Starting phenix.real_space_refine
on Mon Apr 28 08:32:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wny_37675/04_2025/8wny_37675.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wny_37675/04_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_37675/04_2025/8wny_37675.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wny_37675/04_2025/8wny_37675.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wny_37675/04_2025/8wny_37675.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wny_37675/04_2025/8wny_37675.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.002 sd=   0.077
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      32      5.16       5
     C    4713      2.51       5
     N    1190      2.21       5
     O    1298      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 7233
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3645
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 468, 3645
          Classifications: {'peptide': 468}
          Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 445}
    Chain: "B"
      Number of atoms: 3525
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 456, 3525
          Classifications: {'peptide': 456}
          Link IDs: {'PTRANS': 23, 'TRANS': 432}
    Chain: "A"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "B"
      Number of atoms: 7
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 7
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1, 'PEPT-D': 1}
  Time building chain proxies: 4.60, per 1000 atoms: 0.64
  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: 1.87
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 5 sheets defined
      63.4% alpha, 6.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.70
  Creating SS restraints...
    Processing helix  chain 'A' and resid 167 through 175
    Processing helix  chain 'A' and resid 178 through 207
      removed outlier: 3.511A  pdb=" N   THR A 182 " --> pdb=" O   GLY A 178 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 236
      removed outlier: 3.693A  pdb=" N   PHE A 234 " --> pdb=" O   ASP A 230 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   GLN A 235 " --> pdb=" O   LEU A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 247
      removed outlier: 3.580A  pdb=" N   GLY A 247 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 248 through 255
    Processing helix  chain 'A' and resid 287 through 301
    Processing helix  chain 'A' and resid 324 through 342
    Processing helix  chain 'A' and resid 350 through 354
      removed outlier: 3.559A  pdb=" N   ASN A 353 " --> pdb=" O   ASP A 350 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 356 through 372
      removed outlier: 3.780A  pdb=" N   PHE A 360 " --> pdb=" O   ASP A 356 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   PHE A 371 " --> pdb=" O   ILE A 367 " (cutoff:3.500A)
      removed outlier: 4.104A  pdb=" N   SER A 372 " --> pdb=" O   THR A 368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 394
      removed outlier: 4.219A  pdb=" N   ILE A 389 " --> pdb=" O   ASP A 385 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   LEU A 390 " --> pdb=" O   LEU A 386 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   SER A 391 " --> pdb=" O   GLN A 387 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   LEU A 392 " --> pdb=" O   GLN A 388 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 412 through 428
    Processing helix  chain 'A' and resid 441 through 445
      removed outlier: 3.724A  pdb=" N   SER A 444 " --> pdb=" O   LEU A 441 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 450 through 460
      removed outlier: 3.975A  pdb=" N   LEU A 456 " --> pdb=" O   ARG A 452 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 519 through 534
      removed outlier: 3.596A  pdb=" N   LEU A 523 " --> pdb=" O   SER A 519 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 534 through 540
    Processing helix  chain 'A' and resid 585 through 589
      removed outlier: 4.240A  pdb=" N   SER A 589 " --> pdb=" O   ALA A 586 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 43 through 54
      removed outlier: 3.536A  pdb=" N   THR B  47 " --> pdb=" O   LEU B  43 " (cutoff:3.500A)
      removed outlier: 4.386A  pdb=" N   ILE B  48 " --> pdb=" O   SER B  44 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ILE B  53 " --> pdb=" O   ILE B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 56 through 59
    Processing helix  chain 'B' and resid 60 through 70
      removed outlier: 3.845A  pdb=" N   GLY B  64 " --> pdb=" O   ILE B  60 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   HIS B  68 " --> pdb=" O   GLY B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 71 through 100
      removed outlier: 3.765A  pdb=" N   VAL B  80 " --> pdb=" O   LEU B  76 " (cutoff:3.500A)
      removed outlier: 4.149A  pdb=" N   ALA B  87 " --> pdb=" O   GLY B  83 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 105 through 114
    Processing helix  chain 'B' and resid 115 through 129
    Processing helix  chain 'B' and resid 129 through 148
    Processing helix  chain 'B' and resid 157 through 179
      removed outlier: 3.547A  pdb=" N   SER B 179 " --> pdb=" O   VAL B 175 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 180 through 211
    Processing helix  chain 'B' and resid 218 through 223
      removed outlier: 3.590A  pdb=" N   PHE B 223 " --> pdb=" O   PRO B 219 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 230 through 242
    Processing helix  chain 'B' and resid 243 through 246
    Processing helix  chain 'B' and resid 247 through 258
      removed outlier: 3.518A  pdb=" N   PHE B 250 " --> pdb=" O   GLY B 247 " (cutoff:3.500A)
      removed outlier: 4.073A  pdb=" N   LEU B 251 " --> pdb=" O   TRP B 248 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   THR B 255 " --> pdb=" O   ASN B 252 " (cutoff:3.500A)
      removed outlier: 5.459A  pdb=" N   GLU B 256 " --> pdb=" O   TYR B 253 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 260 through 291
      removed outlier: 3.506A  pdb=" N   ASN B 264 " --> pdb=" O   ASP B 260 " (cutoff:3.500A)
      Proline residue:  B 266  - end of helix
      Proline residue:  B 274  - end of helix
    Processing helix  chain 'B' and resid 292 through 298
    Processing helix  chain 'B' and resid 301 through 311
    Processing helix  chain 'B' and resid 312 through 315
    Processing helix  chain 'B' and resid 316 through 347
      removed outlier: 3.933A  pdb=" N   VAL B 320 " --> pdb=" O   TRP B 316 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   SER B 325 " --> pdb=" O   SER B 321 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   GLY B 332 " --> pdb=" O   GLY B 328 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   SER B 343 " --> pdb=" O   ARG B 339 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 351 through 356
      removed outlier: 3.588A  pdb=" N   MET B 356 " --> pdb=" O   LEU B 353 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 364 through 380
      removed outlier: 3.727A  pdb=" N   LEU B 380 " --> pdb=" O   ALA B 376 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 383 through 413
    Processing helix  chain 'B' and resid 424 through 445
    Processing helix  chain 'B' and resid 445 through 458
      removed outlier: 3.802A  pdb=" N   CYS B 449 " --> pdb=" O   GLU B 445 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 458 through 467
      removed outlier: 4.190A  pdb=" N   ILE B 462 " --> pdb=" O   THR B 458 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 473 through 492
    Processing sheet with id=AA1, first strand: chain 'A' and resid 400 through 403
      removed outlier: 3.548A  pdb=" N   LEU A 400 " --> pdb=" O   LEU A 377 " (cutoff:3.500A)
      removed outlier: 7.693A  pdb=" N   VAL A 305 " --> pdb=" O   GLY A 345 " (cutoff:3.500A)
      removed outlier: 8.553A  pdb=" N   GLN A 347 " --> pdb=" O   VAL A 305 " (cutoff:3.500A)
      removed outlier: 6.811A  pdb=" N   LEU A 307 " --> pdb=" O   GLN A 347 " (cutoff:3.500A)
      removed outlier: 5.969A  pdb=" N   LEU A 260 " --> pdb=" O   ILE A 306 " (cutoff:3.500A)
      removed outlier: 6.764A  pdb=" N   ASP A 308 " --> pdb=" O   LEU A 260 " (cutoff:3.500A)
      removed outlier: 7.142A  pdb=" N   LEU A 262 " --> pdb=" O   ASP A 308 " (cutoff:3.500A)
      removed outlier: 6.425A  pdb=" N   TRP A 434 " --> pdb=" O   VAL A 466 " (cutoff:3.500A)
      removed outlier: 8.475A  pdb=" N   SER A 468 " --> pdb=" O   TRP A 434 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 266 through 267
    Processing sheet with id=AA3, first strand: chain 'A' and resid 541 through 544
      removed outlier: 6.144A  pdb=" N   ARG A 626 " --> pdb=" O   LEU A 596 " (cutoff:3.500A)
      removed outlier: 5.146A  pdb=" N   LEU A 596 " --> pdb=" O   ARG A 626 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 575 through 576
    Processing sheet with id=AA5, first strand: chain 'B' and resid 357 through 358

    425 hydrogen bonds defined for protein.
    1218 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.07

  Time building geometry restraints manager: 2.19 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:             1.100
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     20.310
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.000
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7528
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.068   7424  Z= 0.177
  Angle     :  0.776  24.437  10113  Z= 0.389
  Chirality :  0.064   1.346   1166
  Planarity :  0.004   0.072   1258
  Dihedral  : 15.851  87.990   2681
  Min Nonbonded Distance : 2.225

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

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

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

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

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

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

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

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 94
  time to evaluate  : 0.904 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 3
  outliers final: 3
  residues processed: 96
  average time/residue: 0.1700
  time to fit residues: 23.1434
Evaluate side-chains
  92 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 89
  time to evaluate  : 0.797 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  366 ASN
Chi-restraints excluded: chain A residue  507 ASN
Chi-restraints excluded: chain A residue  508 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 76 optimal weight:    5.9990
   chunk 68 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 23 optimal weight:    0.2980
   chunk 46 optimal weight:    2.9990
   chunk 36 optimal weight:    0.7980
   chunk 71 optimal weight:    5.9990
   chunk 27 optimal weight:    3.9990
   chunk 43 optimal weight:    9.9990
   chunk 53 optimal weight:    0.8980
   chunk 82 optimal weight:    0.6980
   overall best weight:    0.9382

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.178543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.137843 restraints weight = 9245.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.136566 restraints weight = 8858.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.138035 restraints weight = 9110.287|
|-----------------------------------------------------------------------------|
r_work (final): 0.3611
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7586
moved from start:          0.0885

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

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

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

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

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00354 (    4)
  link_NAG-ASN         : angle       4.97785 (   12)
  hydrogen bonds       : bond        0.05270 (  425)
  hydrogen bonds       : angle       4.27351 ( 1218)
  SS BOND              : bond        0.00133 (    1)
  SS BOND              : angle       1.97689 (    2)
  covalent geometry    : bond        0.00358 ( 7419)
  covalent geometry    : angle       0.57320 (10099)

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

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

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

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 100
  time to evaluate  : 0.859 
Fit side-chains
   revert: symmetry clash
REVERT: A  310 THR cc_start: 0.8514 (m) cc_final: 0.8116 (t)
REVERT: A  452 ARG cc_start: 0.7824 (mtt-85) cc_final: 0.6489 (mtt90)
REVERT: B  170 MET cc_start: 0.7796 (mtt) cc_final: 0.7524 (mtp)
REVERT: B  227 MET cc_start: 0.6236 (OUTLIER) cc_final: 0.5828 (ttp)
  outliers start: 24
  outliers final: 18
  residues processed: 115
  average time/residue: 0.1681
  time to fit residues: 27.3823
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  : 0.747 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  211 CYS
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  504 VAL
Chi-restraints excluded: chain A residue  508 MET
Chi-restraints excluded: chain A residue  522 SER
Chi-restraints excluded: chain B residue  106 ASP
Chi-restraints excluded: chain B residue  227 MET
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  295 GLU
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  416 LEU
Chi-restraints excluded: chain B residue  420 ILE
Chi-restraints excluded: chain B residue  438 LEU
Chi-restraints excluded: chain B residue  467 VAL
Chi-restraints excluded: chain B residue  477 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 86 optimal weight:    0.0980
   chunk 77 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 34 optimal weight:    4.9990
   chunk 80 optimal weight:    2.9990
   chunk 87 optimal weight:    1.9990
   chunk 70 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   overall best weight:    1.1986

-------------------------------------------------------------------------------
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**
B 488 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.175904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.137012 restraints weight = 9387.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.134915 restraints weight = 8892.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.136622 restraints weight = 10227.620|
|-----------------------------------------------------------------------------|
r_work (final): 0.3578
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7611
moved from start:          0.1460

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7424  Z= 0.172
  Angle     :  0.596   7.470  10113  Z= 0.297
  Chirality :  0.041   0.170   1166
  Planarity :  0.004   0.053   1258
  Dihedral  :  4.397  59.706   1075
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 19.87 %
    Favored  : 76.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.58 (0.28), residues: 920
  helix:  2.20 (0.23), residues: 520
  sheet:  0.66 (0.67), residues: 57
  loop : -0.73 (0.33), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 434 
 HIS   0.003   0.001   HIS A 557 
 PHE   0.018   0.002   PHE A 545 
 TYR   0.017   0.002   TYR B 385 
 ARG   0.003   0.000   ARG A 227 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00460 (    4)
  link_NAG-ASN         : angle       3.06834 (   12)
  hydrogen bonds       : bond        0.05591 (  425)
  hydrogen bonds       : angle       4.21444 ( 1218)
  SS BOND              : bond        0.00041 (    1)
  SS BOND              : angle       1.96608 (    2)
  covalent geometry    : bond        0.00410 ( 7419)
  covalent geometry    : angle       0.58583 (10099)

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

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

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

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 98
  time to evaluate  : 0.894 
Fit side-chains
   revert: symmetry clash
REVERT: A  210 ARG cc_start: 0.6655 (tpp80) cc_final: 0.6381 (tpp80)
REVERT: A  310 THR cc_start: 0.8546 (m) cc_final: 0.8202 (t)
REVERT: A  452 ARG cc_start: 0.7861 (mtt-85) cc_final: 0.6445 (mtt90)
REVERT: B   60 ILE cc_start: 0.8331 (OUTLIER) cc_final: 0.7907 (mt)
REVERT: B  170 MET cc_start: 0.7701 (mtt) cc_final: 0.7409 (mtp)
REVERT: B  227 MET cc_start: 0.6307 (OUTLIER) cc_final: 0.5897 (ttp)
REVERT: B  318 MET cc_start: 0.6942 (OUTLIER) cc_final: 0.6691 (ttp)
REVERT: B  335 PHE cc_start: 0.7078 (m-80) cc_final: 0.6846 (m-80)
  outliers start: 32
  outliers final: 18
  residues processed: 120
  average time/residue: 0.1805
  time to fit residues: 30.0540
Evaluate side-chains
  113 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 92
  time to evaluate  : 0.772 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  485 MET
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   60 ILE
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  168 CYS
Chi-restraints excluded: chain B residue  227 MET
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  281 THR
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  318 MET
Chi-restraints excluded: chain B residue  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 70 optimal weight:    0.5980
   chunk 44 optimal weight:    0.2980
   chunk 9 optimal weight:    1.9990
   chunk 19 optimal weight:    4.9990
   chunk 27 optimal weight:    2.9990
   chunk 28 optimal weight:    0.7980
   chunk 17 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 3 optimal weight:    0.5980
   chunk 31 optimal weight:    1.9990
   chunk 80 optimal weight:    2.9990
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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**
B 264 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.177539 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.136776 restraints weight = 9380.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.135425 restraints weight = 10165.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.137497 restraints weight = 9044.792|
|-----------------------------------------------------------------------------|
r_work (final): 0.3591
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7599
moved from start:          0.1562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7424  Z= 0.139
  Angle     :  0.562   7.359  10113  Z= 0.276
  Chirality :  0.039   0.218   1166
  Planarity :  0.004   0.048   1258
  Dihedral  :  4.188  52.588   1075
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 20.39 %
    Favored  : 75.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.68 (0.28), residues: 920
  helix:  2.32 (0.23), residues: 519
  sheet:  0.72 (0.68), residues: 57
  loop : -0.75 (0.32), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 434 
 HIS   0.003   0.001   HIS A 557 
 PHE   0.015   0.001   PHE A 542 
 TYR   0.014   0.001   TYR B 385 
 ARG   0.007   0.000   ARG A 314 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00443 (    4)
  link_NAG-ASN         : angle       2.94613 (   12)
  hydrogen bonds       : bond        0.05015 (  425)
  hydrogen bonds       : angle       4.05587 ( 1218)
  SS BOND              : bond        0.00653 (    1)
  SS BOND              : angle       2.31241 (    2)
  covalent geometry    : bond        0.00321 ( 7419)
  covalent geometry    : angle       0.55220 (10099)

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

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

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

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 100
  time to evaluate  : 0.852 
Fit side-chains
   revert: symmetry clash
REVERT: A  210 ARG cc_start: 0.6635 (tpp80) cc_final: 0.6317 (tpp80)
REVERT: A  310 THR cc_start: 0.8556 (m) cc_final: 0.8146 (t)
REVERT: A  340 GLN cc_start: 0.7570 (mm-40) cc_final: 0.7331 (mm-40)
REVERT: A  452 ARG cc_start: 0.7854 (mtt-85) cc_final: 0.6461 (mtt90)
REVERT: B   60 ILE cc_start: 0.8252 (OUTLIER) cc_final: 0.7808 (mt)
REVERT: B  170 MET cc_start: 0.7685 (mtt) cc_final: 0.7385 (mtp)
REVERT: B  208 GLN cc_start: 0.7586 (mm-40) cc_final: 0.6871 (tt0)
REVERT: B  227 MET cc_start: 0.6307 (OUTLIER) cc_final: 0.5898 (ttp)
REVERT: B  318 MET cc_start: 0.6924 (OUTLIER) cc_final: 0.6185 (ttp)
  outliers start: 29
  outliers final: 17
  residues processed: 120
  average time/residue: 0.1965
  time to fit residues: 32.8495
Evaluate side-chains
  118 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 98
  time to evaluate  : 0.749 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 MET
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  508 MET
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  522 SER
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain B residue   60 ILE
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue  106 ASP
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  227 MET
Chi-restraints excluded: chain B residue  281 THR
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  318 MET
Chi-restraints excluded: chain B residue  438 LEU
Chi-restraints excluded: chain B residue  477 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 7 optimal weight:    0.8980
   chunk 75 optimal weight:    1.9990
   chunk 72 optimal weight:    0.8980
   chunk 10 optimal weight:    2.9990
   chunk 21 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9980
   chunk 6 optimal weight:    0.7980
   chunk 30 optimal weight:    0.8980
   chunk 53 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 83 optimal weight:    0.2980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.4009 r_free = 0.4009 target = 0.178322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.137956 restraints weight = 9157.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.137213 restraints weight = 9029.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.138648 restraints weight = 9610.512|
|-----------------------------------------------------------------------------|
r_work (final): 0.3608
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7569
moved from start:          0.1664

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= 0.127
  Angle     :  0.553  10.778  10113  Z= 0.270
  Chirality :  0.038   0.160   1166
  Planarity :  0.004   0.043   1258
  Dihedral  :  4.029  47.984   1075
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 21.81 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.80 (0.28), residues: 920
  helix:  2.46 (0.23), residues: 513
  sheet:  0.84 (0.68), residues: 57
  loop : -0.72 (0.33), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 316 
 HIS   0.002   0.001   HIS A 557 
 PHE   0.015   0.001   PHE A 542 
 TYR   0.012   0.001   TYR B 385 
 ARG   0.007   0.000   ARG A 314 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00443 (    4)
  link_NAG-ASN         : angle       2.60468 (   12)
  hydrogen bonds       : bond        0.04660 (  425)
  hydrogen bonds       : angle       3.95915 ( 1218)
  SS BOND              : bond        0.00147 (    1)
  SS BOND              : angle       2.29314 (    2)
  covalent geometry    : bond        0.00291 ( 7419)
  covalent geometry    : angle       0.54504 (10099)

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

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

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

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 100
  time to evaluate  : 0.851 
Fit side-chains
   revert: symmetry clash
REVERT: A  290 ASP cc_start: 0.7763 (m-30) cc_final: 0.7407 (t0)
REVERT: A  310 THR cc_start: 0.8550 (m) cc_final: 0.8139 (t)
REVERT: A  340 GLN cc_start: 0.7678 (mm-40) cc_final: 0.7188 (mm-40)
REVERT: A  452 ARG cc_start: 0.7831 (mtt-85) cc_final: 0.6440 (mtt90)
REVERT: B   60 ILE cc_start: 0.8197 (OUTLIER) cc_final: 0.7761 (mt)
REVERT: B  170 MET cc_start: 0.7640 (mtt) cc_final: 0.7415 (mtp)
REVERT: B  208 GLN cc_start: 0.7642 (mm-40) cc_final: 0.6930 (tt0)
REVERT: B  227 MET cc_start: 0.6238 (OUTLIER) cc_final: 0.5844 (ttp)
REVERT: B  318 MET cc_start: 0.6735 (OUTLIER) cc_final: 0.6089 (ttp)
  outliers start: 26
  outliers final: 17
  residues processed: 118
  average time/residue: 0.2000
  time to fit residues: 33.4117
Evaluate side-chains
  117 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 97
  time to evaluate  : 0.842 
-------------------------------------------------------------------------------
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  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   60 ILE
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue  106 ASP
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  168 CYS
Chi-restraints excluded: chain B residue  227 MET
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  281 THR
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  318 MET
Chi-restraints excluded: chain B residue  438 LEU
Chi-restraints excluded: chain B residue  477 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 63 optimal weight:    5.9990
   chunk 39 optimal weight:    1.9990
   chunk 68 optimal weight:    3.9990
   chunk 47 optimal weight:    0.2980
   chunk 61 optimal weight:    3.9990
   chunk 76 optimal weight:    0.7980
   chunk 74 optimal weight:    0.5980
   chunk 86 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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**
A 340 GLN
A 365 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.178029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.137551 restraints weight = 9189.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.135955 restraints weight = 9625.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.137648 restraints weight = 8692.463|
|-----------------------------------------------------------------------------|
r_work (final): 0.3597
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7588
moved from start:          0.1808

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= 0.127
  Angle     :  0.543   7.866  10113  Z= 0.267
  Chirality :  0.038   0.162   1166
  Planarity :  0.004   0.040   1258
  Dihedral  :  3.906  40.521   1075
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 21.81 %
    Favored  : 73.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.88 (0.28), residues: 920
  helix:  2.51 (0.23), residues: 514
  sheet:  0.64 (0.63), residues: 65
  loop : -0.66 (0.33), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 316 
 HIS   0.002   0.001   HIS A 557 
 PHE   0.015   0.001   PHE A 542 
 TYR   0.012   0.001   TYR B 385 
 ARG   0.002   0.000   ARG B 418 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00428 (    4)
  link_NAG-ASN         : angle       2.35478 (   12)
  hydrogen bonds       : bond        0.04570 (  425)
  hydrogen bonds       : angle       3.90964 ( 1218)
  SS BOND              : bond        0.00046 (    1)
  SS BOND              : angle       2.49862 (    2)
  covalent geometry    : bond        0.00292 ( 7419)
  covalent geometry    : angle       0.53654 (10099)

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

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

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

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 98
  time to evaluate  : 0.836 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  290 ASP cc_start: 0.7834 (m-30) cc_final: 0.7462 (t0)
REVERT: A  310 THR cc_start: 0.8480 (m) cc_final: 0.8041 (t)
REVERT: A  340 GLN cc_start: 0.7867 (mm110) cc_final: 0.7456 (mm-40)
REVERT: A  452 ARG cc_start: 0.7931 (mtt-85) cc_final: 0.6496 (mtt90)
REVERT: B   60 ILE cc_start: 0.8221 (OUTLIER) cc_final: 0.7789 (mt)
REVERT: B  208 GLN cc_start: 0.7676 (mm-40) cc_final: 0.6972 (tt0)
REVERT: B  227 MET cc_start: 0.6236 (OUTLIER) cc_final: 0.5843 (ttp)
REVERT: B  318 MET cc_start: 0.6719 (OUTLIER) cc_final: 0.6063 (ttp)
  outliers start: 33
  outliers final: 22
  residues processed: 121
  average time/residue: 0.1794
  time to fit residues: 30.6068
Evaluate side-chains
  120 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 95
  time to evaluate  : 0.813 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  184 TRP
Chi-restraints excluded: chain A residue  197 MET
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  508 MET
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  522 SER
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain B residue   60 ILE
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue  106 ASP
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  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  281 THR
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  318 MET
Chi-restraints excluded: chain B residue  438 LEU
Chi-restraints excluded: chain B residue  467 VAL
Chi-restraints excluded: chain B residue  477 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 74 optimal weight:    2.9990
   chunk 87 optimal weight:    0.9990
   chunk 69 optimal weight:    0.9980
   chunk 4 optimal weight:    0.0010
   chunk 20 optimal weight:    6.9990
   chunk 86 optimal weight:    0.6980
   chunk 76 optimal weight:    0.8980
   chunk 82 optimal weight:    0.9990
   chunk 16 optimal weight:    0.0980
   chunk 48 optimal weight:    2.9990
   overall best weight:    0.5386

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

Flipped N/Q/H residues before XYZ refinement:
A 268 ASN
** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 365 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.179229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.138712 restraints weight = 9141.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.137996 restraints weight = 8848.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.139419 restraints weight = 9688.480|
|-----------------------------------------------------------------------------|
r_work (final): 0.3627
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7571
moved from start:          0.1844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7424  Z= 0.116
  Angle     :  0.549   7.166  10113  Z= 0.269
  Chirality :  0.039   0.204   1166
  Planarity :  0.004   0.038   1258
  Dihedral  :  3.856  35.765   1075
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 22.45 %
    Favored  : 74.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.89 (0.28), residues: 920
  helix:  2.54 (0.23), residues: 513
  sheet:  0.82 (0.67), residues: 57
  loop : -0.67 (0.33), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 316 
 HIS   0.002   0.000   HIS A 557 
 PHE   0.015   0.001   PHE A 542 
 TYR   0.011   0.001   TYR B 390 
 ARG   0.002   0.000   ARG B 418 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00413 (    4)
  link_NAG-ASN         : angle       2.27787 (   12)
  hydrogen bonds       : bond        0.04269 (  425)
  hydrogen bonds       : angle       3.84580 ( 1218)
  SS BOND              : bond        0.00030 (    1)
  SS BOND              : angle       3.02881 (    2)
  covalent geometry    : bond        0.00264 ( 7419)
  covalent geometry    : angle       0.54205 (10099)

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

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

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

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 95
  time to evaluate  : 0.987 
Fit side-chains
REVERT: A  267 LYS cc_start: 0.7643 (tppt) cc_final: 0.7402 (tttp)
REVERT: A  290 ASP cc_start: 0.7732 (m-30) cc_final: 0.7408 (t0)
REVERT: A  340 GLN cc_start: 0.7812 (mm110) cc_final: 0.7363 (mm-40)
REVERT: A  452 ARG cc_start: 0.7914 (mtt-85) cc_final: 0.6493 (mtt90)
REVERT: A  534 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7610 (tp30)
REVERT: B   60 ILE cc_start: 0.8239 (OUTLIER) cc_final: 0.7794 (mt)
REVERT: B  208 GLN cc_start: 0.7693 (mm-40) cc_final: 0.6975 (tt0)
REVERT: B  227 MET cc_start: 0.6227 (OUTLIER) cc_final: 0.5848 (ttp)
REVERT: B  318 MET cc_start: 0.6647 (OUTLIER) cc_final: 0.6274 (ttp)
  outliers start: 24
  outliers final: 17
  residues processed: 111
  average time/residue: 0.2192
  time to fit residues: 33.8858
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  : 1.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  184 TRP
Chi-restraints excluded: chain A residue  197 MET
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  522 SER
Chi-restraints excluded: chain A residue  617 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  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  477 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 33 optimal weight:    0.1980
   chunk 71 optimal weight:    2.9990
   chunk 88 optimal weight:    0.9990
   chunk 8 optimal weight:    0.8980
   chunk 67 optimal weight:    0.9990
   chunk 87 optimal weight:    5.9990
   chunk 42 optimal weight:    5.9990
   chunk 72 optimal weight:    1.9990
   chunk 77 optimal weight:    2.9990
   chunk 66 optimal weight:    0.0980
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.6384

-------------------------------------------------------------------------------
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**
B 488 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.178896 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.140356 restraints weight = 9226.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.138926 restraints weight = 9068.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.140839 restraints weight = 8944.775|
|-----------------------------------------------------------------------------|
r_work (final): 0.3631
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7542
moved from start:          0.1956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7424  Z= 0.121
  Angle     :  0.553   8.075  10113  Z= 0.270
  Chirality :  0.039   0.163   1166
  Planarity :  0.004   0.039   1258
  Dihedral  :  3.645  16.236   1072
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 22.97 %
    Favored  : 73.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.94 (0.28), residues: 920
  helix:  2.54 (0.23), residues: 514
  sheet:  1.29 (0.65), residues: 58
  loop : -0.68 (0.33), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 316 
 HIS   0.002   0.000   HIS A 557 
 PHE   0.014   0.001   PHE A 542 
 TYR   0.011   0.001   TYR B 385 
 ARG   0.002   0.000   ARG B 418 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00410 (    4)
  link_NAG-ASN         : angle       2.14692 (   12)
  hydrogen bonds       : bond        0.04327 (  425)
  hydrogen bonds       : angle       3.81181 ( 1218)
  SS BOND              : bond        0.00232 (    1)
  SS BOND              : angle       2.80373 (    2)
  covalent geometry    : bond        0.00279 ( 7419)
  covalent geometry    : angle       0.54733 (10099)

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

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

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

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 95
  time to evaluate  : 0.903 
Fit side-chains
   revert: symmetry clash
REVERT: A  290 ASP cc_start: 0.7685 (m-30) cc_final: 0.7411 (t0)
REVERT: A  340 GLN cc_start: 0.7905 (mm110) cc_final: 0.7452 (mm-40)
REVERT: A  452 ARG cc_start: 0.7927 (mtt-85) cc_final: 0.6486 (mtt90)
REVERT: A  534 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7682 (mm-30)
REVERT: B   60 ILE cc_start: 0.8193 (OUTLIER) cc_final: 0.7787 (mt)
REVERT: B  208 GLN cc_start: 0.7690 (mm-40) cc_final: 0.6984 (tt0)
REVERT: B  318 MET cc_start: 0.6651 (OUTLIER) cc_final: 0.6250 (ttp)
  outliers start: 28
  outliers final: 21
  residues processed: 116
  average time/residue: 0.2468
  time to fit residues: 40.9616
Evaluate side-chains
  113 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 90
  time to evaluate  : 1.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  184 TRP
Chi-restraints excluded: chain A residue  197 MET
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  508 MET
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  522 SER
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain B residue   60 ILE
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue  106 ASP
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  154 CYS
Chi-restraints excluded: chain B residue  168 CYS
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  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 65 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 76 optimal weight:    1.9990
   chunk 40 optimal weight:    0.8980
   chunk 4 optimal weight:    0.0970
   chunk 30 optimal weight:    1.9990
   chunk 10 optimal weight:    0.3980
   chunk 0 optimal weight:    6.9990
   chunk 31 optimal weight:    1.9990
   chunk 58 optimal weight:    0.5980
   chunk 70 optimal weight:    0.7980
   overall best weight:    0.5578

-------------------------------------------------------------------------------
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**
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 = 0.4022 r_free = 0.4022 target = 0.179394 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.140710 restraints weight = 9251.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.138754 restraints weight = 8963.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.140337 restraints weight = 10080.004|
|-----------------------------------------------------------------------------|
r_work (final): 0.3625
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7553
moved from start:          0.2006

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= 0.117
  Angle     :  0.554   8.494  10113  Z= 0.269
  Chirality :  0.038   0.164   1166
  Planarity :  0.004   0.038   1258
  Dihedral  :  3.603  15.373   1072
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 22.97 %
    Favored  : 73.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.96 (0.28), residues: 920
  helix:  2.56 (0.23), residues: 514
  sheet:  1.57 (0.69), residues: 51
  loop : -0.69 (0.33), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.001   TRP B 316 
 HIS   0.002   0.000   HIS A 557 
 PHE   0.015   0.001   PHE A 542 
 TYR   0.049   0.002   TYR A 251 
 ARG   0.002   0.000   ARG B 418 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00403 (    4)
  link_NAG-ASN         : angle       2.11375 (   12)
  hydrogen bonds       : bond        0.04200 (  425)
  hydrogen bonds       : angle       3.79325 ( 1218)
  SS BOND              : bond        0.00054 (    1)
  SS BOND              : angle       3.22132 (    2)
  covalent geometry    : bond        0.00267 ( 7419)
  covalent geometry    : angle       0.54746 (10099)

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

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

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

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 95
  time to evaluate  : 1.262 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  290 ASP cc_start: 0.7684 (m-30) cc_final: 0.7422 (t0)
REVERT: A  340 GLN cc_start: 0.7932 (mm110) cc_final: 0.7452 (mm-40)
REVERT: A  452 ARG cc_start: 0.7929 (mtt-85) cc_final: 0.6509 (mtt90)
REVERT: A  534 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7695 (mm-30)
REVERT: B   60 ILE cc_start: 0.8234 (OUTLIER) cc_final: 0.7791 (mt)
REVERT: B  208 GLN cc_start: 0.7694 (mm-40) cc_final: 0.6985 (tt0)
REVERT: B  227 MET cc_start: 0.6222 (OUTLIER) cc_final: 0.5849 (ttp)
REVERT: B  318 MET cc_start: 0.6675 (OUTLIER) cc_final: 0.6258 (ttp)
  outliers start: 27
  outliers final: 21
  residues processed: 114
  average time/residue: 0.2241
  time to fit residues: 36.1234
Evaluate side-chains
  119 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 95
  time to evaluate  : 1.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  184 TRP
Chi-restraints excluded: chain A residue  197 MET
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  508 MET
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  522 SER
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain B residue   60 ILE
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue  106 ASP
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  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  488 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 4 optimal weight:    0.6980
   chunk 47 optimal weight:    0.5980
   chunk 8 optimal weight:    0.6980
   chunk 12 optimal weight:    6.9990
   chunk 40 optimal weight:    0.9980
   chunk 18 optimal weight:    0.7980
   chunk 34 optimal weight:    0.0050
   chunk 62 optimal weight:    4.9990
   chunk 45 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9980
   overall best weight:    0.5594

-------------------------------------------------------------------------------
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**
A 483 GLN
B 240 GLN
B 488 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.179572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.140914 restraints weight = 9326.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.139277 restraints weight = 9171.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.140950 restraints weight = 9896.466|
|-----------------------------------------------------------------------------|
r_work (final): 0.3636
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7545
moved from start:          0.2078

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= 0.117
  Angle     :  0.554   8.380  10113  Z= 0.269
  Chirality :  0.038   0.165   1166
  Planarity :  0.004   0.039   1258
  Dihedral  :  3.572  14.951   1072
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 23.23 %
    Favored  : 73.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.99 (0.28), residues: 920
  helix:  2.57 (0.23), residues: 514
  sheet:  1.57 (0.69), residues: 51
  loop : -0.66 (0.33), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.001   TRP B 316 
 HIS   0.002   0.000   HIS A 557 
 PHE   0.014   0.001   PHE A 542 
 TYR   0.042   0.002   TYR A 251 
 ARG   0.002   0.000   ARG B 418 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00401 (    4)
  link_NAG-ASN         : angle       2.05076 (   12)
  hydrogen bonds       : bond        0.04165 (  425)
  hydrogen bonds       : angle       3.77568 ( 1218)
  SS BOND              : bond        0.00025 (    1)
  SS BOND              : angle       3.04180 (    2)
  covalent geometry    : bond        0.00266 ( 7419)
  covalent geometry    : angle       0.54861 (10099)

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

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

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

  1840 Ramachandran restraints generated.
    920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 96
  time to evaluate  : 0.749 
Fit side-chains
   revert: symmetry clash
REVERT: A  290 ASP cc_start: 0.7625 (m-30) cc_final: 0.7420 (t0)
REVERT: A  340 GLN cc_start: 0.7938 (mm110) cc_final: 0.7459 (mm-40)
REVERT: A  452 ARG cc_start: 0.7934 (mtt-85) cc_final: 0.6508 (mtt90)
REVERT: A  534 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7694 (mm-30)
REVERT: B   60 ILE cc_start: 0.8297 (OUTLIER) cc_final: 0.7847 (mt)
REVERT: B  208 GLN cc_start: 0.7695 (mm-40) cc_final: 0.6997 (tt0)
REVERT: B  227 MET cc_start: 0.6230 (OUTLIER) cc_final: 0.5862 (ttp)
REVERT: B  318 MET cc_start: 0.6631 (OUTLIER) cc_final: 0.6230 (ttp)
  outliers start: 27
  outliers final: 21
  residues processed: 115
  average time/residue: 0.1640
  time to fit residues: 26.6170
Evaluate side-chains
  116 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 92
  time to evaluate  : 0.757 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  184 TRP
Chi-restraints excluded: chain A residue  197 MET
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  412 THR
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  508 MET
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  522 SER
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain B residue   60 ILE
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue  106 ASP
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  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  477 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 1 optimal weight:    0.4980
   chunk 36 optimal weight:    4.9990
   chunk 46 optimal weight:    5.9990
   chunk 85 optimal weight:    0.5980
   chunk 28 optimal weight:    0.6980
   chunk 84 optimal weight:    0.8980
   chunk 15 optimal weight:    7.9990
   chunk 56 optimal weight:    0.9980
   chunk 62 optimal weight:    4.9990
   chunk 53 optimal weight:    2.9990
   chunk 20 optimal weight:    0.6980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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**
A 483 GLN
B 240 GLN
B 488 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.179137 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.140658 restraints weight = 9172.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.139318 restraints weight = 8774.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.141183 restraints weight = 8846.167|
|-----------------------------------------------------------------------------|
r_work (final): 0.3640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7545
moved from start:          0.2107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7424  Z= 0.130
  Angle     :  0.600  12.592  10113  Z= 0.291
  Chirality :  0.039   0.167   1166
  Planarity :  0.004   0.039   1258
  Dihedral  :  3.604  15.874   1072
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 23.61 %
    Favored  : 73.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.95 (0.28), residues: 920
  helix:  2.52 (0.23), residues: 514
  sheet:  1.56 (0.69), residues: 51
  loop : -0.64 (0.33), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP B 316 
 HIS   0.002   0.000   HIS A 557 
 PHE   0.014   0.001   PHE A 542 
 TYR   0.015   0.001   TYR A 251 
 ARG   0.002   0.000   ARG B 418 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00389 (    4)
  link_NAG-ASN         : angle       2.03301 (   12)
  hydrogen bonds       : bond        0.04348 (  425)
  hydrogen bonds       : angle       3.85704 ( 1218)
  SS BOND              : bond        0.00055 (    1)
  SS BOND              : angle       2.99171 (    2)
  covalent geometry    : bond        0.00303 ( 7419)
  covalent geometry    : angle       0.59460 (10099)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2863.67 seconds
wall clock time: 53 minutes 16.92 seconds (3196.92 seconds total)