Starting phenix.real_space_refine
on Sun May 11 01:50:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wny_37675/05_2025/8wny_37675.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wny_37675/05_2025/8wny_37675.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wny_37675/05_2025/8wny_37675.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wny_37675/05_2025/8wny_37675.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wny_37675/05_2025/8wny_37675.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wny_37675/05_2025/8wny_37675.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.002 sd=   0.077
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      32      5.16       5
     C    4713      2.51       5
     N    1190      2.21       5
     O    1298      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 7233
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3645
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 468, 3645
          Classifications: {'peptide': 468}
          Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 445}
    Chain: "B"
      Number of atoms: 3525
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 456, 3525
          Classifications: {'peptide': 456}
          Link IDs: {'PTRANS': 23, 'TRANS': 432}
    Chain: "A"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "B"
      Number of atoms: 7
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 7
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1, 'PEPT-D': 1}
  Time building chain proxies: 5.27, per 1000 atoms: 0.73
  Number of scatterers: 7233
  At special positions: 0
  Unit cell: (105.12, 77.745, 122.64, 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      32     16.00
     O    1298      8.00
     N    1190      7.00
     C    4713      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 154 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 701 " - " ASN A 366 "
      " NAG A 702 " - " ASN A 382 "
      " NAG A 703 " - " ASN A 425 "
      " NAG A 704 " - " ASN A 507 "
  Time building additional restraints: 2.32
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
    Skipped
      Input residue name is d-peptide
        pdb=" CB  DSN B1001 "
  Number of C-beta restraints generated:  1688

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 5 sheets defined
      63.4% alpha, 6.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.16
  Creating SS restraints...
    Processing helix  chain 'A' and resid 167 through 175
    Processing helix  chain 'A' and resid 178 through 207
      removed outlier: 3.511A  pdb=" N   THR A 182 " --> pdb=" O   GLY A 178 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 236
      removed outlier: 3.693A  pdb=" N   PHE A 234 " --> pdb=" O   ASP A 230 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   GLN A 235 " --> pdb=" O   LEU A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 247
      removed outlier: 3.580A  pdb=" N   GLY A 247 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 248 through 255
    Processing helix  chain 'A' and resid 287 through 301
    Processing helix  chain 'A' and resid 324 through 342
    Processing helix  chain 'A' and resid 350 through 354
      removed outlier: 3.559A  pdb=" N   ASN A 353 " --> pdb=" O   ASP A 350 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 356 through 372
      removed outlier: 3.780A  pdb=" N   PHE A 360 " --> pdb=" O   ASP A 356 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   PHE A 371 " --> pdb=" O   ILE A 367 " (cutoff:3.500A)
      removed outlier: 4.104A  pdb=" N   SER A 372 " --> pdb=" O   THR A 368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 394
      removed outlier: 4.219A  pdb=" N   ILE A 389 " --> pdb=" O   ASP A 385 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   LEU A 390 " --> pdb=" O   LEU A 386 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   SER A 391 " --> pdb=" O   GLN A 387 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   LEU A 392 " --> pdb=" O   GLN A 388 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 412 through 428
    Processing helix  chain 'A' and resid 441 through 445
      removed outlier: 3.724A  pdb=" N   SER A 444 " --> pdb=" O   LEU A 441 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 450 through 460
      removed outlier: 3.975A  pdb=" N   LEU A 456 " --> pdb=" O   ARG A 452 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 519 through 534
      removed outlier: 3.596A  pdb=" N   LEU A 523 " --> pdb=" O   SER A 519 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 534 through 540
    Processing helix  chain 'A' and resid 585 through 589
      removed outlier: 4.240A  pdb=" N   SER A 589 " --> pdb=" O   ALA A 586 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 43 through 54
      removed outlier: 3.536A  pdb=" N   THR B  47 " --> pdb=" O   LEU B  43 " (cutoff:3.500A)
      removed outlier: 4.386A  pdb=" N   ILE B  48 " --> pdb=" O   SER B  44 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ILE B  53 " --> pdb=" O   ILE B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 56 through 59
    Processing helix  chain 'B' and resid 60 through 70
      removed outlier: 3.845A  pdb=" N   GLY B  64 " --> pdb=" O   ILE B  60 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   HIS B  68 " --> pdb=" O   GLY B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 71 through 100
      removed outlier: 3.765A  pdb=" N   VAL B  80 " --> pdb=" O   LEU B  76 " (cutoff:3.500A)
      removed outlier: 4.149A  pdb=" N   ALA B  87 " --> pdb=" O   GLY B  83 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 105 through 114
    Processing helix  chain 'B' and resid 115 through 129
    Processing helix  chain 'B' and resid 129 through 148
    Processing helix  chain 'B' and resid 157 through 179
      removed outlier: 3.547A  pdb=" N   SER B 179 " --> pdb=" O   VAL B 175 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 180 through 211
    Processing helix  chain 'B' and resid 218 through 223
      removed outlier: 3.590A  pdb=" N   PHE B 223 " --> pdb=" O   PRO B 219 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 230 through 242
    Processing helix  chain 'B' and resid 243 through 246
    Processing helix  chain 'B' and resid 247 through 258
      removed outlier: 3.518A  pdb=" N   PHE B 250 " --> pdb=" O   GLY B 247 " (cutoff:3.500A)
      removed outlier: 4.073A  pdb=" N   LEU B 251 " --> pdb=" O   TRP B 248 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   THR B 255 " --> pdb=" O   ASN B 252 " (cutoff:3.500A)
      removed outlier: 5.459A  pdb=" N   GLU B 256 " --> pdb=" O   TYR B 253 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 260 through 291
      removed outlier: 3.506A  pdb=" N   ASN B 264 " --> pdb=" O   ASP B 260 " (cutoff:3.500A)
      Proline residue:  B 266  - end of helix
      Proline residue:  B 274  - end of helix
    Processing helix  chain 'B' and resid 292 through 298
    Processing helix  chain 'B' and resid 301 through 311
    Processing helix  chain 'B' and resid 312 through 315
    Processing helix  chain 'B' and resid 316 through 347
      removed outlier: 3.933A  pdb=" N   VAL B 320 " --> pdb=" O   TRP B 316 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   SER B 325 " --> pdb=" O   SER B 321 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   GLY B 332 " --> pdb=" O   GLY B 328 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   SER B 343 " --> pdb=" O   ARG B 339 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 351 through 356
      removed outlier: 3.588A  pdb=" N   MET B 356 " --> pdb=" O   LEU B 353 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 364 through 380
      removed outlier: 3.727A  pdb=" N   LEU B 380 " --> pdb=" O   ALA B 376 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 383 through 413
    Processing helix  chain 'B' and resid 424 through 445
    Processing helix  chain 'B' and resid 445 through 458
      removed outlier: 3.802A  pdb=" N   CYS B 449 " --> pdb=" O   GLU B 445 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 458 through 467
      removed outlier: 4.190A  pdb=" N   ILE B 462 " --> pdb=" O   THR B 458 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 473 through 492
    Processing sheet with id=AA1, first strand: chain 'A' and resid 400 through 403
      removed outlier: 3.548A  pdb=" N   LEU A 400 " --> pdb=" O   LEU A 377 " (cutoff:3.500A)
      removed outlier: 7.693A  pdb=" N   VAL A 305 " --> pdb=" O   GLY A 345 " (cutoff:3.500A)
      removed outlier: 8.553A  pdb=" N   GLN A 347 " --> pdb=" O   VAL A 305 " (cutoff:3.500A)
      removed outlier: 6.811A  pdb=" N   LEU A 307 " --> pdb=" O   GLN A 347 " (cutoff:3.500A)
      removed outlier: 5.969A  pdb=" N   LEU A 260 " --> pdb=" O   ILE A 306 " (cutoff:3.500A)
      removed outlier: 6.764A  pdb=" N   ASP A 308 " --> pdb=" O   LEU A 260 " (cutoff:3.500A)
      removed outlier: 7.142A  pdb=" N   LEU A 262 " --> pdb=" O   ASP A 308 " (cutoff:3.500A)
      removed outlier: 6.425A  pdb=" N   TRP A 434 " --> pdb=" O   VAL A 466 " (cutoff:3.500A)
      removed outlier: 8.475A  pdb=" N   SER A 468 " --> pdb=" O   TRP A 434 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 266 through 267
    Processing sheet with id=AA3, first strand: chain 'A' and resid 541 through 544
      removed outlier: 6.144A  pdb=" N   ARG A 626 " --> pdb=" O   LEU A 596 " (cutoff:3.500A)
      removed outlier: 5.146A  pdb=" N   LEU A 596 " --> pdb=" O   ARG A 626 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 575 through 576
    Processing sheet with id=AA5, first strand: chain 'B' and resid 357 through 358

    425 hydrogen bonds defined for protein.
    1218 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: 2.56

  Time building geometry restraints manager: 2.56 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 1128
        1.31 -     1.44: 2067
        1.44 -     1.56: 4174
        1.56 -     1.69: 0
        1.69 -     1.81: 50
  Bond restraints: 7419
  Sorted by residual:
  bond pdb=" CA  DSN B1001 "
       pdb=" CB  DSN B1001 "
    ideal  model  delta    sigma   weight residual
    1.530  1.462  0.068 2.00e-02 2.50e+03 1.15e+01
  bond pdb=" N   ILE A 367 "
       pdb=" CA  ILE A 367 "
    ideal  model  delta    sigma   weight residual
    1.461  1.493 -0.032 1.17e-02 7.31e+03 7.56e+00
  bond pdb=" N   ASN A 366 "
       pdb=" CA  ASN A 366 "
    ideal  model  delta    sigma   weight residual
    1.457  1.487 -0.029 1.17e-02 7.31e+03 6.30e+00
  bond pdb=" N   SER A 505 "
       pdb=" CA  SER A 505 "
    ideal  model  delta    sigma   weight residual
    1.454  1.485 -0.031 1.23e-02 6.61e+03 6.22e+00
  bond pdb=" N   THR A 276 "
       pdb=" CA  THR A 276 "
    ideal  model  delta    sigma   weight residual
    1.457  1.488 -0.030 1.29e-02 6.01e+03 5.57e+00
  ... (remaining 7414 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.20: 9944
        2.20 -     4.39: 122
        4.39 -     6.59: 23
        6.59 -     8.78: 5
        8.78 -    10.98: 5
  Bond angle restraints: 10099
  Sorted by residual:
  angle pdb=" C   ASN A 507 "
        pdb=" CA  ASN A 507 "
        pdb=" CB  ASN A 507 "
      ideal   model   delta    sigma   weight residual
     109.16  120.14  -10.98 1.29e+00 6.01e-01 7.25e+01
  angle pdb=" N   ASN A 507 "
        pdb=" CA  ASN A 507 "
        pdb=" C   ASN A 507 "
      ideal   model   delta    sigma   weight residual
     114.75  105.39    9.36 1.26e+00 6.30e-01 5.52e+01
  angle pdb=" CA  ASN A 507 "
        pdb=" CB  ASN A 507 "
        pdb=" CG  ASN A 507 "
      ideal   model   delta    sigma   weight residual
     112.60  118.46   -5.86 1.00e+00 1.00e+00 3.44e+01
  angle pdb=" O   ASN A 507 "
        pdb=" C   ASN A 507 "
        pdb=" N   MET A 508 "
      ideal   model   delta    sigma   weight residual
     121.64  128.12   -6.48 1.23e+00 6.61e-01 2.78e+01
  angle pdb=" CA  ASN A 507 "
        pdb=" C   ASN A 507 "
        pdb=" N   MET A 508 "
      ideal   model   delta    sigma   weight residual
     119.80  113.05    6.75 1.34e+00 5.57e-01 2.54e+01
  ... (remaining 10094 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.60: 3830
       17.60 -    35.20: 397
       35.20 -    52.79: 120
       52.79 -    70.39: 17
       70.39 -    87.99: 8
  Dihedral angle restraints: 4372
    sinusoidal: 1736
      harmonic: 2636
  Sorted by residual:
  dihedral pdb=" CB  CYS A 211 "
           pdb=" SG  CYS A 211 "
           pdb=" SG  CYS B 154 "
           pdb=" CB  CYS B 154 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -139.09   53.09     1      1.00e+01 1.00e-02 3.83e+01
  dihedral pdb=" CA  ASN A 366 "
           pdb=" CB  ASN A 366 "
           pdb=" CG  ASN A 366 "
           pdb=" OD1 ASN A 366 "
      ideal   model   delta sinusoidal    sigma   weight residual
     120.00 -166.23  -73.77     2      2.00e+01 2.50e-03 1.11e+01
  dihedral pdb=" CG  ARG B 360 "
           pdb=" CD  ARG B 360 "
           pdb=" NE  ARG B 360 "
           pdb=" CZ  ARG B 360 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  135.36   44.64     2      1.50e+01 4.44e-03 1.05e+01
  ... (remaining 4369 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.269: 1163
       0.269 -    0.538: 1
       0.538 -    0.808: 0
       0.808 -    1.077: 1
       1.077 -    1.346: 1
  Chirality restraints: 1166
  Sorted by residual:
  chirality pdb=" C1  NAG A 703 "
            pdb=" ND2 ASN A 425 "
            pdb=" C2  NAG A 703 "
            pdb=" O5  NAG A 703 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.05   -1.35 2.00e-01 2.50e+01 4.53e+01
  chirality pdb=" C1  NAG A 701 "
            pdb=" ND2 ASN A 366 "
            pdb=" C2  NAG A 701 "
            pdb=" O5  NAG A 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.44   -0.96 2.00e-01 2.50e+01 2.33e+01
  chirality pdb=" C1  NAG A 704 "
            pdb=" ND2 ASN A 507 "
            pdb=" C2  NAG A 704 "
            pdb=" O5  NAG A 704 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.11   -0.29 2.00e-01 2.50e+01 2.17e+00
  ... (remaining 1163 not shown)

  Planarity restraints: 1262
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 425 "    0.158 2.00e-02 2.50e+03   1.82e-01 4.15e+02
        pdb=" CG  ASN A 425 "   -0.063 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 425 "   -0.023 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 425 "   -0.295 2.00e-02 2.50e+03
        pdb=" C1  NAG A 703 "    0.222 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 382 "    0.106 2.00e-02 2.50e+03   1.69e-01 3.56e+02
        pdb=" CG  ASN A 382 "   -0.054 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 382 "    0.055 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 382 "   -0.298 2.00e-02 2.50e+03
        pdb=" C1  NAG A 702 "    0.191 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 366 "   -0.091 2.00e-02 2.50e+03   1.01e-01 1.27e+02
        pdb=" CG  ASN A 366 "    0.033 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 366 "    0.017 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 366 "    0.162 2.00e-02 2.50e+03
        pdb=" C1  NAG A 701 "   -0.122 2.00e-02 2.50e+03
  ... (remaining 1259 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1203
        2.76 -     3.29: 6852
        3.29 -     3.83: 12011
        3.83 -     4.36: 13013
        4.36 -     4.90: 23510
  Nonbonded interactions: 56589
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 456 "
            pdb=" OG1 THR A 460 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" O   SER A 582 "
            pdb=" OG  SER A 582 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" OD1 ASP A 493 "
            pdb=" OG  SER A 495 "
     model   vdw
     2.238 3.040
  nonbonded pdb=" O   HIS A 266 "
            pdb=" OH  TYR A 313 "
     model   vdw
     2.256 3.040
  nonbonded pdb=" OH  TYR A 251 "
            pdb=" OE2 GLU A 472 "
     model   vdw
     2.263 3.040
  ... (remaining 56584 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             0.840
  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:             0.010
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     22.260
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  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:2.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7528
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      :  0.003   0.068   7424  Z= 0.177
  Angle     :  0.776  24.437  10113  Z= 0.389
  Chirality :  0.064   1.346   1166
  Planarity :  0.004   0.072   1258
  Dihedral  : 15.851  87.990   2681
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  : 21.29 %
    Favored  : 78.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.28 (0.28), residues: 920
  helix:  2.03 (0.23), residues: 508
  sheet:  0.93 (0.70), residues: 57
  loop : -0.94 (0.32), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.001   TRP B 316 
 HIS   0.002   0.000   HIS A 557 
 PHE   0.014   0.001   PHE A 360 
 TYR   0.011   0.001   TYR B 385 
 ARG   0.002   0.000   ARG A 210 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01308 (    4)
  link_NAG-ASN         : angle      11.58486 (   12)
  hydrogen bonds       : bond        0.13428 (  425)
  hydrogen bonds       : angle       5.54371 ( 1218)
  SS BOND              : bond        0.00068 (    1)
  SS BOND              : angle       1.98286 (    2)
  covalent geometry    : bond        0.00347 ( 7419)
  covalent geometry    : angle       0.66512 (10099)

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

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

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 94
  time to evaluate  : 0.846 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 3
  outliers final: 3
  residues processed: 96
  average time/residue: 0.1670
  time to fit residues: 22.5702
Evaluate side-chains
  92 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 89
  time to evaluate  : 0.721 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  366 ASN
Chi-restraints excluded: chain A residue  507 ASN
Chi-restraints excluded: chain A residue  508 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 76 optimal weight:    5.9990
   chunk 68 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 23 optimal weight:    0.2980
   chunk 46 optimal weight:    2.9990
   chunk 36 optimal weight:    0.7980
   chunk 71 optimal weight:    5.9990
   chunk 27 optimal weight:    3.9990
   chunk 43 optimal weight:    9.9990
   chunk 53 optimal weight:    0.8980
   chunk 82 optimal weight:    0.6980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A 280 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.178538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.137896 restraints weight = 9245.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.136715 restraints weight = 8861.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.138299 restraints weight = 9141.359|
|-----------------------------------------------------------------------------|
r_work (final): 0.3612
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7582
moved from start:          0.0885

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   7424  Z= 0.155
  Angle     :  0.599   8.389  10113  Z= 0.294
  Chirality :  0.040   0.141   1166
  Planarity :  0.004   0.060   1258
  Dihedral  :  4.866  59.754   1079
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 18.97 %
    Favored  : 77.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.57 (0.28), residues: 920
  helix:  2.26 (0.23), residues: 515
  sheet:  0.78 (0.68), residues: 57
  loop : -0.82 (0.32), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 316 
 HIS   0.003   0.001   HIS A 557 
 PHE   0.014   0.001   PHE B 327 
 TYR   0.015   0.002   TYR B 385 
 ARG   0.004   0.000   ARG A 227 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00354 (    4)
  link_NAG-ASN         : angle       4.97785 (   12)
  hydrogen bonds       : bond        0.05270 (  425)
  hydrogen bonds       : angle       4.27351 ( 1218)
  SS BOND              : bond        0.00133 (    1)
  SS BOND              : angle       1.97688 (    2)
  covalent geometry    : bond        0.00358 ( 7419)
  covalent geometry    : angle       0.57320 (10099)

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

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

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 100
  time to evaluate  : 0.708 
Fit side-chains
   revert: symmetry clash
REVERT: A  310 THR cc_start: 0.8517 (m) cc_final: 0.8120 (t)
REVERT: A  452 ARG cc_start: 0.7822 (mtt-85) cc_final: 0.6488 (mtt90)
REVERT: B  170 MET cc_start: 0.7792 (mtt) cc_final: 0.7519 (mtp)
REVERT: B  227 MET cc_start: 0.6237 (OUTLIER) cc_final: 0.5828 (ttp)
  outliers start: 24
  outliers final: 18
  residues processed: 115
  average time/residue: 0.1601
  time to fit residues: 25.8060
Evaluate side-chains
  112 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 93
  time to evaluate  : 0.726 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  211 CYS
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  504 VAL
Chi-restraints excluded: chain A residue  508 MET
Chi-restraints excluded: chain A residue  522 SER
Chi-restraints excluded: chain B residue  106 ASP
Chi-restraints excluded: chain B residue  227 MET
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  295 GLU
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  416 LEU
Chi-restraints excluded: chain B residue  420 ILE
Chi-restraints excluded: chain B residue  438 LEU
Chi-restraints excluded: chain B residue  467 VAL
Chi-restraints excluded: chain B residue  477 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 86 optimal weight:    0.7980
   chunk 77 optimal weight:    0.7980
   chunk 9 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9980
   chunk 80 optimal weight:    2.9990
   chunk 87 optimal weight:    0.9990
   chunk 70 optimal weight:    2.9990
   chunk 58 optimal weight:    0.7980
   chunk 24 optimal weight:    0.6980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 488 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.178689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.138479 restraints weight = 9345.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.137607 restraints weight = 9230.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.139320 restraints weight = 9143.198|
|-----------------------------------------------------------------------------|
r_work (final): 0.3628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7577
moved from start:          0.1312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7424  Z= 0.136
  Angle     :  0.549   7.516  10113  Z= 0.272
  Chirality :  0.039   0.170   1166
  Planarity :  0.004   0.051   1258
  Dihedral  :  4.212  57.978   1075
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 20.65 %
    Favored  : 76.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.73 (0.28), residues: 920
  helix:  2.35 (0.23), residues: 521
  sheet:  0.77 (0.67), residues: 57
  loop : -0.73 (0.33), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 316 
 HIS   0.003   0.001   HIS A 557 
 PHE   0.014   0.001   PHE A 542 
 TYR   0.013   0.001   TYR B 385 
 ARG   0.003   0.000   ARG A 227 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00500 (    4)
  link_NAG-ASN         : angle       3.02098 (   12)
  hydrogen bonds       : bond        0.04850 (  425)
  hydrogen bonds       : angle       4.04099 ( 1218)
  SS BOND              : bond        0.00000 (    1)
  SS BOND              : angle       1.92322 (    2)
  covalent geometry    : bond        0.00312 ( 7419)
  covalent geometry    : angle       0.53905 (10099)

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

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

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 102
  time to evaluate  : 0.843 
Fit side-chains
   revert: symmetry clash
REVERT: A  310 THR cc_start: 0.8486 (m) cc_final: 0.8117 (t)
REVERT: A  452 ARG cc_start: 0.7882 (mtt-85) cc_final: 0.6483 (mtt90)
REVERT: B   60 ILE cc_start: 0.8230 (OUTLIER) cc_final: 0.7785 (mt)
REVERT: B  170 MET cc_start: 0.7651 (mtt) cc_final: 0.7365 (mtp)
REVERT: B  227 MET cc_start: 0.6250 (OUTLIER) cc_final: 0.5830 (ttp)
REVERT: B  318 MET cc_start: 0.6796 (OUTLIER) cc_final: 0.6237 (ttp)
  outliers start: 21
  outliers final: 9
  residues processed: 117
  average time/residue: 0.1882
  time to fit residues: 30.3187
Evaluate side-chains
  108 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 96
  time to evaluate  : 0.779 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  211 CYS
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  508 MET
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  522 SER
Chi-restraints excluded: chain B residue   60 ILE
Chi-restraints excluded: chain B residue  227 MET
Chi-restraints excluded: chain B residue  281 THR
Chi-restraints excluded: chain B residue  318 MET
Chi-restraints excluded: chain B residue  438 LEU
Chi-restraints excluded: chain B residue  477 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 70 optimal weight:    0.8980
   chunk 44 optimal weight:    0.1980
   chunk 9 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 27 optimal weight:    3.9990
   chunk 28 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 80 optimal weight:    0.0870
   overall best weight:    0.8362

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

Flipped N/Q/H residues before XYZ refinement:
** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.178440 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.137290 restraints weight = 9369.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.136912 restraints weight = 9189.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.138260 restraints weight = 9489.270|
|-----------------------------------------------------------------------------|
r_work (final): 0.3604
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7578
moved from start:          0.1517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7424  Z= 0.137
  Angle     :  0.560   9.906  10113  Z= 0.274
  Chirality :  0.039   0.161   1166
  Planarity :  0.004   0.046   1258
  Dihedral  :  4.107  54.719   1075
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 19.48 %
    Favored  : 76.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.79 (0.28), residues: 920
  helix:  2.40 (0.23), residues: 519
  sheet:  0.81 (0.68), residues: 57
  loop : -0.68 (0.33), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 316 
 HIS   0.003   0.001   HIS A 557 
 PHE   0.014   0.001   PHE A 542 
 TYR   0.013   0.001   TYR B 385 
 ARG   0.007   0.000   ARG A 314 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00444 (    4)
  link_NAG-ASN         : angle       2.91188 (   12)
  hydrogen bonds       : bond        0.04834 (  425)
  hydrogen bonds       : angle       3.99964 ( 1218)
  SS BOND              : bond        0.00104 (    1)
  SS BOND              : angle       1.73706 (    2)
  covalent geometry    : bond        0.00320 ( 7419)
  covalent geometry    : angle       0.55042 (10099)

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

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

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 100
  time to evaluate  : 0.814 
Fit side-chains
   revert: symmetry clash
REVERT: A  310 THR cc_start: 0.8537 (m) cc_final: 0.8112 (t)
REVERT: A  452 ARG cc_start: 0.7823 (mtt-85) cc_final: 0.6441 (mtt90)
REVERT: B   60 ILE cc_start: 0.8302 (OUTLIER) cc_final: 0.7862 (mt)
REVERT: B  170 MET cc_start: 0.7682 (mtt) cc_final: 0.7378 (mtp)
REVERT: B  208 GLN cc_start: 0.7643 (mm-40) cc_final: 0.6907 (tt0)
REVERT: B  227 MET cc_start: 0.6294 (OUTLIER) cc_final: 0.5887 (ttp)
REVERT: B  318 MET cc_start: 0.6641 (OUTLIER) cc_final: 0.6398 (ttp)
  outliers start: 32
  outliers final: 20
  residues processed: 123
  average time/residue: 0.1945
  time to fit residues: 32.7726
Evaluate side-chains
  118 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 95
  time to evaluate  : 0.827 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  184 TRP
Chi-restraints excluded: chain A residue  197 MET
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  508 MET
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  522 SER
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain B residue   48 ILE
Chi-restraints excluded: chain B residue   60 ILE
Chi-restraints excluded: chain B residue  106 ASP
Chi-restraints excluded: chain B residue  168 CYS
Chi-restraints excluded: chain B residue  227 MET
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  281 THR
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  318 MET
Chi-restraints excluded: chain B residue  438 LEU
Chi-restraints excluded: chain B residue  477 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 7 optimal weight:    0.9980
   chunk 75 optimal weight:    0.9990
   chunk 72 optimal weight:    0.9980
   chunk 10 optimal weight:    4.9990
   chunk 21 optimal weight:    0.0270
   chunk 3 optimal weight:    0.9990
   chunk 6 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9980
   chunk 53 optimal weight:    2.9990
   chunk 19 optimal weight:    0.1980
   chunk 83 optimal weight:    4.9990
   overall best weight:    0.5838

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

Flipped N/Q/H residues before XYZ refinement:
** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 365 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.179638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.139010 restraints weight = 9133.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.136949 restraints weight = 9583.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.138583 restraints weight = 8752.494|
|-----------------------------------------------------------------------------|
r_work (final): 0.3607
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7565
moved from start:          0.1580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7424  Z= 0.117
  Angle     :  0.550   9.953  10113  Z= 0.267
  Chirality :  0.039   0.266   1166
  Planarity :  0.004   0.043   1258
  Dihedral  :  3.982  51.628   1075
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 21.03 %
    Favored  : 75.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.94 (0.28), residues: 920
  helix:  2.61 (0.23), residues: 508
  sheet:  0.90 (0.68), residues: 57
  loop : -0.68 (0.33), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 316 
 HIS   0.002   0.000   HIS A 557 
 PHE   0.014   0.001   PHE A 542 
 TYR   0.012   0.001   TYR B 385 
 ARG   0.002   0.000   ARG A 227 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00445 (    4)
  link_NAG-ASN         : angle       2.59841 (   12)
  hydrogen bonds       : bond        0.04446 (  425)
  hydrogen bonds       : angle       3.88703 ( 1218)
  SS BOND              : bond        0.00202 (    1)
  SS BOND              : angle       2.37638 (    2)
  covalent geometry    : bond        0.00264 ( 7419)
  covalent geometry    : angle       0.54177 (10099)

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

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

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 100
  time to evaluate  : 0.768 
Fit side-chains
   revert: symmetry clash
REVERT: A  290 ASP cc_start: 0.7835 (m-30) cc_final: 0.7448 (t0)
REVERT: A  310 THR cc_start: 0.8520 (m) cc_final: 0.8069 (t)
REVERT: A  452 ARG cc_start: 0.7866 (mtt-85) cc_final: 0.6410 (mtt90)
REVERT: B   60 ILE cc_start: 0.8269 (OUTLIER) cc_final: 0.7825 (mt)
REVERT: B  208 GLN cc_start: 0.7601 (mm-40) cc_final: 0.6864 (tt0)
REVERT: B  227 MET cc_start: 0.6194 (OUTLIER) cc_final: 0.5796 (ttp)
REVERT: B  318 MET cc_start: 0.6716 (OUTLIER) cc_final: 0.6330 (ttp)
REVERT: B  481 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7716 (mt-10)
  outliers start: 27
  outliers final: 21
  residues processed: 117
  average time/residue: 0.1682
  time to fit residues: 27.4636
Evaluate side-chains
  121 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 97
  time to evaluate  : 0.775 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  184 TRP
Chi-restraints excluded: chain A residue  197 MET
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  508 MET
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  522 SER
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain A residue  625 LEU
Chi-restraints excluded: chain B residue   48 ILE
Chi-restraints excluded: chain B residue   60 ILE
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue  106 ASP
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  168 CYS
Chi-restraints excluded: chain B residue  227 MET
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  318 MET
Chi-restraints excluded: chain B residue  438 LEU
Chi-restraints excluded: chain B residue  467 VAL
Chi-restraints excluded: chain B residue  477 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 63 optimal weight:    0.3980
   chunk 39 optimal weight:    4.9990
   chunk 68 optimal weight:    3.9990
   chunk 47 optimal weight:    0.8980
   chunk 61 optimal weight:    1.9990
   chunk 76 optimal weight:    0.9990
   chunk 74 optimal weight:    0.9990
   chunk 86 optimal weight:    0.8980
   chunk 30 optimal weight:    0.7980
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.178306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.139398 restraints weight = 9194.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.137529 restraints weight = 9151.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.139108 restraints weight = 10290.862|
|-----------------------------------------------------------------------------|
r_work (final): 0.3614
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7566
moved from start:          0.1734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7424  Z= 0.132
  Angle     :  0.543   7.711  10113  Z= 0.267
  Chirality :  0.039   0.164   1166
  Planarity :  0.004   0.040   1258
  Dihedral  :  3.921  46.099   1075
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 21.03 %
    Favored  : 74.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.89 (0.28), residues: 920
  helix:  2.49 (0.23), residues: 514
  sheet:  0.72 (0.65), residues: 62
  loop : -0.61 (0.33), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 316 
 HIS   0.003   0.001   HIS A 557 
 PHE   0.014   0.001   PHE A 542 
 TYR   0.013   0.001   TYR B 385 
 ARG   0.002   0.000   ARG A 314 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00419 (    4)
  link_NAG-ASN         : angle       2.39377 (   12)
  hydrogen bonds       : bond        0.04647 (  425)
  hydrogen bonds       : angle       3.89332 ( 1218)
  SS BOND              : bond        0.00061 (    1)
  SS BOND              : angle       2.98221 (    2)
  covalent geometry    : bond        0.00306 ( 7419)
  covalent geometry    : angle       0.53540 (10099)

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

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

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 98
  time to evaluate  : 0.865 
Fit side-chains
   revert: symmetry clash
REVERT: A  290 ASP cc_start: 0.7742 (m-30) cc_final: 0.7413 (t0)
REVERT: A  310 THR cc_start: 0.8484 (m) cc_final: 0.8062 (t)
REVERT: A  452 ARG cc_start: 0.7936 (mtt-85) cc_final: 0.6508 (mtt90)
REVERT: B   60 ILE cc_start: 0.8210 (OUTLIER) cc_final: 0.7789 (mt)
REVERT: B  170 MET cc_start: 0.7627 (mtt) cc_final: 0.7334 (mtp)
REVERT: B  208 GLN cc_start: 0.7675 (mm-40) cc_final: 0.6946 (tt0)
REVERT: B  227 MET cc_start: 0.6230 (OUTLIER) cc_final: 0.5846 (ttp)
REVERT: B  318 MET cc_start: 0.6658 (OUTLIER) cc_final: 0.6437 (ttp)
  outliers start: 34
  outliers final: 24
  residues processed: 123
  average time/residue: 0.1727
  time to fit residues: 29.3288
Evaluate side-chains
  121 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 94
  time to evaluate  : 0.746 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  184 TRP
Chi-restraints excluded: chain A residue  197 MET
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  508 MET
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  522 SER
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue   48 ILE
Chi-restraints excluded: chain B residue   60 ILE
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue  106 ASP
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  168 CYS
Chi-restraints excluded: chain B residue  227 MET
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  281 THR
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  318 MET
Chi-restraints excluded: chain B residue  438 LEU
Chi-restraints excluded: chain B residue  467 VAL
Chi-restraints excluded: chain B residue  477 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 1 optimal weight:    0.0670
   chunk 74 optimal weight:    1.9990
   chunk 87 optimal weight:    0.9980
   chunk 69 optimal weight:    0.2980
   chunk 4 optimal weight:    0.4980
   chunk 20 optimal weight:    5.9990
   chunk 86 optimal weight:    0.0980
   chunk 76 optimal weight:    0.8980
   chunk 82 optimal weight:    0.6980
   chunk 16 optimal weight:    0.0970
   chunk 48 optimal weight:    2.9990
   overall best weight:    0.2116

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

Flipped N/Q/H residues before XYZ refinement:
** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 488 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.182779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.143061 restraints weight = 9101.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.141887 restraints weight = 8673.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.143153 restraints weight = 8816.666|
|-----------------------------------------------------------------------------|
r_work (final): 0.3662
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7492
moved from start:          0.1856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   7424  Z= 0.100
  Angle     :  0.542  13.270  10113  Z= 0.261
  Chirality :  0.037   0.164   1166
  Planarity :  0.003   0.038   1258
  Dihedral  :  3.780  39.644   1075
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 22.32 %
    Favored  : 74.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.96 (0.28), residues: 920
  helix:  2.61 (0.23), residues: 514
  sheet:  0.94 (0.67), residues: 57
  loop : -0.71 (0.33), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 316 
 HIS   0.002   0.000   HIS A 539 
 PHE   0.015   0.001   PHE A 542 
 TYR   0.012   0.001   TYR B 390 
 ARG   0.002   0.000   ARG A 314 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00434 (    4)
  link_NAG-ASN         : angle       2.21900 (   12)
  hydrogen bonds       : bond        0.03705 (  425)
  hydrogen bonds       : angle       3.74407 ( 1218)
  SS BOND              : bond        0.00622 (    1)
  SS BOND              : angle       2.88364 (    2)
  covalent geometry    : bond        0.00210 ( 7419)
  covalent geometry    : angle       0.53555 (10099)

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

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

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 97
  time to evaluate  : 0.838 
Fit side-chains
REVERT: A  210 ARG cc_start: 0.6320 (tpp80) cc_final: 0.6022 (tpp80)
REVERT: A  290 ASP cc_start: 0.7717 (m-30) cc_final: 0.7384 (t0)
REVERT: A  452 ARG cc_start: 0.7952 (mtt-85) cc_final: 0.6453 (mtt90)
REVERT: B   60 ILE cc_start: 0.8173 (OUTLIER) cc_final: 0.7722 (mt)
REVERT: B  208 GLN cc_start: 0.7545 (mm-40) cc_final: 0.6725 (tt0)
REVERT: B  227 MET cc_start: 0.6256 (OUTLIER) cc_final: 0.5906 (ttp)
REVERT: B  318 MET cc_start: 0.6326 (OUTLIER) cc_final: 0.5735 (ttp)
  outliers start: 25
  outliers final: 16
  residues processed: 116
  average time/residue: 0.1961
  time to fit residues: 31.6162
Evaluate side-chains
  109 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 90
  time to evaluate  : 0.756 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  184 TRP
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  508 MET
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  522 SER
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue   48 ILE
Chi-restraints excluded: chain B residue   60 ILE
Chi-restraints excluded: chain B residue  106 ASP
Chi-restraints excluded: chain B residue  154 CYS
Chi-restraints excluded: chain B residue  168 CYS
Chi-restraints excluded: chain B residue  227 MET
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  318 MET
Chi-restraints excluded: chain B residue  438 LEU
Chi-restraints excluded: chain B residue  477 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 33 optimal weight:    0.5980
   chunk 71 optimal weight:    0.9980
   chunk 88 optimal weight:    0.0670
   chunk 8 optimal weight:    0.9980
   chunk 67 optimal weight:    0.0870
   chunk 87 optimal weight:    4.9990
   chunk 42 optimal weight:    6.9990
   chunk 72 optimal weight:    0.7980
   chunk 77 optimal weight:    3.9990
   chunk 66 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.5096

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

Flipped N/Q/H residues before XYZ refinement:
** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 488 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.180753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.140044 restraints weight = 9220.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.139426 restraints weight = 9117.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.140743 restraints weight = 9148.592|
|-----------------------------------------------------------------------------|
r_work (final): 0.3631
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7522
moved from start:          0.1915

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7424  Z= 0.114
  Angle     :  0.562  12.395  10113  Z= 0.271
  Chirality :  0.039   0.202   1166
  Planarity :  0.003   0.037   1258
  Dihedral  :  3.684  34.395   1075
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 23.23 %
    Favored  : 73.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.02 (0.28), residues: 920
  helix:  2.58 (0.23), residues: 515
  sheet:  1.65 (0.70), residues: 51
  loop : -0.65 (0.33), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.001   TRP B 316 
 HIS   0.002   0.000   HIS B 358 
 PHE   0.013   0.001   PHE A 542 
 TYR   0.011   0.001   TYR B 390 
 ARG   0.002   0.000   ARG B 418 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00417 (    4)
  link_NAG-ASN         : angle       2.09373 (   12)
  hydrogen bonds       : bond        0.04038 (  425)
  hydrogen bonds       : angle       3.78594 ( 1218)
  SS BOND              : bond        0.00121 (    1)
  SS BOND              : angle       2.80631 (    2)
  covalent geometry    : bond        0.00260 ( 7419)
  covalent geometry    : angle       0.55673 (10099)

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

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

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 93
  time to evaluate  : 0.746 
Fit side-chains
   revert: symmetry clash
REVERT: A  290 ASP cc_start: 0.7738 (m-30) cc_final: 0.7450 (t0)
REVERT: A  452 ARG cc_start: 0.7889 (mtt-85) cc_final: 0.6487 (mtt90)
REVERT: B   60 ILE cc_start: 0.8198 (OUTLIER) cc_final: 0.7769 (mt)
REVERT: B  208 GLN cc_start: 0.7561 (mm-40) cc_final: 0.6950 (tt0)
REVERT: B  318 MET cc_start: 0.6446 (OUTLIER) cc_final: 0.5798 (ttp)
  outliers start: 24
  outliers final: 16
  residues processed: 110
  average time/residue: 0.1746
  time to fit residues: 26.6930
Evaluate side-chains
  107 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 89
  time to evaluate  : 0.852 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  184 TRP
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  522 SER
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain B residue   48 ILE
Chi-restraints excluded: chain B residue   60 ILE
Chi-restraints excluded: chain B residue  106 ASP
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  154 CYS
Chi-restraints excluded: chain B residue  168 CYS
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  318 MET
Chi-restraints excluded: chain B residue  438 LEU
Chi-restraints excluded: chain B residue  488 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 65 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 76 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9980
   chunk 4 optimal weight:    0.0370
   chunk 30 optimal weight:    0.0030
   chunk 10 optimal weight:    2.9990
   chunk 0 optimal weight:    6.9990
   chunk 31 optimal weight:    0.2980
   chunk 58 optimal weight:    0.4980
   chunk 70 optimal weight:    0.8980
   overall best weight:    0.3468

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

Flipped N/Q/H residues before XYZ refinement:
** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.181719 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.141372 restraints weight = 9225.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.140452 restraints weight = 9214.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.141940 restraints weight = 8977.056|
|-----------------------------------------------------------------------------|
r_work (final): 0.3660
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7524
moved from start:          0.1976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   7424  Z= 0.106
  Angle     :  0.555  11.058  10113  Z= 0.266
  Chirality :  0.038   0.163   1166
  Planarity :  0.003   0.037   1258
  Dihedral  :  3.478  16.580   1072
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 23.61 %
    Favored  : 73.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.03 (0.28), residues: 920
  helix:  2.68 (0.23), residues: 508
  sheet:  1.66 (0.69), residues: 51
  loop : -0.72 (0.32), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP B 316 
 HIS   0.001   0.000   HIS B 358 
 PHE   0.014   0.001   PHE A 542 
 TYR   0.013   0.001   TYR A 251 
 ARG   0.002   0.000   ARG B 418 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00415 (    4)
  link_NAG-ASN         : angle       2.03660 (   12)
  hydrogen bonds       : bond        0.03799 (  425)
  hydrogen bonds       : angle       3.75699 ( 1218)
  SS BOND              : bond        0.00016 (    1)
  SS BOND              : angle       3.04952 (    2)
  covalent geometry    : bond        0.00235 ( 7419)
  covalent geometry    : angle       0.54924 (10099)

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

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

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 93
  time to evaluate  : 0.828 
Fit side-chains
   revert: symmetry clash
REVERT: A  290 ASP cc_start: 0.7703 (m-30) cc_final: 0.7436 (t0)
REVERT: A  452 ARG cc_start: 0.7882 (mtt-85) cc_final: 0.6498 (mtt90)
REVERT: B   60 ILE cc_start: 0.8146 (OUTLIER) cc_final: 0.7688 (mt)
REVERT: B  208 GLN cc_start: 0.7589 (mm-40) cc_final: 0.6986 (tt0)
REVERT: B  227 MET cc_start: 0.6252 (OUTLIER) cc_final: 0.5894 (ttp)
REVERT: B  318 MET cc_start: 0.6391 (OUTLIER) cc_final: 0.5776 (ttp)
  outliers start: 19
  outliers final: 14
  residues processed: 105
  average time/residue: 0.1820
  time to fit residues: 26.5608
Evaluate side-chains
  106 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 89
  time to evaluate  : 0.808 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  184 TRP
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  522 SER
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain B residue   48 ILE
Chi-restraints excluded: chain B residue   60 ILE
Chi-restraints excluded: chain B residue  106 ASP
Chi-restraints excluded: chain B residue  154 CYS
Chi-restraints excluded: chain B residue  168 CYS
Chi-restraints excluded: chain B residue  227 MET
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  318 MET
Chi-restraints excluded: chain B residue  438 LEU
Chi-restraints excluded: chain B residue  477 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 4 optimal weight:    0.5980
   chunk 47 optimal weight:    0.6980
   chunk 8 optimal weight:    0.7980
   chunk 12 optimal weight:    0.6980
   chunk 40 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9980
   chunk 62 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 488 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.178486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.139247 restraints weight = 9359.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.137959 restraints weight = 8893.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.139891 restraints weight = 8938.181|
|-----------------------------------------------------------------------------|
r_work (final): 0.3628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7559
moved from start:          0.2032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7424  Z= 0.134
  Angle     :  0.582  10.321  10113  Z= 0.282
  Chirality :  0.040   0.177   1166
  Planarity :  0.004   0.038   1258
  Dihedral  :  3.570  15.152   1072
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 23.61 %
    Favored  : 73.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.93 (0.28), residues: 920
  helix:  2.49 (0.23), residues: 514
  sheet:  1.57 (0.69), residues: 51
  loop : -0.62 (0.33), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP B 316 
 HIS   0.002   0.000   HIS B 358 
 PHE   0.013   0.001   PHE A 542 
 TYR   0.014   0.001   TYR B 385 
 ARG   0.002   0.000   ARG B 418 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00384 (    4)
  link_NAG-ASN         : angle       1.99700 (   12)
  hydrogen bonds       : bond        0.04521 (  425)
  hydrogen bonds       : angle       3.88934 ( 1218)
  SS BOND              : bond        0.00022 (    1)
  SS BOND              : angle       3.01517 (    2)
  covalent geometry    : bond        0.00315 ( 7419)
  covalent geometry    : angle       0.57656 (10099)

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

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

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 96
  time to evaluate  : 0.730 
Fit side-chains
   revert: symmetry clash
REVERT: A  290 ASP cc_start: 0.7651 (m-30) cc_final: 0.7443 (t0)
REVERT: A  452 ARG cc_start: 0.7949 (mtt-85) cc_final: 0.6527 (mtt90)
REVERT: B   60 ILE cc_start: 0.8282 (OUTLIER) cc_final: 0.7861 (mt)
REVERT: B  170 MET cc_start: 0.7632 (mtt) cc_final: 0.7348 (mtp)
REVERT: B  208 GLN cc_start: 0.7697 (mm-40) cc_final: 0.7122 (tt0)
REVERT: B  227 MET cc_start: 0.6345 (OUTLIER) cc_final: 0.6031 (ttp)
REVERT: B  318 MET cc_start: 0.6590 (OUTLIER) cc_final: 0.6196 (ttp)
  outliers start: 22
  outliers final: 18
  residues processed: 113
  average time/residue: 0.1799
  time to fit residues: 28.1243
Evaluate side-chains
  115 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 94
  time to evaluate  : 0.787 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  184 TRP
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  522 SER
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain B residue   48 ILE
Chi-restraints excluded: chain B residue   60 ILE
Chi-restraints excluded: chain B residue  106 ASP
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  154 CYS
Chi-restraints excluded: chain B residue  168 CYS
Chi-restraints excluded: chain B residue  186 ILE
Chi-restraints excluded: chain B residue  227 MET
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  318 MET
Chi-restraints excluded: chain B residue  438 LEU
Chi-restraints excluded: chain B residue  477 HIS
Chi-restraints excluded: chain B residue  488 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 1 optimal weight:    0.0980
   chunk 36 optimal weight:    0.9980
   chunk 46 optimal weight:    1.9990
   chunk 85 optimal weight:    0.8980
   chunk 28 optimal weight:    0.4980
   chunk 84 optimal weight:    0.9990
   chunk 15 optimal weight:    0.7980
   chunk 56 optimal weight:    0.5980
   chunk 62 optimal weight:    3.9990
   chunk 53 optimal weight:    2.9990
   chunk 20 optimal weight:    4.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 240 GLN
B 488 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.179494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.140616 restraints weight = 9167.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.138404 restraints weight = 8688.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.139802 restraints weight = 10005.702|
|-----------------------------------------------------------------------------|
r_work (final): 0.3634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7569
moved from start:          0.2095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7424  Z= 0.120
  Angle     :  0.570  10.560  10113  Z= 0.276
  Chirality :  0.039   0.167   1166
  Planarity :  0.004   0.039   1258
  Dihedral  :  3.529  15.058   1072
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 23.87 %
    Favored  : 73.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.88 (0.28), residues: 920
  helix:  2.43 (0.23), residues: 520
  sheet:  1.52 (0.68), residues: 51
  loop : -0.66 (0.33), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP B 316 
 HIS   0.002   0.000   HIS B 358 
 PHE   0.014   0.001   PHE A 542 
 TYR   0.048   0.002   TYR A 251 
 ARG   0.002   0.000   ARG B 418 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00389 (    4)
  link_NAG-ASN         : angle       1.96795 (   12)
  hydrogen bonds       : bond        0.04249 (  425)
  hydrogen bonds       : angle       3.83119 ( 1218)
  SS BOND              : bond        0.00069 (    1)
  SS BOND              : angle       2.92221 (    2)
  covalent geometry    : bond        0.00275 ( 7419)
  covalent geometry    : angle       0.56524 (10099)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2335.00 seconds
wall clock time: 41 minutes 48.86 seconds (2508.86 seconds total)