Starting phenix.real_space_refine
on Fri Aug 22 19:46:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j8m_36074/08_2025/8j8m_36074_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j8m_36074/08_2025/8j8m_36074.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.58
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j8m_36074/08_2025/8j8m_36074_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j8m_36074/08_2025/8j8m_36074_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8j8m_36074/08_2025/8j8m_36074.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j8m_36074/08_2025/8j8m_36074.map"
  }
  resolution = 3.58
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.039
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      27      5.16       5
     C    4811      2.51       5
     N    1188      2.21       5
     O    1336      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7362
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 3656
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 469, 3656
          Classifications: {'peptide': 469}
          Link IDs: {'PTRANS': 22, 'TRANS': 446}
    Chain: "B"
      Number of atoms: 3579
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 463, 3579
          Classifications: {'peptide': 463}
          Link IDs: {'PTRANS': 24, 'TRANS': 438}
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      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: "E"
      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: "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: "B"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Time building chain proxies: 1.88, per 1000 atoms: 0.26
  Number of scatterers: 7362
  At special positions: 0
  Unit cell: (99.645, 83.22, 125.925, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      27     16.00
     O    1336      8.00
     N    1188      7.00
     C    4811      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 211 " - pdb=" SG  CYS B 164 " 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 D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
    NAG-ASN
      " NAG C   1 " - " ASN A 507 "
      " NAG D   1 " - " ASN A 382 "
      " NAG E   1 " - " ASN A 366 "
      " NAG F   1 " - " ASN A 425 "
  Time building additional restraints: 0.60
  Conformation dependent library (CDL) restraints added in 392.6 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1718

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 4 sheets defined
      58.8% alpha, 5.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 166 through 174
    Processing helix  chain 'A' and resid 178 through 207
      removed outlier: 3.672A  pdb=" N   ARG A 183 " --> pdb=" O   TRP A 179 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   TRP A 184 " --> pdb=" O   VAL A 180 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 256
      removed outlier: 5.276A  pdb=" N   ASP A 250 " --> pdb=" O   LYS A 246 " (cutoff:3.500A)
      removed outlier: 5.480A  pdb=" N   TYR A 251 " --> pdb=" O   GLY A 247 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   LEU A 252 " --> pdb=" O   ARG A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 301
    Processing helix  chain 'A' and resid 324 through 340
      removed outlier: 4.371A  pdb=" N   GLU A 336 " --> pdb=" O   LYS A 332 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   PHE A 337 " --> pdb=" O   ASP A 333 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 351 through 354
    Processing helix  chain 'A' and resid 356 through 372
      removed outlier: 3.747A  pdb=" N   PHE A 360 " --> pdb=" O   ASP A 356 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   PHE A 371 " --> pdb=" O   ILE A 367 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   SER A 372 " --> pdb=" O   THR A 368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 393
    Processing helix  chain 'A' and resid 404 through 409
      removed outlier: 3.552A  pdb=" N   ASP A 408 " --> pdb=" O   TYR A 405 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   SER A 409 " --> pdb=" O   LEU A 406 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 428
    Processing helix  chain 'A' and resid 450 through 459
      removed outlier: 3.817A  pdb=" N   PHE A 459 " --> pdb=" O   GLN A 455 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 509 through 516
      removed outlier: 4.218A  pdb=" N   GLU A 515 " --> pdb=" O   LYS A 511 " (cutoff:3.500A)
      removed outlier: 4.249A  pdb=" N   ASP A 516 " --> pdb=" O   GLY A 512 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 519 through 532
      removed outlier: 3.800A  pdb=" N   SER A 532 " --> pdb=" O   SER A 528 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 534 through 540
    Processing helix  chain 'B' and resid 51 through 64
      removed outlier: 3.593A  pdb=" N   ILE B  59 " --> pdb=" O   GLY B  55 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 66 through 79
      removed outlier: 3.648A  pdb=" N   VAL B  70 " --> pdb=" O   SER B  66 " (cutoff:3.500A)
      Proline residue:  B  72  - end of helix
    Processing helix  chain 'B' and resid 81 through 110
    Processing helix  chain 'B' and resid 115 through 123
      removed outlier: 3.732A  pdb=" N   LEU B 121 " --> pdb=" O   TYR B 117 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 125 through 139
      removed outlier: 3.796A  pdb=" N   ALA B 129 " --> pdb=" O   GLY B 125 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 139 through 158
      removed outlier: 3.702A  pdb=" N   GLN B 145 " --> pdb=" O   ARG B 141 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   TYR B 146 " --> pdb=" O   PRO B 142 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 159 through 161
      No H-bonds generated for 'chain 'B' and resid 159 through 161'
    Processing helix  chain 'B' and resid 167 through 189
      removed outlier: 3.581A  pdb=" N   SER B 189 " --> pdb=" O   VAL B 185 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 189 through 221
      removed outlier: 3.661A  pdb=" N   ALA B 193 " --> pdb=" O   SER B 189 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 242 through 254
      removed outlier: 3.724A  pdb=" N   PHE B 252 " --> pdb=" O   TYR B 248 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   ALA B 253 " --> pdb=" O   SER B 249 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   TYR B 254 " --> pdb=" O   GLY B 250 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 260 through 264
    Processing helix  chain 'B' and resid 269 through 300
      removed outlier: 3.596A  pdb=" N   LEU B 274 " --> pdb=" O   PRO B 270 " (cutoff:3.500A)
      Proline residue:  B 275  - end of helix
      Proline residue:  B 283  - end of helix
      removed outlier: 3.795A  pdb=" N   THR B 299 " --> pdb=" O   ALA B 295 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   LEU B 300 " --> pdb=" O   TYR B 296 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 301 through 308
    Processing helix  chain 'B' and resid 310 through 320
    Processing helix  chain 'B' and resid 325 through 356
      removed outlier: 3.795A  pdb=" N   VAL B 329 " --> pdb=" O   TRP B 325 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   GLY B 337 " --> pdb=" O   LEU B 333 " (cutoff:3.500A)
      removed outlier: 4.233A  pdb=" N   SER B 338 " --> pdb=" O   SER B 334 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   LEU B 349 " --> pdb=" O   THR B 345 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   GLU B 356 " --> pdb=" O   VAL B 352 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 373 through 386
    Processing helix  chain 'B' and resid 387 through 390
      removed outlier: 3.566A  pdb=" N   SER B 390 " --> pdb=" O   TYR B 387 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 387 through 390'
    Processing helix  chain 'B' and resid 393 through 395
      No H-bonds generated for 'chain 'B' and resid 393 through 395'
    Processing helix  chain 'B' and resid 396 through 422
      removed outlier: 3.534A  pdb=" N   PHE B 400 " --> pdb=" O   VAL B 396 " (cutoff:3.500A)
      removed outlier: 4.600A  pdb=" N   PHE B 402 " --> pdb=" O   ASN B 398 " (cutoff:3.500A)
      removed outlier: 4.527A  pdb=" N   TRP B 405 " --> pdb=" O   SER B 401 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   VAL B 408 " --> pdb=" O   ASN B 404 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   ALA B 409 " --> pdb=" O   TRP B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 434 through 454
    Processing helix  chain 'B' and resid 454 through 466
      removed outlier: 3.726A  pdb=" N   ILE B 465 " --> pdb=" O   GLY B 461 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   LEU B 466 " --> pdb=" O   PHE B 462 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 467 through 476
      removed outlier: 4.359A  pdb=" N   VAL B 471 " --> pdb=" O   SER B 467 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 482 through 500
    Processing sheet with id=AA1, first strand: chain 'A' and resid 225 through 227
      removed outlier: 6.320A  pdb=" N   LEU A 225 " --> pdb=" O   PHE A 467 " (cutoff:3.500A)
      removed outlier: 6.799A  pdb=" N   CYS A 432 " --> pdb=" O   THR A 464 " (cutoff:3.500A)
      removed outlier: 7.774A  pdb=" N   VAL A 466 " --> pdb=" O   CYS A 432 " (cutoff:3.500A)
      removed outlier: 6.542A  pdb=" N   TRP A 434 " --> pdb=" O   VAL A 466 " (cutoff:3.500A)
      removed outlier: 8.478A  pdb=" N   SER A 468 " --> pdb=" O   TRP A 434 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 260 through 261
      removed outlier: 5.917A  pdb=" N   LEU A 260 " --> pdb=" O   ILE A 306 " (cutoff:3.500A)
      removed outlier: 7.301A  pdb=" N   ASP A 308 " --> pdb=" O   LEU A 260 " (cutoff:3.500A)
      removed outlier: 8.496A  pdb=" N   GLN A 347 " --> pdb=" O   VAL A 305 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   LEU A 307 " --> pdb=" O   GLN A 347 " (cutoff:3.500A)
      removed outlier: 8.712A  pdb=" N   ARG A 349 " --> pdb=" O   LEU A 307 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   LEU A 377 " --> pdb=" O   LEU A 400 " (cutoff:3.500A)
      removed outlier: 7.486A  pdb=" N   THR A 402 " --> pdb=" O   LEU A 377 " (cutoff:3.500A)
      removed outlier: 6.124A  pdb=" N   ALA A 379 " --> pdb=" O   THR A 402 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 541 through 545
      removed outlier: 4.203A  pdb=" N   SER A 553 " --> pdb=" O   PHE A 545 " (cutoff:3.500A)
      removed outlier: 6.997A  pdb=" N   GLY A 622 " --> pdb=" O   SER A 599 " (cutoff:3.500A)
      removed outlier: 4.997A  pdb=" N   SER A 599 " --> pdb=" O   GLY A 622 " (cutoff:3.500A)
      removed outlier: 7.751A  pdb=" N   LEU A 624 " --> pdb=" O   LEU A 597 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   LEU A 597 " --> pdb=" O   LEU A 624 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   ALA A 594 " --> pdb=" O   LEU A 610 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 575 through 576

    379 hydrogen bonds defined for protein.
    1113 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: 1.10

  Time building geometry restraints manager: 0.81 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: 2229
        1.34 -     1.45: 1114
        1.45 -     1.57: 4161
        1.57 -     1.69: 0
        1.69 -     1.81: 40
  Bond restraints: 7544
  Sorted by residual:
  bond pdb=" CD2 TRP B 601 "
       pdb=" CE3 TRP B 601 "
    ideal  model  delta    sigma   weight residual
    1.398  1.555 -0.157 1.60e-02 3.91e+03 9.64e+01
  bond pdb=" CE2 TRP B 601 "
       pdb=" CZ2 TRP B 601 "
    ideal  model  delta    sigma   weight residual
    1.394  1.549 -0.155 2.10e-02 2.27e+03 5.47e+01
  bond pdb=" CZ2 TRP B 601 "
       pdb=" CH2 TRP B 601 "
    ideal  model  delta    sigma   weight residual
    1.368  1.491 -0.123 1.90e-02 2.77e+03 4.17e+01
  bond pdb=" CG  TRP B 601 "
       pdb=" CD2 TRP B 601 "
    ideal  model  delta    sigma   weight residual
    1.433  1.341  0.092 1.80e-02 3.09e+03 2.61e+01
  bond pdb=" CE3 TRP B 601 "
       pdb=" CZ3 TRP B 601 "
    ideal  model  delta    sigma   weight residual
    1.382  1.493 -0.111 3.00e-02 1.11e+03 1.36e+01
  ... (remaining 7539 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.61: 9945
        1.61 -     3.22: 249
        3.22 -     4.83: 53
        4.83 -     6.43: 19
        6.43 -     8.04: 8
  Bond angle restraints: 10274
  Sorted by residual:
  angle pdb=" C   PHE B 231 "
        pdb=" CA  PHE B 231 "
        pdb=" CB  PHE B 231 "
      ideal   model   delta    sigma   weight residual
     116.54  110.91    5.63 1.15e+00 7.56e-01 2.40e+01
  angle pdb=" CA  ILE B 327 "
        pdb=" C   ILE B 327 "
        pdb=" N   PRO B 328 "
      ideal   model   delta    sigma   weight residual
     120.83  118.02    2.81 5.90e-01 2.87e+00 2.27e+01
  angle pdb=" N   TRP B 325 "
        pdb=" CA  TRP B 325 "
        pdb=" C   TRP B 325 "
      ideal   model   delta    sigma   weight residual
     114.31  109.78    4.53 1.29e+00 6.01e-01 1.23e+01
  angle pdb=" CG  TRP B 601 "
        pdb=" CD2 TRP B 601 "
        pdb=" CE3 TRP B 601 "
      ideal   model   delta    sigma   weight residual
     133.90  130.50    3.40 1.00e+00 1.00e+00 1.16e+01
  angle pdb=" N   GLY B 321 "
        pdb=" CA  GLY B 321 "
        pdb=" C   GLY B 321 "
      ideal   model   delta    sigma   weight residual
     115.59  111.10    4.49 1.32e+00 5.74e-01 1.16e+01
  ... (remaining 10269 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.12: 4096
       23.12 -    46.23: 306
       46.23 -    69.35: 56
       69.35 -    92.47: 30
       92.47 -   115.58: 32
  Dihedral angle restraints: 4520
    sinusoidal: 1847
      harmonic: 2673
  Sorted by residual:
  dihedral pdb=" CB  CYS A 211 "
           pdb=" SG  CYS A 211 "
           pdb=" SG  CYS B 164 "
           pdb=" CB  CYS B 164 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00 -177.18  -89.82     1      1.00e+01 1.00e-02 9.57e+01
  dihedral pdb=" O3  NAG C   2 "
           pdb=" C3  NAG C   2 "
           pdb=" C4  NAG C   2 "
           pdb=" O4  NAG C   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
     295.45  179.87  115.58     1      3.00e+01 1.11e-03 1.53e+01
  dihedral pdb=" C2  NAG C   2 "
           pdb=" C3  NAG C   2 "
           pdb=" C4  NAG C   2 "
           pdb=" O4  NAG C   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
     175.11   60.03  115.08     1      3.00e+01 1.11e-03 1.52e+01
  ... (remaining 4517 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.194: 1207
       0.194 -    0.389: 3
       0.389 -    0.583: 1
       0.583 -    0.778: 0
       0.778 -    0.972: 1
  Chirality restraints: 1212
  Sorted by residual:
  chirality pdb=" C1  NAG F   2 "
            pdb=" O4  NAG F   1 "
            pdb=" C2  NAG F   2 "
            pdb=" O5  NAG F   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.43   -0.97 2.00e-02 2.50e+03 2.36e+03
  chirality pdb=" C1  NAG E   2 "
            pdb=" O4  NAG E   1 "
            pdb=" C2  NAG E   2 "
            pdb=" O5  NAG E   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.17   -0.23 2.00e-02 2.50e+03 1.37e+02
  chirality pdb=" C1  NAG C   2 "
            pdb=" O4  NAG C   1 "
            pdb=" C2  NAG C   2 "
            pdb=" O5  NAG C   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.28   -0.12 2.00e-02 2.50e+03 3.89e+01
  ... (remaining 1209 not shown)

  Planarity restraints: 1275
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 366 "    0.160 2.00e-02 2.50e+03   3.78e-01 1.78e+03
        pdb=" CG  ASN A 366 "   -0.111 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 366 "    0.177 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 366 "   -0.669 2.00e-02 2.50e+03
        pdb=" C1  NAG E   1 "    0.443 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 425 "   -0.217 2.00e-02 2.50e+03   2.84e-01 1.01e+03
        pdb=" CG  ASN A 425 "    0.094 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 425 "   -0.016 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 425 "    0.481 2.00e-02 2.50e+03
        pdb=" C1  NAG F   1 "   -0.341 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG D   2 "   -0.332 2.00e-02 2.50e+03   2.82e-01 9.96e+02
        pdb=" C7  NAG D   2 "    0.083 2.00e-02 2.50e+03
        pdb=" C8  NAG D   2 "   -0.178 2.00e-02 2.50e+03
        pdb=" N2  NAG D   2 "    0.495 2.00e-02 2.50e+03
        pdb=" O7  NAG D   2 "   -0.068 2.00e-02 2.50e+03
  ... (remaining 1272 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 717
        2.74 -     3.28: 7868
        3.28 -     3.82: 12483
        3.82 -     4.36: 13722
        4.36 -     4.90: 23686
  Nonbonded interactions: 58476
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN B 145 "
            pdb=" OG  SER B 342 "
     model   vdw
     2.203 3.120
  nonbonded pdb=" OG1 THR A 460 "
            pdb=" OH  TYR A 554 "
     model   vdw
     2.207 3.040
  nonbonded pdb=" OH  TYR A 469 "
            pdb=" O   PRO A 488 "
     model   vdw
     2.220 3.040
  nonbonded pdb=" OD1 ASP A 493 "
            pdb=" OG  SER A 496 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" O   TYR A 251 "
            pdb=" OG  SER A 254 "
     model   vdw
     2.246 3.040
  ... (remaining 58471 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'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.080
  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:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     8.180
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
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   0.157   7553  Z= 0.266
  Angle     :  0.821  32.255  10300  Z= 0.380
  Chirality :  0.053   0.972   1212
  Planarity :  0.016   0.282   1271
  Dihedral  : 20.770 115.585   2799
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  :  0.63 %
    Favored  : 98.48 %
  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 aren not related in a simple way.
  whole:  0.67 (0.29), residues: 928
  helix:  1.64 (0.25), residues: 498
  sheet: -0.59 (0.58), residues: 63
  loop : -1.04 (0.32), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 421 
 TYR   0.013   0.001   TYR B 318 
 PHE   0.022   0.001   PHE A 320 
 TRP   0.026   0.001   TRP B 478 
 HIS   0.004   0.001   HIS A 221 

Details of bonding type rmsd
  covalent geometry    : bond        0.00469 ( 7544)
  covalent geometry    : angle       0.67716 (10274)
  SS BOND              : bond        0.00003 (    1)
  SS BOND              : angle       1.99797 (    2)
  hydrogen bonds       : bond        0.14646 (  379)
  hydrogen bonds       : angle       5.80093 ( 1113)
  link_BETA1-4         : bond        0.00446 (    4)
  link_BETA1-4         : angle       3.15818 (   12)
  link_NAG-ASN         : bond        0.08465 (    4)
  link_NAG-ASN         : angle      13.24288 (   12)

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 90
  time to evaluate  : 0.299 
Fit side-chains
   revert: symmetry clash
REVERT: A  508 MET cc_start: 0.7810 (mpp) cc_final: 0.7484 (mpp)
REVERT: B  120 MET cc_start: 0.8447 (ttp) cc_final: 0.7933 (tmm)
REVERT: B  132 LYS cc_start: 0.8921 (tptp) cc_final: 0.8695 (tptp)
REVERT: B  305 MET cc_start: 0.9077 (mtt) cc_final: 0.8713 (mtt)
REVERT: B  365 MET cc_start: 0.8216 (mpp) cc_final: 0.7951 (mpp)
  outliers start: 7
  outliers final: 2
  residues processed: 93
  average time/residue: 0.0597
  time to fit residues: 8.4400
Evaluate side-chains
  60 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 58
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  260 LEU
Chi-restraints excluded: chain B residue  327 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 49 optimal weight:    7.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    0.1980
   chunk 33 optimal weight:    9.9990
   chunk 65 optimal weight:    9.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    0.7980
   chunk 74 optimal weight:    0.7980
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
A 438 GLN
** A 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 561 ASN
** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 367 HIS
B 505 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.074698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.053305 restraints weight = 31562.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.055351 restraints weight = 15368.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.056565 restraints weight = 10676.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.057267 restraints weight = 8839.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.057688 restraints weight = 7995.109|
|-----------------------------------------------------------------------------|
r_work (final): 0.3084
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7867
moved from start:          0.1299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7553  Z= 0.150
  Angle     :  0.842  20.015  10300  Z= 0.358
  Chirality :  0.047   0.323   1212
  Planarity :  0.004   0.044   1271
  Dihedral  : 20.240 117.862   1160
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  :  7.87 %
    Favored  : 90.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.87 (0.29), residues: 928
  helix:  1.78 (0.24), residues: 505
  sheet: -0.62 (0.59), residues: 63
  loop : -0.94 (0.33), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 348 
 TYR   0.014   0.001   TYR B 117 
 PHE   0.022   0.002   PHE B 439 
 TRP   0.014   0.001   TRP B 478 
 HIS   0.005   0.001   HIS B 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 7544)
  covalent geometry    : angle       0.74811 (10274)
  SS BOND              : bond        0.00035 (    1)
  SS BOND              : angle       0.65185 (    2)
  hydrogen bonds       : bond        0.04795 (  379)
  hydrogen bonds       : angle       4.33575 ( 1113)
  link_BETA1-4         : bond        0.01707 (    4)
  link_BETA1-4         : angle       3.96744 (   12)
  link_NAG-ASN         : bond        0.00810 (    4)
  link_NAG-ASN         : angle      10.63398 (   12)

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 63
  time to evaluate  : 0.274 
Fit side-chains
REVERT: A  271 ASP cc_start: 0.8695 (m-30) cc_final: 0.8406 (t0)
REVERT: A  508 MET cc_start: 0.8280 (mpp) cc_final: 0.7768 (mpp)
REVERT: B  120 MET cc_start: 0.9196 (ttp) cc_final: 0.8594 (tmm)
REVERT: B  365 MET cc_start: 0.8403 (mpp) cc_final: 0.7942 (mpp)
REVERT: B  500 MET cc_start: 0.8638 (mtm) cc_final: 0.8013 (mmt)
  outliers start: 9
  outliers final: 4
  residues processed: 67
  average time/residue: 0.0577
  time to fit residues: 6.1282
Evaluate side-chains
  54 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 50
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 ILE
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  285 VAL
Chi-restraints excluded: chain B residue  400 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 55 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 7 optimal weight:    3.9990
   chunk 43 optimal weight:    7.9990
   chunk 80 optimal weight:    1.9990
   chunk 6 optimal weight:    4.9990
   chunk 41 optimal weight:    0.2980
   chunk 63 optimal weight:    9.9990
   chunk 46 optimal weight:    4.9990
   chunk 82 optimal weight:    0.6980
   chunk 56 optimal weight:    0.8980
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
A 539 HIS
B 273 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.073816 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.052599 restraints weight = 31395.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.054596 restraints weight = 15280.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.055771 restraints weight = 10637.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.056488 restraints weight = 8820.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.056880 restraints weight = 7981.657|
|-----------------------------------------------------------------------------|
r_work (final): 0.3069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7891
moved from start:          0.1710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7553  Z= 0.139
  Angle     :  0.763  15.494  10300  Z= 0.330
  Chirality :  0.045   0.293   1212
  Planarity :  0.004   0.041   1271
  Dihedral  : 16.744 110.393   1156
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 7.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 11.29 %
    Favored  : 86.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.04 (0.29), residues: 928
  helix:  2.00 (0.24), residues: 500
  sheet: -0.79 (0.60), residues: 65
  loop : -0.91 (0.33), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 348 
 TYR   0.012   0.001   TYR B 117 
 PHE   0.013   0.001   PHE B 130 
 TRP   0.014   0.001   TRP B 405 
 HIS   0.003   0.001   HIS B 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 7544)
  covalent geometry    : angle       0.69847 (10274)
  SS BOND              : bond        0.00009 (    1)
  SS BOND              : angle       0.51822 (    2)
  hydrogen bonds       : bond        0.04308 (  379)
  hydrogen bonds       : angle       4.01363 ( 1113)
  link_BETA1-4         : bond        0.01754 (    4)
  link_BETA1-4         : angle       2.78300 (   12)
  link_NAG-ASN         : bond        0.00799 (    4)
  link_NAG-ASN         : angle       8.63458 (   12)

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 55
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  271 ASP cc_start: 0.8751 (m-30) cc_final: 0.8447 (t0)
REVERT: A  508 MET cc_start: 0.8432 (mpp) cc_final: 0.7896 (mpp)
REVERT: B  120 MET cc_start: 0.9160 (ttp) cc_final: 0.8938 (ttp)
REVERT: B  365 MET cc_start: 0.8353 (mpp) cc_final: 0.7942 (mpp)
REVERT: B  500 MET cc_start: 0.8687 (mtm) cc_final: 0.7995 (mmt)
  outliers start: 14
  outliers final: 10
  residues processed: 62
  average time/residue: 0.0505
  time to fit residues: 5.1703
Evaluate side-chains
  62 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 52
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 ILE
Chi-restraints excluded: chain A residue  382 ASN
Chi-restraints excluded: chain B residue   66 SER
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  285 VAL
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  396 VAL
Chi-restraints excluded: chain B residue  400 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 46 optimal weight:    4.9990
   chunk 91 optimal weight:    6.9990
   chunk 9 optimal weight:    6.9990
   chunk 32 optimal weight:   20.0000
   chunk 80 optimal weight:    0.6980
   chunk 72 optimal weight:    5.9990
   chunk 64 optimal weight:    8.9990
   chunk 63 optimal weight:    5.9990
   chunk 14 optimal weight:    0.9990
   chunk 15 optimal weight:    4.9990
   chunk 50 optimal weight:    3.9990
   overall best weight:    3.1388

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

Flipped N/Q/H residues before XYZ refinement:
A 561 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.074022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.052963 restraints weight = 32411.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.054788 restraints weight = 17676.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.055850 restraints weight = 13189.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.056476 restraints weight = 11269.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.056772 restraints weight = 10373.117|
|-----------------------------------------------------------------------------|
r_work (final): 0.3160
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8259
moved from start:          0.2199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   7553  Z= 0.226
  Angle     :  0.785  12.583  10300  Z= 0.356
  Chirality :  0.046   0.315   1212
  Planarity :  0.004   0.047   1271
  Dihedral  : 15.113 112.038   1156
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 9.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.14 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 13.83 %
    Favored  : 84.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.88 (0.28), residues: 928
  helix:  1.82 (0.24), residues: 504
  sheet: -0.93 (0.60), residues: 65
  loop : -0.91 (0.33), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 348 
 TYR   0.011   0.001   TYR B 117 
 PHE   0.018   0.002   PHE B 344 
 TRP   0.013   0.001   TRP B 405 
 HIS   0.003   0.001   HIS A 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00508 ( 7544)
  covalent geometry    : angle       0.73754 (10274)
  SS BOND              : bond        0.00014 (    1)
  SS BOND              : angle       0.63472 (    2)
  hydrogen bonds       : bond        0.04987 (  379)
  hydrogen bonds       : angle       4.21934 ( 1113)
  link_BETA1-4         : bond        0.01453 (    4)
  link_BETA1-4         : angle       2.82416 (   12)
  link_NAG-ASN         : bond        0.00534 (    4)
  link_NAG-ASN         : angle       7.44816 (   12)

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 50
  time to evaluate  : 0.294 
Fit side-chains
REVERT: A  271 ASP cc_start: 0.8295 (m-30) cc_final: 0.8055 (t0)
REVERT: A  508 MET cc_start: 0.8633 (mpp) cc_final: 0.8011 (mpp)
REVERT: B  120 MET cc_start: 0.9086 (ttp) cc_final: 0.8688 (ttp)
REVERT: B  247 LEU cc_start: 0.9316 (mm) cc_final: 0.9068 (tt)
REVERT: B  365 MET cc_start: 0.8588 (mpp) cc_final: 0.8328 (mpp)
  outliers start: 16
  outliers final: 11
  residues processed: 59
  average time/residue: 0.0569
  time to fit residues: 5.4776
Evaluate side-chains
  61 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 50
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 ILE
Chi-restraints excluded: chain B residue   66 SER
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  239 ASP
Chi-restraints excluded: chain B residue  251 LEU
Chi-restraints excluded: chain B residue  260 LEU
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  285 VAL
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  396 VAL
Chi-restraints excluded: chain B residue  400 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 42 optimal weight:    0.0040
   chunk 7 optimal weight:    0.5980
   chunk 80 optimal weight:    2.9990
   chunk 31 optimal weight:    6.9990
   chunk 11 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   chunk 48 optimal weight:    2.9990
   chunk 49 optimal weight:    3.9990
   chunk 60 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   overall best weight:    1.7198

-------------------------------------------------------------------------------
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 = 0.3589 r_free = 0.3589 target = 0.074921 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.054393 restraints weight = 32396.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.056318 restraints weight = 17312.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.057469 restraints weight = 12660.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.058005 restraints weight = 10759.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.058461 restraints weight = 9931.000|
|-----------------------------------------------------------------------------|
r_work (final): 0.3147
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8231
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   0.037   7553  Z= 0.146
  Angle     :  0.722  10.695  10300  Z= 0.320
  Chirality :  0.045   0.282   1212
  Planarity :  0.004   0.040   1271
  Dihedral  : 14.630 111.560   1156
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.06 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 15.86 %
    Favored  : 82.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.11 (0.29), residues: 928
  helix:  2.03 (0.24), residues: 504
  sheet: -0.92 (0.61), residues: 65
  loop : -0.83 (0.33), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 348 
 TYR   0.012   0.001   TYR B 472 
 PHE   0.013   0.001   PHE B 130 
 TRP   0.011   0.001   TRP B 405 
 HIS   0.002   0.001   HIS B 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 7544)
  covalent geometry    : angle       0.67633 (10274)
  SS BOND              : bond        0.00023 (    1)
  SS BOND              : angle       0.52719 (    2)
  hydrogen bonds       : bond        0.04423 (  379)
  hydrogen bonds       : angle       4.01243 ( 1113)
  link_BETA1-4         : bond        0.01394 (    4)
  link_BETA1-4         : angle       2.76303 (   12)
  link_NAG-ASN         : bond        0.00524 (    4)
  link_NAG-ASN         : angle       6.93989 (   12)

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 49
  time to evaluate  : 0.285 
Fit side-chains
REVERT: A  271 ASP cc_start: 0.8045 (m-30) cc_final: 0.7833 (t0)
REVERT: A  508 MET cc_start: 0.8679 (mpp) cc_final: 0.8056 (mpp)
REVERT: B  120 MET cc_start: 0.9037 (ttp) cc_final: 0.8656 (ttp)
REVERT: B  247 LEU cc_start: 0.9333 (mm) cc_final: 0.9069 (tp)
REVERT: B  305 MET cc_start: 0.8966 (mtt) cc_final: 0.8757 (mtt)
REVERT: B  365 MET cc_start: 0.8518 (mpp) cc_final: 0.8255 (mpp)
REVERT: B  500 MET cc_start: 0.8546 (mtm) cc_final: 0.8151 (mmt)
  outliers start: 11
  outliers final: 10
  residues processed: 55
  average time/residue: 0.0618
  time to fit residues: 5.4121
Evaluate side-chains
  57 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 47
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 ILE
Chi-restraints excluded: chain B residue   66 SER
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  239 ASP
Chi-restraints excluded: chain B residue  260 LEU
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  285 VAL
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  396 VAL
Chi-restraints excluded: chain B residue  400 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 29 optimal weight:    3.9990
   chunk 6 optimal weight:    5.9990
   chunk 62 optimal weight:    5.9990
   chunk 26 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 28 optimal weight:    0.0020
   chunk 89 optimal weight:    0.0870
   chunk 53 optimal weight:    5.9990
   chunk 33 optimal weight:    0.0050
   chunk 1 optimal weight:    3.9990
   chunk 31 optimal weight:    0.0980
   overall best weight:    0.4382

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

Flipped N/Q/H residues before XYZ refinement:
A 217 GLN
A 347 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.076827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.056662 restraints weight = 32032.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.058636 restraints weight = 17114.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.059802 restraints weight = 12455.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.060508 restraints weight = 10553.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.060841 restraints weight = 9641.683|
|-----------------------------------------------------------------------------|
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8176
moved from start:          0.2353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   7553  Z= 0.107
  Angle     :  0.697  12.150  10300  Z= 0.304
  Chirality :  0.043   0.290   1212
  Planarity :  0.003   0.041   1271
  Dihedral  : 13.972 112.231   1156
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 16.37 %
    Favored  : 82.49 %
  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 aren not related in a simple way.
  whole:  1.19 (0.29), residues: 928
  helix:  2.05 (0.24), residues: 508
  sheet: -0.73 (0.62), residues: 65
  loop : -0.78 (0.33), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 563 
 TYR   0.009   0.001   TYR B 117 
 PHE   0.015   0.001   PHE B 130 
 TRP   0.010   0.001   TRP B 405 
 HIS   0.002   0.001   HIS B 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00215 ( 7544)
  covalent geometry    : angle       0.65505 (10274)
  SS BOND              : bond        0.00038 (    1)
  SS BOND              : angle       0.36132 (    2)
  hydrogen bonds       : bond        0.03705 (  379)
  hydrogen bonds       : angle       3.76077 ( 1113)
  link_BETA1-4         : bond        0.01339 (    4)
  link_BETA1-4         : angle       2.65806 (   12)
  link_NAG-ASN         : bond        0.00642 (    4)
  link_NAG-ASN         : angle       6.50978 (   12)

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 54
  time to evaluate  : 0.268 
Fit side-chains
REVERT: A  271 ASP cc_start: 0.8146 (m-30) cc_final: 0.7875 (t0)
REVERT: A  508 MET cc_start: 0.8689 (mpp) cc_final: 0.7991 (mpp)
REVERT: B  120 MET cc_start: 0.8885 (ttp) cc_final: 0.8450 (tmm)
REVERT: B  247 LEU cc_start: 0.9300 (mm) cc_final: 0.9046 (tp)
REVERT: B  305 MET cc_start: 0.8980 (mtt) cc_final: 0.8763 (mtt)
REVERT: B  365 MET cc_start: 0.8414 (mpp) cc_final: 0.8112 (mpp)
  outliers start: 9
  outliers final: 6
  residues processed: 59
  average time/residue: 0.0585
  time to fit residues: 5.5012
Evaluate side-chains
  55 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 49
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 ILE
Chi-restraints excluded: chain B residue   66 SER
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  239 ASP
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  400 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 38 optimal weight:   10.0000
   chunk 36 optimal weight:    4.9990
   chunk 54 optimal weight:    0.8980
   chunk 39 optimal weight:    1.9990
   chunk 32 optimal weight:    8.9990
   chunk 68 optimal weight:    4.9990
   chunk 37 optimal weight:    4.9990
   chunk 80 optimal weight:    3.9990
   chunk 49 optimal weight:    8.9990
   chunk 71 optimal weight:    6.9990
   chunk 14 optimal weight:    4.9990
   overall best weight:    3.3788

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

Flipped N/Q/H residues before XYZ refinement:
B 218 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.081088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.059371 restraints weight = 33720.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.061321 restraints weight = 17049.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.062437 restraints weight = 12348.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.062924 restraints weight = 10561.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.063326 restraints weight = 9840.971|
|-----------------------------------------------------------------------------|
r_work (final): 0.3353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8217
moved from start:          0.2673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   7553  Z= 0.241
  Angle     :  0.785  12.563  10300  Z= 0.358
  Chirality :  0.045   0.289   1212
  Planarity :  0.004   0.043   1271
  Dihedral  : 13.843 111.933   1156
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 9.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 17.64 %
    Favored  : 80.84 %
  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 aren not related in a simple way.
  whole:  1.05 (0.29), residues: 928
  helix:  1.97 (0.24), residues: 503
  sheet: -0.91 (0.63), residues: 65
  loop : -0.83 (0.33), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 348 
 TYR   0.011   0.001   TYR B 117 
 PHE   0.019   0.002   PHE B 439 
 TRP   0.010   0.001   TRP A 431 
 HIS   0.004   0.001   HIS A 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00544 ( 7544)
  covalent geometry    : angle       0.74946 (10274)
  SS BOND              : bond        0.00006 (    1)
  SS BOND              : angle       0.52324 (    2)
  hydrogen bonds       : bond        0.04861 (  379)
  hydrogen bonds       : angle       4.15064 ( 1113)
  link_BETA1-4         : bond        0.01278 (    4)
  link_BETA1-4         : angle       2.54927 (   12)
  link_NAG-ASN         : bond        0.00393 (    4)
  link_NAG-ASN         : angle       6.39997 (   12)

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 45
  time to evaluate  : 0.306 
Fit side-chains
REVERT: A  271 ASP cc_start: 0.8519 (m-30) cc_final: 0.8172 (t0)
REVERT: A  307 LEU cc_start: 0.9493 (tp) cc_final: 0.9279 (tp)
REVERT: A  508 MET cc_start: 0.8655 (mpp) cc_final: 0.7996 (mpp)
REVERT: B  247 LEU cc_start: 0.9264 (mm) cc_final: 0.9031 (tp)
REVERT: B  289 TYR cc_start: 0.8682 (OUTLIER) cc_final: 0.8347 (m-10)
REVERT: B  365 MET cc_start: 0.8559 (mpp) cc_final: 0.8250 (mpp)
  outliers start: 12
  outliers final: 9
  residues processed: 55
  average time/residue: 0.0575
  time to fit residues: 5.1811
Evaluate side-chains
  55 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 45
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 ILE
Chi-restraints excluded: chain B residue   66 SER
Chi-restraints excluded: chain B residue  103 TYR
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  239 ASP
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  285 VAL
Chi-restraints excluded: chain B residue  289 TYR
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  400 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 50 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9980
   chunk 4 optimal weight:    5.9990
   chunk 61 optimal weight:    0.7980
   chunk 26 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9980
   chunk 39 optimal weight:    1.9990
   chunk 19 optimal weight:    7.9990
   chunk 25 optimal weight:    5.9990
   chunk 44 optimal weight:    0.9990
   chunk 87 optimal weight:    7.9990
   overall best weight:    0.9584

-------------------------------------------------------------------------------
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 = 0.3689 r_free = 0.3689 target = 0.077631 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.058461 restraints weight = 30160.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.060394 restraints weight = 15883.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.061582 restraints weight = 11331.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.062262 restraints weight = 9457.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.062480 restraints weight = 8577.294|
|-----------------------------------------------------------------------------|
r_work (final): 0.3247
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8203
moved from start:          0.2652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   7553  Z= 0.118
  Angle     :  0.701  13.386  10300  Z= 0.313
  Chirality :  0.043   0.280   1212
  Planarity :  0.003   0.039   1271
  Dihedral  : 13.598 111.314   1156
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 18.27 %
    Favored  : 80.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.26 (0.29), residues: 928
  helix:  2.14 (0.24), residues: 506
  sheet: -0.72 (0.62), residues: 65
  loop : -0.79 (0.33), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 348 
 TYR   0.010   0.001   TYR B 117 
 PHE   0.017   0.001   PHE B 439 
 TRP   0.010   0.001   TRP B 405 
 HIS   0.002   0.001   HIS A 620 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 7544)
  covalent geometry    : angle       0.66410 (10274)
  SS BOND              : bond        0.00007 (    1)
  SS BOND              : angle       0.37396 (    2)
  hydrogen bonds       : bond        0.04117 (  379)
  hydrogen bonds       : angle       3.85253 ( 1113)
  link_BETA1-4         : bond        0.01229 (    4)
  link_BETA1-4         : angle       2.48414 (   12)
  link_NAG-ASN         : bond        0.00583 (    4)
  link_NAG-ASN         : angle       6.21153 (   12)

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 51
  time to evaluate  : 0.296 
Fit side-chains
REVERT: A  508 MET cc_start: 0.8686 (mpp) cc_final: 0.7965 (mpp)
REVERT: A  615 LEU cc_start: 0.8727 (mt) cc_final: 0.8414 (mt)
REVERT: B  120 MET cc_start: 0.9033 (ttp) cc_final: 0.8411 (tmm)
REVERT: B  247 LEU cc_start: 0.9352 (mm) cc_final: 0.9069 (tp)
REVERT: B  289 TYR cc_start: 0.8802 (OUTLIER) cc_final: 0.8397 (m-10)
REVERT: B  365 MET cc_start: 0.8450 (mpp) cc_final: 0.8110 (mpp)
REVERT: B  500 MET cc_start: 0.8374 (mtm) cc_final: 0.8091 (mmt)
  outliers start: 10
  outliers final: 6
  residues processed: 56
  average time/residue: 0.0612
  time to fit residues: 5.4286
Evaluate side-chains
  56 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 49
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 ILE
Chi-restraints excluded: chain B residue   66 SER
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  239 ASP
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  289 TYR
Chi-restraints excluded: chain B residue  400 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 69 optimal weight:    0.9980
   chunk 51 optimal weight:    2.9990
   chunk 72 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9980
   chunk 91 optimal weight:    0.9980
   chunk 27 optimal weight:    3.9990
   chunk 31 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9980
   chunk 35 optimal weight:    1.9990
   chunk 37 optimal weight:    0.6980
   chunk 20 optimal weight:    1.9990
   overall best weight:    0.9180

-------------------------------------------------------------------------------
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 = 0.3697 r_free = 0.3697 target = 0.080042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.060299 restraints weight = 30129.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.062138 restraints weight = 16739.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.063258 restraints weight = 12316.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.063735 restraints weight = 10444.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.064171 restraints weight = 9659.020|
|-----------------------------------------------------------------------------|
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8208
moved from start:          0.2706

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   7553  Z= 0.115
  Angle     :  0.716  14.487  10300  Z= 0.316
  Chirality :  0.043   0.279   1212
  Planarity :  0.003   0.040   1271
  Dihedral  : 13.297 111.096   1156
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 7.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.06 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 18.78 %
    Favored  : 80.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.30 (0.29), residues: 928
  helix:  2.16 (0.24), residues: 505
  sheet: -0.58 (0.63), residues: 65
  loop : -0.77 (0.33), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 348 
 TYR   0.010   0.001   TYR B 117 
 PHE   0.017   0.001   PHE B 439 
 TRP   0.022   0.001   TRP B 405 
 HIS   0.002   0.001   HIS A 620 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 7544)
  covalent geometry    : angle       0.68072 (10274)
  SS BOND              : bond        0.00013 (    1)
  SS BOND              : angle       0.32980 (    2)
  hydrogen bonds       : bond        0.03933 (  379)
  hydrogen bonds       : angle       3.83359 ( 1113)
  link_BETA1-4         : bond        0.01156 (    4)
  link_BETA1-4         : angle       2.44194 (   12)
  link_NAG-ASN         : bond        0.00576 (    4)
  link_NAG-ASN         : angle       6.11570 (   12)

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 48
  time to evaluate  : 0.286 
Fit side-chains
REVERT: A  508 MET cc_start: 0.8680 (mpp) cc_final: 0.7975 (mpp)
REVERT: A  615 LEU cc_start: 0.8743 (mt) cc_final: 0.8382 (mt)
REVERT: B  120 MET cc_start: 0.8924 (ttp) cc_final: 0.8320 (tmm)
REVERT: B  247 LEU cc_start: 0.9342 (mm) cc_final: 0.9049 (tt)
REVERT: B  289 TYR cc_start: 0.8801 (OUTLIER) cc_final: 0.8397 (m-10)
REVERT: B  304 GLN cc_start: 0.9651 (mt0) cc_final: 0.9293 (tm-30)
REVERT: B  365 MET cc_start: 0.8415 (mpp) cc_final: 0.8072 (mpp)
REVERT: B  500 MET cc_start: 0.8347 (mtm) cc_final: 0.8069 (mmt)
  outliers start: 8
  outliers final: 5
  residues processed: 54
  average time/residue: 0.0636
  time to fit residues: 5.4424
Evaluate side-chains
  52 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 46
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 ILE
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  239 ASP
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  289 TYR
Chi-restraints excluded: chain B residue  400 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 18 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9990
   chunk 69 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9990
   chunk 36 optimal weight:    4.9990
   chunk 44 optimal weight:    4.9990
   chunk 72 optimal weight:    3.9990
   chunk 42 optimal weight:    0.0770
   chunk 14 optimal weight:    0.9980
   chunk 81 optimal weight:    5.9990
   chunk 3 optimal weight:    6.9990
   overall best weight:    0.7740

-------------------------------------------------------------------------------
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 = 0.3619 r_free = 0.3619 target = 0.076105 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.055854 restraints weight = 31631.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.057806 restraints weight = 16848.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.059004 restraints weight = 12227.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.059691 restraints weight = 10298.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.060073 restraints weight = 9394.385|
|-----------------------------------------------------------------------------|
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8178
moved from start:          0.2795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   7553  Z= 0.110
  Angle     :  0.718  13.048  10300  Z= 0.315
  Chirality :  0.043   0.277   1212
  Planarity :  0.003   0.041   1271
  Dihedral  : 12.879 110.793   1156
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  : 18.78 %
    Favored  : 80.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.35 (0.29), residues: 928
  helix:  2.18 (0.24), residues: 507
  sheet: -0.54 (0.63), residues: 65
  loop : -0.72 (0.33), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 348 
 TYR   0.008   0.001   TYR B 117 
 PHE   0.016   0.001   PHE B 439 
 TRP   0.019   0.001   TRP B 405 
 HIS   0.003   0.001   HIS A 620 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 ( 7544)
  covalent geometry    : angle       0.68440 (10274)
  SS BOND              : bond        0.00021 (    1)
  SS BOND              : angle       0.24029 (    2)
  hydrogen bonds       : bond        0.03743 (  379)
  hydrogen bonds       : angle       3.73663 ( 1113)
  link_BETA1-4         : bond        0.01102 (    4)
  link_BETA1-4         : angle       2.38828 (   12)
  link_NAG-ASN         : bond        0.00624 (    4)
  link_NAG-ASN         : angle       6.01577 (   12)

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 46
  time to evaluate  : 0.289 
Fit side-chains
REVERT: A  170 LEU cc_start: 0.9160 (tp) cc_final: 0.8951 (tt)
REVERT: A  508 MET cc_start: 0.8686 (mpp) cc_final: 0.7985 (mpp)
REVERT: A  615 LEU cc_start: 0.8852 (mt) cc_final: 0.8471 (mt)
REVERT: B  120 MET cc_start: 0.9058 (ttp) cc_final: 0.8387 (tmm)
REVERT: B  247 LEU cc_start: 0.9305 (mm) cc_final: 0.9024 (tt)
REVERT: B  289 TYR cc_start: 0.8802 (OUTLIER) cc_final: 0.8423 (m-10)
REVERT: B  304 GLN cc_start: 0.9678 (mt0) cc_final: 0.9307 (tm-30)
REVERT: B  365 MET cc_start: 0.8492 (mpp) cc_final: 0.8144 (mpp)
  outliers start: 6
  outliers final: 4
  residues processed: 51
  average time/residue: 0.0604
  time to fit residues: 5.0355
Evaluate side-chains
  51 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 46
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 ILE
Chi-restraints excluded: chain B residue  239 ASP
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  289 TYR
Chi-restraints excluded: chain B residue  400 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 75 optimal weight:    1.9990
   chunk 36 optimal weight:    5.9990
   chunk 45 optimal weight:    4.9990
   chunk 84 optimal weight:    0.0060
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 16 optimal weight:    7.9990
   chunk 79 optimal weight:    0.9980
   overall best weight:    1.4002

-------------------------------------------------------------------------------
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 = 0.3689 r_free = 0.3689 target = 0.079655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.060106 restraints weight = 30306.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.061905 restraints weight = 16912.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.063012 restraints weight = 12452.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.063575 restraints weight = 10541.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.063996 restraints weight = 9700.553|
|-----------------------------------------------------------------------------|
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8210
moved from start:          0.2869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7553  Z= 0.127
  Angle     :  0.712  13.001  10300  Z= 0.313
  Chirality :  0.043   0.278   1212
  Planarity :  0.003   0.040   1271
  Dihedral  : 12.709 110.376   1156
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.06 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 18.78 %
    Favored  : 80.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.42 (0.29), residues: 928
  helix:  2.23 (0.24), residues: 509
  sheet: -0.57 (0.62), residues: 65
  loop : -0.69 (0.33), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 348 
 TYR   0.008   0.001   TYR B 117 
 PHE   0.015   0.001   PHE B 439 
 TRP   0.018   0.001   TRP B 405 
 HIS   0.003   0.001   HIS A 620 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 7544)
  covalent geometry    : angle       0.67881 (10274)
  SS BOND              : bond        0.00011 (    1)
  SS BOND              : angle       0.26900 (    2)
  hydrogen bonds       : bond        0.03866 (  379)
  hydrogen bonds       : angle       3.79385 ( 1113)
  link_BETA1-4         : bond        0.01012 (    4)
  link_BETA1-4         : angle       2.36631 (   12)
  link_NAG-ASN         : bond        0.00571 (    4)
  link_NAG-ASN         : angle       5.89664 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1346.11 seconds
wall clock time: 23 minutes 57.82 seconds (1437.82 seconds total)