excluded: chain B residue  226 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 66 optimal weight:    2.9990
   chunk 2 optimal weight:    6.9990
   chunk 63 optimal weight:    0.9980
   chunk 30 optimal weight:    1.9990
   chunk 35 optimal weight:    0.7980
   chunk 65 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   chunk 33 optimal weight:    0.6980
   chunk 25 optimal weight:    0.7980
   chunk 51 optimal weight:    0.7980
   chunk 57 optimal weight:    0.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 315 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4385 r_free = 0.4385 target = 0.162157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.143805 restraints weight = 10800.848|
|-----------------------------------------------------------------------------|
r_work (start): 0.4172 rms_B_bonded: 2.62
r_work: 0.4073 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.4073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7030
moved from start:          0.1503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5778  Z= 0.141
  Angle     :  0.672  10.006   7916  Z= 0.307
  Chirality :  0.042   0.318    982
  Planarity :  0.004   0.040    963
  Dihedral  : 11.863  86.439   1064
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 13.95 %
    Favored  : 83.84 %
  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:  2.15 (0.33), residues: 693
  helix:  2.15 (0.22), residues: 555
  sheet:  None (None), residues: 0
  loop : -1.70 (0.51), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 117 
 TYR   0.011   0.001   TYR A 373 
 PHE   0.026   0.002   PHE A 402 
 TRP   0.008   0.001   TRP A  11 
 HIS   0.003   0.001   HIS B 315 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 5759)
  covalent geometry    : angle       0.63814 ( 7863)
  SS BOND              : bond        0.00226 (    4)
  SS BOND              : angle       0.92175 (    8)
  hydrogen bonds       : bond        0.05206 (  441)
  hydrogen bonds       : angle       4.33598 ( 1317)
  link_BETA1-4         : bond        0.00444 (    9)
  link_BETA1-4         : angle       2.93896 (   27)
  link_NAG-ASN         : bond        0.00664 (    6)
  link_NAG-ASN         : angle       2.69649 (   18)

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

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

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 67
  time to evaluate  : 0.206 
Fit side-chains
REVERT: A   53 CYS cc_start: 0.8979 (m) cc_final: 0.8712 (t)
REVERT: A  348 GLU cc_start: 0.7922 (tp30) cc_final: 0.7657 (tp30)
  outliers start: 13
  outliers final: 10
  residues processed: 74
  average time/residue: 0.0765
  time to fit residues: 7.4389
Evaluate side-chains
  76 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 66
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  224 CYS
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  273 ASP
Chi-restraints excluded: chain A residue  295 TYR
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain B residue  197 VAL
Chi-restraints excluded: chain B residue  226 LEU
Chi-restraints excluded: chain B residue  325 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 17 optimal weight:    0.6980
   chunk 56 optimal weight:    2.9990
   chunk 35 optimal weight:    5.9990
   chunk 37 optimal weight:    4.9990
   chunk 9 optimal weight:    0.8980
   chunk 68 optimal weight:   10.0000
   chunk 15 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9980
   chunk 31 optimal weight:    0.0010
   chunk 7 optimal weight:    0.5980
   chunk 16 optimal weight:    0.6980
   overall best weight:    0.5386

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

Flipped N/Q/H residues before XYZ refinement:
** A  41 GLN ** 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 = 0.4420 r_free = 0.4420 target = 0.164056 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.146156 restraints weight = 10962.642|
|-----------------------------------------------------------------------------|
r_work (start): 0.4254 rms_B_bonded: 2.60
r_work: 0.4152 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.4152
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7006
moved from start:          0.1683

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5778  Z= 0.128
  Angle     :  0.644  10.896   7916  Z= 0.294
  Chirality :  0.040   0.293    982
  Planarity :  0.003   0.035    963
  Dihedral  :  9.873  77.512   1064
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 16.16 %
    Favored  : 81.63 %
  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:  2.32 (0.33), residues: 693
  helix:  2.26 (0.23), residues: 557
  sheet:  None (None), residues: 0
  loop : -1.67 (0.52), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 117 
 TYR   0.011   0.001   TYR A 373 
 PHE   0.020   0.001   PHE A  60 
 TRP   0.008   0.001   TRP A  11 
 HIS   0.002   0.000   HIS A 124 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 5759)
  covalent geometry    : angle       0.61234 ( 7863)
  SS BOND              : bond        0.00244 (    4)
  SS BOND              : angle       0.86880 (    8)
  hydrogen bonds       : bond        0.04796 (  441)
  hydrogen bonds       : angle       4.16095 ( 1317)
  link_BETA1-4         : bond        0.00478 (    9)
  link_BETA1-4         : angle       2.75480 (   27)
  link_NAG-ASN         : bond        0.00639 (    6)
  link_NAG-ASN         : angle       2.67473 (   18)

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

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

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 68
  time to evaluate  : 0.198 
Fit side-chains
REVERT: A   53 CYS cc_start: 0.8848 (m) cc_final: 0.8597 (t)
REVERT: A  348 GLU cc_start: 0.7860 (tp30) cc_final: 0.7584 (tp30)
  outliers start: 13
  outliers final: 9
  residues processed: 76
  average time/residue: 0.0736
  time to fit residues: 7.4199
Evaluate side-chains
  72 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 63
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  273 ASP
Chi-restraints excluded: chain A residue  295 TYR
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  409 ILE
Chi-restraints excluded: chain B residue  197 VAL
Chi-restraints excluded: chain B residue  226 LEU
Chi-restraints excluded: chain B residue  325 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 39 optimal weight:    3.9990
   chunk 37 optimal weight:    4.9990
   chunk 18 optimal weight:    0.9990
   chunk 7 optimal weight:    0.8980
   chunk 1 optimal weight:    9.9990
   chunk 68 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 54 optimal weight:    9.9990
   chunk 47 optimal weight:    2.9990
   chunk 58 optimal weight:    0.4980
   chunk 53 optimal weight:    0.7980
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
** A  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 315 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4375 r_free = 0.4375 target = 0.159837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.141687 restraints weight = 11263.032|
|-----------------------------------------------------------------------------|
r_work (start): 0.4176 rms_B_bonded: 2.61
r_work: 0.4073 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.4073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7102
moved from start:          0.1920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   5778  Z= 0.158
  Angle     :  0.690  11.699   7916  Z= 0.316
  Chirality :  0.042   0.330    982
  Planarity :  0.004   0.033    963
  Dihedral  :  8.878  64.578   1064
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 17.52 %
    Favored  : 79.59 %
  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:  2.14 (0.33), residues: 693
  helix:  2.14 (0.22), residues: 556
  sheet:  None (None), residues: 0
  loop : -1.72 (0.51), residues: 137

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 330 
 TYR   0.012   0.001   TYR A 373 
 PHE   0.009   0.001   PHE A 380 
 TRP   0.007   0.001   TRP B 210 
 HIS   0.003   0.001   HIS B 336 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 5759)
  covalent geometry    : angle       0.65869 ( 7863)
  SS BOND              : bond        0.00311 (    4)
  SS BOND              : angle       1.03677 (    8)
  hydrogen bonds       : bond        0.05360 (  441)
  hydrogen bonds       : angle       4.24182 ( 1317)
  link_BETA1-4         : bond        0.00403 (    9)
  link_BETA1-4         : angle       2.66157 (   27)
  link_NAG-ASN         : bond        0.00546 (    6)
  link_NAG-ASN         : angle       2.98346 (   18)

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

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

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 62
  time to evaluate  : 0.190 
Fit side-chains
REVERT: A   53 CYS cc_start: 0.8852 (m) cc_final: 0.8625 (t)
REVERT: A  348 GLU cc_start: 0.7850 (tp30) cc_final: 0.7601 (tp30)
  outliers start: 17
  outliers final: 13
  residues processed: 72
  average time/residue: 0.0743
  time to fit residues: 7.1787
Evaluate side-chains
  75 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 62
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  273 ASP
Chi-restraints excluded: chain A residue  295 TYR
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  409 ILE
Chi-restraints excluded: chain B residue  197 VAL
Chi-restraints excluded: chain B residue  206 ASP
Chi-restraints excluded: chain B residue  226 LEU
Chi-restraints excluded: chain B residue  270 PHE
Chi-restraints excluded: chain B residue  325 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 37 optimal weight:    4.9990
   chunk 40 optimal weight:    8.9990
   chunk 51 optimal weight:    0.9980
   chunk 12 optimal weight:    0.8980
   chunk 0 optimal weight:    5.9990
   chunk 42 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9990
   chunk 62 optimal weight:    0.0000
   chunk 14 optimal weight:    1.9990
   chunk 32 optimal weight:    0.6980
   overall best weight:    0.7184

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

Flipped N/Q/H residues before XYZ refinement:
** A  41 GLN ** 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 = 0.4299 r_free = 0.4299 target = 0.159047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.140756 restraints weight = 11190.095|
|-----------------------------------------------------------------------------|
r_work (start): 0.4147 rms_B_bonded: 2.54
r_work: 0.4060 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.4060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7058
moved from start:          0.1996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5778  Z= 0.132
  Angle     :  0.648  11.116   7916  Z= 0.296
  Chirality :  0.040   0.295    982
  Planarity :  0.003   0.033    963
  Dihedral  :  7.703  54.863   1064
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 18.88 %
    Favored  : 78.57 %
  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 are not related in a simple way.
  whole:  2.33 (0.33), residues: 693
  helix:  2.27 (0.22), residues: 557
  sheet:  None (None), residues: 0
  loop : -1.72 (0.51), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 345 
 TYR   0.011   0.001   TYR A 373 
 PHE   0.020   0.001   PHE A  60 
 TRP   0.008   0.001   TRP A  11 
 HIS   0.003   0.001   HIS B 124 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 5759)
  covalent geometry    : angle       0.61257 ( 7863)
  SS BOND              : bond        0.00257 (    4)
  SS BOND              : angle       0.84598 (    8)
  hydrogen bonds       : bond        0.04950 (  441)
  hydrogen bonds       : angle       4.13754 ( 1317)
  link_BETA1-4         : bond        0.00478 (    9)
  link_BETA1-4         : angle       2.55411 (   27)
  link_NAG-ASN         : bond        0.00607 (    6)
  link_NAG-ASN         : angle       3.24062 (   18)

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

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

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 65
  time to evaluate  : 0.202 
Fit side-chains
REVERT: A   53 CYS cc_start: 0.8824 (m) cc_final: 0.8593 (t)
REVERT: A  348 GLU cc_start: 0.7798 (tp30) cc_final: 0.7558 (tp30)
REVERT: B  226 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7682 (mp)
  outliers start: 15
  outliers final: 10
  residues processed: 75
  average time/residue: 0.0790
  time to fit residues: 7.7153
Evaluate side-chains
  74 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 63
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  273 ASP
Chi-restraints excluded: chain A residue  295 TYR
Chi-restraints excluded: chain A residue  354 GLU
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  409 ILE
Chi-restraints excluded: chain B residue  197 VAL
Chi-restraints excluded: chain B residue  226 LEU
Chi-restraints excluded: chain B residue  325 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 41 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9990
   chunk 1 optimal weight:    9.9990
   chunk 50 optimal weight:    0.1980
   chunk 36 optimal weight:    0.8980
   chunk 56 optimal weight:    0.5980
   chunk 24 optimal weight:    2.9990
   chunk 62 optimal weight:    0.0670
   chunk 26 optimal weight:    0.9990
   chunk 5 optimal weight:    5.9990
   chunk 42 optimal weight:    0.7980
   overall best weight:    0.5118

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

Flipped N/Q/H residues before XYZ refinement:
** A  41 GLN ** 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 = 0.4315 r_free = 0.4315 target = 0.160174 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.141886 restraints weight = 11283.523|
|-----------------------------------------------------------------------------|
r_work (start): 0.4147 rms_B_bonded: 2.56
r_work: 0.4059 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.4059
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7038
moved from start:          0.2126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   5778  Z= 0.127
  Angle     :  0.628   8.286   7916  Z= 0.289
  Chirality :  0.039   0.286    982
  Planarity :  0.003   0.034    963
  Dihedral  :  6.824  54.664   1064
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 19.90 %
    Favored  : 77.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.42 (0.33), residues: 693
  helix:  2.35 (0.23), residues: 557
  sheet:  None (None), residues: 0
  loop : -1.74 (0.51), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 117 
 TYR   0.011   0.001   TYR A 373 
 PHE   0.016   0.001   PHE B 277 
 TRP   0.007   0.001   TRP A  11 
 HIS   0.003   0.001   HIS B 124 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 5759)
  covalent geometry    : angle       0.59288 ( 7863)
  SS BOND              : bond        0.00199 (    4)
  SS BOND              : angle       0.79421 (    8)
  hydrogen bonds       : bond        0.04725 (  441)
  hydrogen bonds       : angle       4.06596 ( 1317)
  link_BETA1-4         : bond        0.00483 (    9)
  link_BETA1-4         : angle       2.38739 (   27)
  link_NAG-ASN         : bond        0.00618 (    6)
  link_NAG-ASN         : angle       3.28723 (   18)

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

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

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 65
  time to evaluate  : 0.207 
Fit side-chains
REVERT: A   53 CYS cc_start: 0.8848 (m) cc_final: 0.8588 (t)
REVERT: A  348 GLU cc_start: 0.7816 (tp30) cc_final: 0.7568 (tp30)
  outliers start: 15
  outliers final: 11
  residues processed: 76
  average time/residue: 0.0714
  time to fit residues: 7.2923
Evaluate side-chains
  72 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 61
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  273 ASP
Chi-restraints excluded: chain A residue  295 TYR
Chi-restraints excluded: chain A residue  354 GLU
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  409 ILE
Chi-restraints excluded: chain B residue  197 VAL
Chi-restraints excluded: chain B residue  325 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 17 optimal weight:    0.8980
   chunk 46 optimal weight:    3.9990
   chunk 2 optimal weight:    0.0470
   chunk 3 optimal weight:    3.9990
   chunk 42 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9990
   chunk 45 optimal weight:    0.6980
   chunk 27 optimal weight:    1.9990
   chunk 47 optimal weight:    0.7980
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.6880

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

Flipped N/Q/H residues before XYZ refinement:
** A  41 GLN ** 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 = 0.4304 r_free = 0.4304 target = 0.159456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.141588 restraints weight = 10909.354|
|-----------------------------------------------------------------------------|
r_work (start): 0.4164 rms_B_bonded: 2.52
r_work: 0.4073 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.4073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7025
moved from start:          0.2214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5778  Z= 0.132
  Angle     :  0.631   7.995   7916  Z= 0.291
  Chirality :  0.039   0.281    982
  Planarity :  0.003   0.031    963
  Dihedral  :  6.678  54.690   1064
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 20.24 %
    Favored  : 76.87 %
  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:  2.46 (0.33), residues: 693
  helix:  2.38 (0.22), residues: 557
  sheet:  None (None), residues: 0
  loop : -1.75 (0.50), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 117 
 TYR   0.011   0.001   TYR A 373 
 PHE   0.022   0.001   PHE A  60 
 TRP   0.007   0.001   TRP A  11 
 HIS   0.002   0.001   HIS B 124 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 5759)
  covalent geometry    : angle       0.60005 ( 7863)
  SS BOND              : bond        0.00226 (    4)
  SS BOND              : angle       0.83167 (    8)
  hydrogen bonds       : bond        0.04758 (  441)
  hydrogen bonds       : angle       4.05250 ( 1317)
  link_BETA1-4         : bond        0.00470 (    9)
  link_BETA1-4         : angle       2.31727 (   27)
  link_NAG-ASN         : bond        0.00589 (    6)
  link_NAG-ASN         : angle       3.08193 (   18)

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

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

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 61
  time to evaluate  : 0.163 
Fit side-chains
REVERT: A   34 PRO cc_start: 0.7327 (Cg_exo) cc_final: 0.7111 (Cg_endo)
REVERT: A   53 CYS cc_start: 0.8846 (m) cc_final: 0.8575 (t)
REVERT: A  321 MET cc_start: 0.7393 (mmm) cc_final: 0.6851 (mtt)
REVERT: A  348 GLU cc_start: 0.7866 (tp30) cc_final: 0.7590 (tp30)
  outliers start: 17
  outliers final: 11
  residues processed: 74
  average time/residue: 0.0706
  time to fit residues: 6.9609
Evaluate side-chains
  71 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 60
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue  224 CYS
Chi-restraints excluded: chain A residue  273 ASP
Chi-restraints excluded: chain A residue  295 TYR
Chi-restraints excluded: chain A residue  354 GLU
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  409 ILE
Chi-restraints excluded: chain B residue  197 VAL
Chi-restraints excluded: chain B residue  206 ASP
Chi-restraints excluded: chain B residue  325 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 47 optimal weight:    0.9990
   chunk 16 optimal weight:    0.0970
   chunk 62 optimal weight:    2.9990
   chunk 53 optimal weight:    0.7980
   chunk 43 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 63 optimal weight:    0.9980
   chunk 37 optimal weight:    2.9990
   chunk 29 optimal weight:    0.6980
   chunk 7 optimal weight:    0.7980
   chunk 45 optimal weight:    0.5980
   overall best weight:    0.5978

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

Flipped N/Q/H residues before XYZ refinement:
** A  41 GLN ** 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 = 0.4311 r_free = 0.4311 target = 0.159994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.142130 restraints weight = 11084.544|
|-----------------------------------------------------------------------------|
r_work (start): 0.4134 rms_B_bonded: 2.56
r_work: 0.4042 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.4042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7016
moved from start:          0.2275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   5778  Z= 0.130
  Angle     :  0.622   7.467   7916  Z= 0.288
  Chirality :  0.039   0.273    982
  Planarity :  0.003   0.029    963
  Dihedral  :  6.546  54.584   1064
  Min Nonbonded Distance : 2.346

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 20.58 %
    Favored  : 76.87 %
  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:  2.48 (0.33), residues: 693
  helix:  2.45 (0.23), residues: 551
  sheet:  None (None), residues: 0
  loop : -1.81 (0.48), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 117 
 TYR   0.011   0.001   TYR A 373 
 PHE   0.021   0.001   PHE B 277 
 TRP   0.007   0.001   TRP A  11 
 HIS   0.002   0.000   HIS B 315 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 5759)
  covalent geometry    : angle       0.59163 ( 7863)
  SS BOND              : bond        0.00214 (    4)
  SS BOND              : angle       0.81983 (    8)
  hydrogen bonds       : bond        0.04704 (  441)
  hydrogen bonds       : angle       4.04587 ( 1317)
  link_BETA1-4         : bond        0.00518 (    9)
  link_BETA1-4         : angle       2.25893 (   27)
  link_NAG-ASN         : bond        0.00594 (    6)
  link_NAG-ASN         : angle       3.01026 (   18)

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

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

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 60
  time to evaluate  : 0.156 
Fit side-chains
REVERT: A   34 PRO cc_start: 0.7415 (Cg_exo) cc_final: 0.7214 (Cg_endo)
REVERT: A   53 CYS cc_start: 0.8854 (m) cc_final: 0.8580 (t)
REVERT: A  348 GLU cc_start: 0.7864 (tp30) cc_final: 0.7598 (tp30)
  outliers start: 15
  outliers final: 14
  residues processed: 72
  average time/residue: 0.0715
  time to fit residues: 6.8076
Evaluate side-chains
  74 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 60
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue  224 CYS
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  273 ASP
Chi-restraints excluded: chain A residue  295 TYR
Chi-restraints excluded: chain A residue  354 GLU
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  409 ILE
Chi-restraints excluded: chain B residue  197 VAL
Chi-restraints excluded: chain B residue  206 ASP
Chi-restraints excluded: chain B residue  325 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 57 optimal weight:    0.0980
   chunk 49 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9990
   chunk 47 optimal weight:    2.9990
   chunk 24 optimal weight:    4.9990
   chunk 68 optimal weight:    7.9990
   chunk 34 optimal weight:    3.9990
   chunk 2 optimal weight:    0.6980
   chunk 37 optimal weight:    3.9990
   overall best weight:    0.9586

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

Flipped N/Q/H residues before XYZ refinement:
** A  41 GLN ** 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 = 0.4295 r_free = 0.4295 target = 0.158399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.139909 restraints weight = 11417.895|
|-----------------------------------------------------------------------------|
r_work (start): 0.4101 rms_B_bonded: 2.59
r_work: 0.4007 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.4007
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7061
moved from start:          0.2327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   5778  Z= 0.145
  Angle     :  0.657   9.361   7916  Z= 0.304
  Chirality :  0.040   0.269    982
  Planarity :  0.004   0.030    963
  Dihedral  :  6.622  54.973   1064
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 20.92 %
    Favored  : 76.53 %
  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:  2.42 (0.33), residues: 693
  helix:  2.36 (0.22), residues: 557
  sheet:  None (None), residues: 0
  loop : -1.77 (0.50), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 117 
 TYR   0.011   0.001   TYR A 373 
 PHE   0.020   0.001   PHE A  60 
 TRP   0.006   0.001   TRP A  11 
 HIS   0.002   0.001   HIS B 315 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 5759)
  covalent geometry    : angle       0.62860 ( 7863)
  SS BOND              : bond        0.00257 (    4)
  SS BOND              : angle       0.93698 (    8)
  hydrogen bonds       : bond        0.04968 (  441)
  hydrogen bonds       : angle       4.10780 ( 1317)
  link_BETA1-4         : bond        0.00455 (    9)
  link_BETA1-4         : angle       2.25350 (   27)
  link_NAG-ASN         : bond        0.00598 (    6)
  link_NAG-ASN         : angle       3.03354 (   18)

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

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

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 60
  time to evaluate  : 0.141 
Fit side-chains
REVERT: A   53 CYS cc_start: 0.8869 (m) cc_final: 0.8598 (t)
REVERT: A  348 GLU cc_start: 0.7828 (tp30) cc_final: 0.7580 (tp30)
  outliers start: 15
  outliers final: 14
  residues processed: 72
  average time/residue: 0.0720
  time to fit residues: 6.7580
Evaluate side-chains
  73 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 59
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue  224 CYS
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  273 ASP
Chi-restraints excluded: chain A residue  295 TYR
Chi-restraints excluded: chain A residue  354 GLU
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  409 ILE
Chi-restraints excluded: chain B residue  197 VAL
Chi-restraints excluded: chain B residue  204 LEU
Chi-restraints excluded: chain B residue  206 ASP
Chi-restraints excluded: chain B residue  325 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 41 optimal weight:    4.9990
   chunk 7 optimal weight:    0.9980
   chunk 18 optimal weight:    0.7980
   chunk 37 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9990
   chunk 64 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 43 optimal weight:    0.7980
   chunk 26 optimal weight:    1.9990
   chunk 38 optimal weight:    5.9990
   chunk 54 optimal weight:    9.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
** A  41 GLN ** 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 = 0.4305 r_free = 0.4305 target = 0.158315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.140147 restraints weight = 10932.091|
|-----------------------------------------------------------------------------|
r_work (start): 0.4104 rms_B_bonded: 2.51
r_work: 0.4015 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.4015
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7085
moved from start:          0.2440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   5778  Z= 0.155
  Angle     :  0.667   7.138   7916  Z= 0.314
  Chirality :  0.040   0.288    982
  Planarity :  0.004   0.042    963
  Dihedral  :  6.738  55.171   1064
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 21.26 %
    Favored  : 76.36 %
  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:  2.26 (0.33), residues: 693
  helix:  2.24 (0.22), residues: 558
  sheet:  None (None), residues: 0
  loop : -1.83 (0.50), residues: 135

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 117 
 TYR   0.011   0.001   TYR A 373 
 PHE   0.023   0.002   PHE B 277 
 TRP   0.006   0.001   TRP B 210 
 HIS   0.002   0.001   HIS A  20 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 5759)
  covalent geometry    : angle       0.63792 ( 7863)
  SS BOND              : bond        0.00267 (    4)
  SS BOND              : angle       1.05109 (    8)
  hydrogen bonds       : bond        0.05239 (  441)
  hydrogen bonds       : angle       4.14741 ( 1317)
  link_BETA1-4         : bond        0.00426 (    9)
  link_BETA1-4         : angle       2.26251 (   27)
  link_NAG-ASN         : bond        0.00567 (    6)
  link_NAG-ASN         : angle       3.07270 (   18)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1188.98 seconds
wall clock time: 21 minutes 9.46 seconds (1269.46 seconds total)