Starting phenix.real_space_refine
on Fri Aug 22 19:28:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wny_37675/08_2025/8wny_37675.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wny_37675/08_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_37675/08_2025/8wny_37675.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wny_37675/08_2025/8wny_37675.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wny_37675/08_2025/8wny_37675.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wny_37675/08_2025/8wny_37675.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.002 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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 1.77, per 1000 atoms: 0.24
  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: 0.59
  Conformation dependent library (CDL) restraints added in 350.8 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.25
  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: 1.12

  Time building geometry restraints manager: 0.72 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:             1.020
  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:             0.020
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     7.740
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.240
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.28 (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
 ARG   0.002   0.000   ARG A 210 
 TYR   0.011   0.001   TYR B 385 
 PHE   0.014   0.001   PHE A 360 
 TRP   0.032   0.001   TRP B 316 
 HIS   0.002   0.000   HIS A 557 

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

*********************** 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  : 0.265 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 3
  outliers final: 3
  residues processed: 96
  average time/residue: 0.0741
  time to fit residues: 10.0960
Evaluate side-chains
  93 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 90
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
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 49 optimal weight:    2.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    0.0030
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    0.5980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.6392

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

Flipped N/Q/H residues before XYZ refinement:
A 280 GLN
A 422 GLN
A 539 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.183461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.144866 restraints weight = 9198.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.144074 restraints weight = 9818.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.145595 restraints weight = 9798.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.146190 restraints weight = 7245.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.146865 restraints weight = 7073.084|
|-----------------------------------------------------------------------------|
r_work (final): 0.3696
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7510
moved from start:          0.0838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7424  Z= 0.132
  Angle     :  0.579   8.689  10113  Z= 0.283
  Chirality :  0.039   0.208   1166
  Planarity :  0.004   0.060   1258
  Dihedral  :  4.781  59.303   1079
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 19.10 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.67 (0.28), residues: 920
  helix:  2.35 (0.23), residues: 515
  sheet:  0.91 (0.69), residues: 57
  loop : -0.80 (0.32), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 227 
 TYR   0.013   0.001   TYR B 333 
 PHE   0.014   0.001   PHE B 327 
 TRP   0.017   0.001   TRP B 316 
 HIS   0.002   0.001   HIS A 557 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 7419)
  covalent geometry    : angle       0.55237 (10099)
  SS BOND              : bond        0.00149 (    1)
  SS BOND              : angle       2.02632 (    2)
  hydrogen bonds       : bond        0.04912 (  425)
  hydrogen bonds       : angle       4.20053 ( 1218)
  link_NAG-ASN         : bond        0.00521 (    4)
  link_NAG-ASN         : angle       4.96374 (   12)

*********************** 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
  120 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 100
  time to evaluate  : 0.177 
Fit side-chains
   revert: symmetry clash
REVERT: A  310 THR cc_start: 0.8443 (m) cc_final: 0.8079 (t)
REVERT: B  227 MET cc_start: 0.6116 (OUTLIER) cc_final: 0.5674 (ttp)
  outliers start: 20
  outliers final: 14
  residues processed: 113
  average time/residue: 0.0699
  time to fit residues: 11.1891
Evaluate side-chains
  110 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 95
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
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  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  522 SER
Chi-restraints excluded: chain A residue  625 LEU
Chi-restraints excluded: chain B residue  106 ASP
Chi-restraints excluded: chain B residue  227 MET
Chi-restraints excluded: chain B residue  295 GLU
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  477 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 41 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 77 optimal weight:    0.8980
   chunk 75 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 80 optimal weight:    2.9990
   chunk 25 optimal weight:    3.9990
   chunk 72 optimal weight:    0.8980
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
A 268 ASN
B 488 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.178076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.138235 restraints weight = 9171.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.136092 restraints weight = 9405.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.138088 restraints weight = 9801.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.138574 restraints weight = 7161.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.139124 restraints weight = 7206.451|
|-----------------------------------------------------------------------------|
r_work (final): 0.3604
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7645
moved from start:          0.1453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   7424  Z= 0.191
  Angle     :  0.616   7.391  10113  Z= 0.308
  Chirality :  0.041   0.169   1166
  Planarity :  0.004   0.053   1258
  Dihedral  :  4.429  58.062   1075
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.54 (0.28), residues: 920
  helix:  2.16 (0.23), residues: 520
  sheet:  0.57 (0.64), residues: 62
  loop : -0.72 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 410 
 TYR   0.018   0.002   TYR B 385 
 PHE   0.020   0.002   PHE A 545 
 TRP   0.012   0.001   TRP B 434 
 HIS   0.004   0.001   HIS A 557 

Details of bonding type rmsd
  covalent geometry    : bond        0.00459 ( 7419)
  covalent geometry    : angle       0.60422 (10099)
  SS BOND              : bond        0.00047 (    1)
  SS BOND              : angle       2.04775 (    2)
  hydrogen bonds       : bond        0.05880 (  425)
  hydrogen bonds       : angle       4.25660 ( 1218)
  link_NAG-ASN         : bond        0.00573 (    4)
  link_NAG-ASN         : angle       3.38781 (   12)

*********************** 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
  126 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 94
  time to evaluate  : 0.277 
Fit side-chains
   revert: symmetry clash
REVERT: A  310 THR cc_start: 0.8558 (m) cc_final: 0.8214 (t)
REVERT: A  452 ARG cc_start: 0.8005 (mtt-85) cc_final: 0.6600 (mtt90)
REVERT: B   60 ILE cc_start: 0.8340 (OUTLIER) cc_final: 0.7932 (mt)
REVERT: B  170 MET cc_start: 0.7743 (mtt) cc_final: 0.7459 (mtp)
REVERT: B  318 MET cc_start: 0.6915 (OUTLIER) cc_final: 0.6585 (ttp)
  outliers start: 32
  outliers final: 18
  residues processed: 115
  average time/residue: 0.0750
  time to fit residues: 12.0328
Evaluate side-chains
  113 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 93
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
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  485 MET
Chi-restraints excluded: chain A residue  504 VAL
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  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  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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 14 optimal weight:    0.9980
   chunk 55 optimal weight:    0.5980
   chunk 71 optimal weight:    0.2980
   chunk 83 optimal weight:    0.2980
   chunk 87 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9980
   chunk 38 optimal weight:    0.8980
   chunk 80 optimal weight:    1.9990
   chunk 21 optimal weight:    0.4980
   chunk 67 optimal weight:    0.5980
   chunk 49 optimal weight:    0.9980
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
A 268 ASN
** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.182817 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.143997 restraints weight = 9248.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.143284 restraints weight = 9706.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.145218 restraints weight = 9644.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.145519 restraints weight = 7320.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.146009 restraints weight = 7454.701|
|-----------------------------------------------------------------------------|
r_work (final): 0.3696
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7521
moved from start:          0.1522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7424  Z= 0.112
  Angle     :  0.531   7.622  10113  Z= 0.261
  Chirality :  0.038   0.228   1166
  Planarity :  0.004   0.047   1258
  Dihedral  :  4.058  52.693   1075
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 20.39 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.89 (0.28), residues: 920
  helix:  2.61 (0.23), residues: 508
  sheet:  0.79 (0.68), residues: 57
  loop : -0.76 (0.32), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 314 
 TYR   0.012   0.001   TYR B 390 
 PHE   0.015   0.001   PHE A 542 
 TRP   0.010   0.001   TRP B 124 
 HIS   0.002   0.000   HIS B 358 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 7419)
  covalent geometry    : angle       0.52165 (10099)
  SS BOND              : bond        0.00094 (    1)
  SS BOND              : angle       1.78018 (    2)
  hydrogen bonds       : bond        0.04403 (  425)
  hydrogen bonds       : angle       3.93475 ( 1218)
  link_NAG-ASN         : bond        0.00517 (    4)
  link_NAG-ASN         : angle       2.86290 (   12)

*********************** 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
  128 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 103
  time to evaluate  : 0.275 
Fit side-chains
   revert: symmetry clash
REVERT: A  310 THR cc_start: 0.8472 (m) cc_final: 0.8099 (t)
REVERT: A  452 ARG cc_start: 0.7959 (mtt-85) cc_final: 0.6559 (mtt90)
REVERT: B   60 ILE cc_start: 0.8270 (OUTLIER) cc_final: 0.7810 (mt)
REVERT: B  208 GLN cc_start: 0.7670 (mm-40) cc_final: 0.6949 (tt0)
REVERT: B  227 MET cc_start: 0.6196 (OUTLIER) cc_final: 0.5772 (ttp)
REVERT: B  318 MET cc_start: 0.6791 (OUTLIER) cc_final: 0.6405 (ttp)
  outliers start: 25
  outliers final: 15
  residues processed: 120
  average time/residue: 0.0791
  time to fit residues: 13.2424
Evaluate side-chains
  114 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 96
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
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  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   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  297 LEU
Chi-restraints excluded: chain B residue  318 MET
Chi-restraints excluded: chain B residue  438 LEU
Chi-restraints excluded: chain B residue  457 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 39 optimal weight:    3.9990
   chunk 75 optimal weight:    0.0370
   chunk 82 optimal weight:    0.9980
   chunk 9 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   chunk 28 optimal weight:    0.0050
   chunk 89 optimal weight:    7.9990
   chunk 59 optimal weight:    0.9990
   chunk 19 optimal weight:    3.9990
   chunk 20 optimal weight:    0.1980
   overall best weight:    0.4472

-------------------------------------------------------------------------------
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 = 0.4059 r_free = 0.4059 target = 0.183340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.144395 restraints weight = 9109.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.142634 restraints weight = 8456.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.144670 restraints weight = 8512.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.144870 restraints weight = 6625.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.145503 restraints weight = 6906.498|
|-----------------------------------------------------------------------------|
r_work (final): 0.3688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7530
moved from start:          0.1613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   7424  Z= 0.110
  Angle     :  0.533  11.002  10113  Z= 0.259
  Chirality :  0.038   0.157   1166
  Planarity :  0.004   0.043   1258
  Dihedral  :  3.936  50.900   1075
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 21.29 %
    Favored  : 75.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.94 (0.28), residues: 920
  helix:  2.65 (0.23), residues: 510
  sheet:  0.86 (0.68), residues: 57
  loop : -0.75 (0.32), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 227 
 TYR   0.012   0.001   TYR B 390 
 PHE   0.014   0.001   PHE A 542 
 TRP   0.011   0.001   TRP B 316 
 HIS   0.002   0.000   HIS A 539 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 7419)
  covalent geometry    : angle       0.52580 (10099)
  SS BOND              : bond        0.00402 (    1)
  SS BOND              : angle       2.31837 (    2)
  hydrogen bonds       : bond        0.04166 (  425)
  hydrogen bonds       : angle       3.82987 ( 1218)
  link_NAG-ASN         : bond        0.00481 (    4)
  link_NAG-ASN         : angle       2.47104 (   12)

*********************** 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
  122 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 98
  time to evaluate  : 0.275 
Fit side-chains
   revert: symmetry clash
REVERT: A  310 THR cc_start: 0.8460 (m) cc_final: 0.8058 (t)
REVERT: A  452 ARG cc_start: 0.7932 (mtt-85) cc_final: 0.6528 (mtt90)
REVERT: B   60 ILE cc_start: 0.8237 (OUTLIER) cc_final: 0.7788 (mt)
REVERT: B  208 GLN cc_start: 0.7569 (mm-40) cc_final: 0.6830 (tt0)
REVERT: B  227 MET cc_start: 0.6162 (OUTLIER) cc_final: 0.5734 (ttp)
REVERT: B  318 MET cc_start: 0.6603 (OUTLIER) cc_final: 0.6209 (ttp)
REVERT: B  481 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7671 (mt-10)
  outliers start: 24
  outliers final: 16
  residues processed: 113
  average time/residue: 0.0765
  time to fit residues: 12.0707
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  : 0.234 
-------------------------------------------------------------------------------
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  508 MET
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  522 SER
Chi-restraints excluded: chain B residue   43 LEU
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  297 LEU
Chi-restraints excluded: chain B residue  318 MET
Chi-restraints excluded: chain B residue  438 LEU
Chi-restraints excluded: chain B residue  457 LEU
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 30 optimal weight:    1.9990
   chunk 72 optimal weight:    0.8980
   chunk 60 optimal weight:    0.6980
   chunk 2 optimal weight:    1.9990
   chunk 80 optimal weight:    0.0670
   chunk 54 optimal weight:    0.5980
   chunk 44 optimal weight:    0.0980
   chunk 88 optimal weight:    0.3980
   chunk 36 optimal weight:    5.9990
   chunk 41 optimal weight:    5.9990
   chunk 90 optimal weight:    0.9980
   overall best weight:    0.3718

-------------------------------------------------------------------------------
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 = 0.4074 r_free = 0.4074 target = 0.184786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.146183 restraints weight = 9157.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.144372 restraints weight = 9048.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.146180 restraints weight = 9733.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.146976 restraints weight = 7186.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.147708 restraints weight = 6854.453|
|-----------------------------------------------------------------------------|
r_work (final): 0.3712
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7493
moved from start:          0.1789

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   7424  Z= 0.102
  Angle     :  0.516   8.480  10113  Z= 0.250
  Chirality :  0.037   0.161   1166
  Planarity :  0.003   0.041   1258
  Dihedral  :  3.744  43.554   1075
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 20.90 %
    Favored  : 75.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.98 (0.28), residues: 920
  helix:  2.64 (0.23), residues: 515
  sheet:  0.69 (0.64), residues: 62
  loop : -0.71 (0.33), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 314 
 TYR   0.012   0.001   TYR B 390 
 PHE   0.014   0.001   PHE A 542 
 TRP   0.014   0.001   TRP B 316 
 HIS   0.002   0.000   HIS A 539 

Details of bonding type rmsd
  covalent geometry    : bond        0.00221 ( 7419)
  covalent geometry    : angle       0.50954 (10099)
  SS BOND              : bond        0.00218 (    1)
  SS BOND              : angle       2.58998 (    2)
  hydrogen bonds       : bond        0.03793 (  425)
  hydrogen bonds       : angle       3.70219 ( 1218)
  link_NAG-ASN         : bond        0.00457 (    4)
  link_NAG-ASN         : angle       2.17167 (   12)

*********************** 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
  125 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 96
  time to evaluate  : 0.207 
Fit side-chains
REVERT: A  210 ARG cc_start: 0.6324 (tpp80) cc_final: 0.6057 (tpp80)
REVERT: A  290 ASP cc_start: 0.7690 (m-30) cc_final: 0.7371 (t0)
REVERT: A  452 ARG cc_start: 0.7941 (mtt-85) cc_final: 0.6519 (mtt90)
REVERT: B   60 ILE cc_start: 0.8125 (OUTLIER) cc_final: 0.7671 (mt)
REVERT: B  208 GLN cc_start: 0.7545 (mm-40) cc_final: 0.6717 (tt0)
REVERT: B  227 MET cc_start: 0.6161 (OUTLIER) cc_final: 0.5777 (ttp)
REVERT: B  318 MET cc_start: 0.6348 (OUTLIER) cc_final: 0.5707 (ttp)
  outliers start: 29
  outliers final: 18
  residues processed: 116
  average time/residue: 0.0838
  time to fit residues: 13.7421
Evaluate side-chains
  111 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 90
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
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  625 LEU
Chi-restraints excluded: chain B residue   43 LEU
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  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  457 LEU
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 18 optimal weight:    0.0980
   chunk 53 optimal weight:    3.9990
   chunk 11 optimal weight:    2.9990
   chunk 54 optimal weight:    0.5980
   chunk 71 optimal weight:    0.0570
   chunk 83 optimal weight:    0.0470
   chunk 12 optimal weight:    0.0270
   chunk 43 optimal weight:    0.9980
   chunk 49 optimal weight:    3.9990
   chunk 45 optimal weight:    0.1980
   chunk 90 optimal weight:    3.9990
   overall best weight:    0.0854

-------------------------------------------------------------------------------
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 211 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.187961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.148341 restraints weight = 9190.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.147237 restraints weight = 8747.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.148376 restraints weight = 9196.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.148828 restraints weight = 7259.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.149200 restraints weight = 7399.070|
|-----------------------------------------------------------------------------|
r_work (final): 0.3721
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7473
moved from start:          0.1966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046   7424  Z= 0.099
  Angle     :  0.532   7.839  10113  Z= 0.258
  Chirality :  0.037   0.160   1166
  Planarity :  0.003   0.040   1258
  Dihedral  :  3.667  39.656   1075
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 21.68 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.12 (0.28), residues: 920
  helix:  2.77 (0.23), residues: 514
  sheet:  0.99 (0.68), residues: 57
  loop : -0.69 (0.33), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 314 
 TYR   0.013   0.001   TYR B 390 
 PHE   0.014   0.001   PHE A 346 
 TRP   0.029   0.001   TRP B 316 
 HIS   0.002   0.000   HIS A 620 

Details of bonding type rmsd
  covalent geometry    : bond        0.00214 ( 7419)
  covalent geometry    : angle       0.52636 (10099)
  SS BOND              : bond        0.00868 (    1)
  SS BOND              : angle       2.74339 (    2)
  hydrogen bonds       : bond        0.03216 (  425)
  hydrogen bonds       : angle       3.58551 ( 1218)
  link_NAG-ASN         : bond        0.00468 (    4)
  link_NAG-ASN         : angle       2.04068 (   12)

*********************** 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
  119 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 97
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  290 ASP cc_start: 0.7723 (m-30) cc_final: 0.7434 (t0)
REVERT: A  452 ARG cc_start: 0.7870 (mtt-85) cc_final: 0.6497 (mtt90)
REVERT: B   60 ILE cc_start: 0.8007 (OUTLIER) cc_final: 0.7551 (mt)
REVERT: B  196 LEU cc_start: 0.7359 (OUTLIER) cc_final: 0.6026 (mm)
REVERT: B  208 GLN cc_start: 0.7417 (mm-40) cc_final: 0.6857 (tt0)
REVERT: B  227 MET cc_start: 0.6073 (OUTLIER) cc_final: 0.5703 (ttp)
  outliers start: 22
  outliers final: 15
  residues processed: 110
  average time/residue: 0.0652
  time to fit residues: 10.2091
Evaluate side-chains
  106 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 88
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
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  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   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  196 LEU
Chi-restraints excluded: chain B residue  211 GLN
Chi-restraints excluded: chain B residue  227 MET
Chi-restraints excluded: chain B residue  297 LEU
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 30 optimal weight:    1.9990
   chunk 39 optimal weight:    0.7980
   chunk 23 optimal weight:    0.6980
   chunk 56 optimal weight:    0.3980
   chunk 76 optimal weight:    5.9990
   chunk 61 optimal weight:    0.9990
   chunk 75 optimal weight:    1.9990
   chunk 68 optimal weight:    0.8980
   chunk 58 optimal weight:    0.3980
   chunk 36 optimal weight:    0.8980
   chunk 50 optimal weight:    2.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 211 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 = 0.4068 r_free = 0.4068 target = 0.184029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.144965 restraints weight = 9148.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.143333 restraints weight = 9071.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.145404 restraints weight = 8767.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.145764 restraints weight = 6820.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.146539 restraints weight = 6888.363|
|-----------------------------------------------------------------------------|
r_work (final): 0.3691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7535
moved from start:          0.2031

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= 0.121
  Angle     :  0.555   9.752  10113  Z= 0.269
  Chirality :  0.038   0.164   1166
  Planarity :  0.004   0.037   1258
  Dihedral  :  3.605  34.721   1075
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 21.68 %
    Favored  : 75.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.03 (0.28), residues: 920
  helix:  2.64 (0.23), residues: 514
  sheet:  0.99 (0.68), residues: 57
  loop : -0.63 (0.33), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 418 
 TYR   0.012   0.001   TYR B 385 
 PHE   0.013   0.001   PHE B 238 
 TRP   0.028   0.001   TRP B 316 
 HIS   0.005   0.001   HIS B 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 7419)
  covalent geometry    : angle       0.55017 (10099)
  SS BOND              : bond        0.00003 (    1)
  SS BOND              : angle       2.77421 (    2)
  hydrogen bonds       : bond        0.03991 (  425)
  hydrogen bonds       : angle       3.70968 ( 1218)
  link_NAG-ASN         : bond        0.00416 (    4)
  link_NAG-ASN         : angle       1.96962 (   12)

*********************** 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
  113 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 89
  time to evaluate  : 0.209 
Fit side-chains
   revert: symmetry clash
REVERT: A  290 ASP cc_start: 0.7615 (m-30) cc_final: 0.7391 (t0)
REVERT: A  452 ARG cc_start: 0.7882 (mtt-85) cc_final: 0.6563 (mtt90)
REVERT: B   60 ILE cc_start: 0.8143 (OUTLIER) cc_final: 0.7680 (mt)
REVERT: B  208 GLN cc_start: 0.7550 (mm-40) cc_final: 0.6985 (tt0)
REVERT: B  227 MET cc_start: 0.6133 (OUTLIER) cc_final: 0.5804 (ttp)
  outliers start: 24
  outliers final: 19
  residues processed: 107
  average time/residue: 0.0696
  time to fit residues: 10.4781
Evaluate side-chains
  105 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 84
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
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  279 LEU
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 A residue  625 LEU
Chi-restraints excluded: chain B residue   43 LEU
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  227 MET
Chi-restraints excluded: chain B residue  297 LEU
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 2 optimal weight:    0.7980
   chunk 24 optimal weight:    0.0170
   chunk 36 optimal weight:    0.8980
   chunk 10 optimal weight:    0.3980
   chunk 21 optimal weight:    1.9990
   chunk 63 optimal weight:    0.0970
   chunk 17 optimal weight:    0.6980
   chunk 48 optimal weight:    3.9990
   chunk 30 optimal weight:    0.0970
   chunk 18 optimal weight:    0.1980
   chunk 40 optimal weight:    0.6980
   overall best weight:    0.1614

-------------------------------------------------------------------------------
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 211 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 = 0.4097 r_free = 0.4097 target = 0.187246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.149046 restraints weight = 9047.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.147015 restraints weight = 9496.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.148463 restraints weight = 9020.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.149179 restraints weight = 7193.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.149597 restraints weight = 7058.844|
|-----------------------------------------------------------------------------|
r_work (final): 0.3722
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7465
moved from start:          0.2126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   7424  Z= 0.099
  Angle     :  0.533   7.521  10113  Z= 0.258
  Chirality :  0.037   0.163   1166
  Planarity :  0.003   0.036   1258
  Dihedral  :  3.343  16.295   1072
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 22.84 %
    Favored  : 74.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.18 (0.29), residues: 920
  helix:  2.73 (0.23), residues: 520
  sheet:  1.81 (0.71), residues: 51
  loop : -0.67 (0.33), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 314 
 TYR   0.043   0.001   TYR A 251 
 PHE   0.013   0.001   PHE A 542 
 TRP   0.027   0.001   TRP B 316 
 HIS   0.002   0.000   HIS A 539 

Details of bonding type rmsd
  covalent geometry    : bond        0.00211 ( 7419)
  covalent geometry    : angle       0.52786 (10099)
  SS BOND              : bond        0.00146 (    1)
  SS BOND              : angle       2.96584 (    2)
  hydrogen bonds       : bond        0.03342 (  425)
  hydrogen bonds       : angle       3.57448 ( 1218)
  link_NAG-ASN         : bond        0.00442 (    4)
  link_NAG-ASN         : angle       1.89756 (   12)

*********************** 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
  106 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 88
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
REVERT: A  290 ASP cc_start: 0.7593 (m-30) cc_final: 0.7383 (t0)
REVERT: A  452 ARG cc_start: 0.7896 (mtt-85) cc_final: 0.6496 (mtt90)
REVERT: B   60 ILE cc_start: 0.7953 (OUTLIER) cc_final: 0.7499 (mt)
REVERT: B  208 GLN cc_start: 0.7438 (mm-40) cc_final: 0.6841 (tt0)
REVERT: B  227 MET cc_start: 0.6118 (OUTLIER) cc_final: 0.5773 (ttp)
  outliers start: 18
  outliers final: 14
  residues processed: 101
  average time/residue: 0.0765
  time to fit residues: 10.8001
Evaluate side-chains
  100 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 84
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   43 LEU
Chi-restraints excluded: chain B residue   60 ILE
Chi-restraints excluded: chain B residue  106 ASP
Chi-restraints excluded: chain B residue  166 MET
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  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 33 optimal weight:    0.2980
   chunk 49 optimal weight:    0.9980
   chunk 55 optimal weight:    0.9980
   chunk 78 optimal weight:    0.7980
   chunk 46 optimal weight:    3.9990
   chunk 37 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9980
   chunk 76 optimal weight:    6.9990
   chunk 71 optimal weight:    5.9990
   chunk 45 optimal weight:    8.9990
   chunk 48 optimal weight:    1.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 211 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 = 0.4052 r_free = 0.4052 target = 0.182302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.144220 restraints weight = 9161.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.142629 restraints weight = 9272.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.144187 restraints weight = 10143.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.144953 restraints weight = 7432.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.145375 restraints weight = 7275.866|
|-----------------------------------------------------------------------------|
r_work (final): 0.3677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7544
moved from start:          0.2168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7424  Z= 0.136
  Angle     :  0.571   7.575  10113  Z= 0.280
  Chirality :  0.039   0.168   1166
  Planarity :  0.004   0.036   1258
  Dihedral  :  3.453  14.758   1072
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 22.19 %
    Favored  : 74.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.03 (0.28), residues: 920
  helix:  2.56 (0.23), residues: 520
  sheet:  1.70 (0.71), residues: 51
  loop : -0.63 (0.33), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 418 
 TYR   0.038   0.002   TYR A 251 
 PHE   0.011   0.001   PHE A 542 
 TRP   0.025   0.001   TRP B 316 
 HIS   0.003   0.001   HIS B 485 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 7419)
  covalent geometry    : angle       0.56657 (10099)
  SS BOND              : bond        0.00045 (    1)
  SS BOND              : angle       3.00505 (    2)
  hydrogen bonds       : bond        0.04353 (  425)
  hydrogen bonds       : angle       3.77253 ( 1218)
  link_NAG-ASN         : bond        0.00398 (    4)
  link_NAG-ASN         : angle       1.88620 (   12)

********************** 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
  109 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 87
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
REVERT: A  452 ARG cc_start: 0.7975 (mtt-85) cc_final: 0.6618 (mtt90)
REVERT: B   60 ILE cc_start: 0.8127 (OUTLIER) cc_final: 0.7719 (mt)
REVERT: B  208 GLN cc_start: 0.7623 (mm-40) cc_final: 0.7043 (tt0)
REVERT: B  227 MET cc_start: 0.6229 (OUTLIER) cc_final: 0.5908 (ttp)
  outliers start: 22
  outliers final: 17
  residues processed: 104
  average time/residue: 0.0799
  time to fit residues: 11.4554
Evaluate side-chains
  104 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 85
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 TRP
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  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   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  227 MET
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  438 LEU
Chi-restraints excluded: chain B residue  457 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 78 optimal weight:    0.6980
   chunk 45 optimal weight:    3.9990
   chunk 15 optimal weight:    0.8980
   chunk 42 optimal weight:    4.9990
   chunk 46 optimal weight:    4.9990
   chunk 49 optimal weight:    3.9990
   chunk 63 optimal weight:    0.6980
   chunk 24 optimal weight:    0.0470
   chunk 30 optimal weight:    0.6980
   chunk 84 optimal weight:    1.9990
   chunk 40 optimal weight:    0.7980
   overall best weight:    0.5878

-------------------------------------------------------------------------------
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 211 GLN
B 240 GLN
B 488 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.183593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.145051 restraints weight = 9173.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.142459 restraints weight = 8748.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.144704 restraints weight = 8260.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.145115 restraints weight = 6491.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.145608 restraints weight = 6588.389|
|-----------------------------------------------------------------------------|
r_work (final): 0.3675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7559
moved from start:          0.2192

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= 0.121
  Angle     :  0.584  14.391  10113  Z= 0.282
  Chirality :  0.039   0.169   1166
  Planarity :  0.003   0.036   1258
  Dihedral  :  3.442  14.414   1072
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 22.58 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.02 (0.28), residues: 920
  helix:  2.55 (0.23), residues: 520
  sheet:  1.69 (0.71), residues: 51
  loop : -0.65 (0.33), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 418 
 TYR   0.035   0.001   TYR A 251 
 PHE   0.013   0.001   PHE A 542 
 TRP   0.023   0.001   TRP B 316 
 HIS   0.002   0.000   HIS A 539 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 7419)
  covalent geometry    : angle       0.57948 (10099)
  SS BOND              : bond        0.00038 (    1)
  SS BOND              : angle       2.91270 (    2)
  hydrogen bonds       : bond        0.04096 (  425)
  hydrogen bonds       : angle       3.77671 ( 1218)
  link_NAG-ASN         : bond        0.00400 (    4)
  link_NAG-ASN         : angle       1.86421 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1172.65 seconds
wall clock time: 20 minutes 55.51 seconds (1255.51 seconds total)