Starting phenix.real_space_refine
on Sun Jun  8 21:35:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7r10_14226/06_2025/7r10_14226.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7r10_14226/06_2025/7r10_14226.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7r10_14226/06_2025/7r10_14226.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7r10_14226/06_2025/7r10_14226.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7r10_14226/06_2025/7r10_14226.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7r10_14226/06_2025/7r10_14226.cif"
  }
  resolution = 4.0
  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=   0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     S      51      5.16       5
     C    6286      2.51       5
     N    1620      2.21       5
     O    1865      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 9823
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "D"
      Number of atoms: 4801
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 588, 4801
          Classifications: {'peptide': 588}
          Link IDs: {'PTRANS': 25, 'TRANS': 562}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 4923
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 622, 4923
          Classifications: {'peptide': 622}
          Link IDs: {'PTRANS': 32, 'TRANS': 589}
          Chain breaks: 4
    Chain: "D"
      Number of atoms: 85
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 85
          Unusual residues: {' ZN': 1, 'NAG': 6}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 6
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 6.14, per 1000 atoms: 0.63
  Number of scatterers: 9823
  At special positions: 0
  Unit cell: (94.864, 108.878, 164.934, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      1     29.99
     S      51     16.00
     O    1865      8.00
     N    1620      7.00
     C    6286      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=13, symmetry=0
    Simple disulfide: pdb=" SG  CYS D 133 " - pdb=" SG  CYS D 141 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 344 " - pdb=" SG  CYS D 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 530 " - pdb=" SG  CYS D 542 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  15 " - pdb=" SG  CYS A 136 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 131 " - pdb=" SG  CYS A 166 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 291 " - pdb=" SG  CYS A 301 " distance=2.07
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 538 " - pdb=" SG  CYS A 590 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 617 " - pdb=" SG  CYS A 649 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 662 " - pdb=" SG  CYS A 671 " 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 A1301 " - " ASN A 343 "
      " NAG D 902 " - " ASN D  53 "
      " NAG D 903 " - " ASN D  90 "
      " NAG D 904 " - " ASN D 322 "
      " NAG D 905 " - " ASN D 432 "
      " NAG D 906 " - " ASN D 546 "
      " NAG D 907 " - " ASN D 103 "
  Time building additional restraints: 2.23
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN D 901 "
        pdb="ZN    ZN D 901 " - pdb=" NE2 HIS D 378 "
        pdb="ZN    ZN D 901 " - pdb=" NE2 HIS D 374 "


  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2272

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 13 sheets defined
      36.7% alpha, 17.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.05
  Creating SS restraints...
    Processing helix  chain 'D' and resid 20 through 53
      removed outlier: 3.684A  pdb=" N   HIS D  34 " --> pdb=" O   ASP D  30 " (cutoff:3.500A)
      removed outlier: 4.879A  pdb=" N   GLU D  35 " --> pdb=" O   LYS D  31 " (cutoff:3.500A)
      removed outlier: 6.184A  pdb=" N   ASP D  38 " --> pdb=" O   HIS D  34 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 55 through 81
    Processing helix  chain 'D' and resid 92 through 101
    Processing helix  chain 'D' and resid 103 through 108
    Processing helix  chain 'D' and resid 109 through 129
    Processing helix  chain 'D' and resid 147 through 155
    Processing helix  chain 'D' and resid 157 through 173
    Processing helix  chain 'D' and resid 176 through 194
    Processing helix  chain 'D' and resid 198 through 205
    Processing helix  chain 'D' and resid 218 through 224
      removed outlier: 3.668A  pdb=" N   LEU D 222 " --> pdb=" O   SER D 218 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   ILE D 223 " --> pdb=" O   ARG D 219 " (cutoff:3.500A)
      removed outlier: 4.136A  pdb=" N   GLU D 224 " --> pdb=" O   GLY D 220 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 218 through 224'
    Processing helix  chain 'D' and resid 226 through 233
    Processing helix  chain 'D' and resid 233 through 249
    Processing helix  chain 'D' and resid 265 through 268
      removed outlier: 4.357A  pdb=" N   GLY D 268 " --> pdb=" O   HIS D 265 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 265 through 268'
    Processing helix  chain 'D' and resid 275 through 281
      removed outlier: 3.650A  pdb=" N   SER D 280 " --> pdb=" O   ASN D 277 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 293 through 301
    Processing helix  chain 'D' and resid 305 through 319
    Processing helix  chain 'D' and resid 326 through 331
      removed outlier: 3.677A  pdb=" N   SER D 331 " --> pdb=" O   PHE D 327 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 365 through 385
      removed outlier: 3.799A  pdb=" N   TYR D 385 " --> pdb=" O   TYR D 381 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 389 through 393
    Processing helix  chain 'D' and resid 399 through 413
      removed outlier: 3.771A  pdb=" N   ALA D 403 " --> pdb=" O   GLY D 399 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   MET D 408 " --> pdb=" O   VAL D 404 " (cutoff:3.500A)
      removed outlier: 4.163A  pdb=" N   SER D 409 " --> pdb=" O   GLY D 405 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 414 through 421
    Processing helix  chain 'D' and resid 431 through 447
      removed outlier: 3.940A  pdb=" N   THR D 445 " --> pdb=" O   LYS D 441 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 449 through 466
    Processing helix  chain 'D' and resid 472 through 484
    Processing helix  chain 'D' and resid 499 through 502
    Processing helix  chain 'D' and resid 503 through 508
    Processing helix  chain 'D' and resid 513 through 533
      removed outlier: 4.651A  pdb=" N   THR D 519 " --> pdb=" O   TYR D 515 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   LEU D 520 " --> pdb=" O   TYR D 516 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 538 through 542
    Processing helix  chain 'D' and resid 547 through 559
      removed outlier: 3.584A  pdb=" N   MET D 557 " --> pdb=" O   LYS D 553 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 565 through 572
    Processing helix  chain 'D' and resid 581 through 588
    Processing helix  chain 'D' and resid 588 through 599
    Processing helix  chain 'A' and resid 294 through 304
    Processing helix  chain 'A' and resid 338 through 343
    Processing helix  chain 'A' and resid 364 through 370
      removed outlier: 3.887A  pdb=" N   LEU A 368 " --> pdb=" O   ASP A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 389
      removed outlier: 3.633A  pdb=" N   ASP A 389 " --> pdb=" O   LYS A 386 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 410
      removed outlier: 4.009A  pdb=" N   ARG A 408 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 422
    Processing helix  chain 'A' and resid 502 through 505
    Processing sheet with id=AA1, first strand: chain 'D' and resid 262 through 263
      removed outlier: 5.661A  pdb=" N   LEU D 262 " --> pdb=" O   VAL D 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'D' and resid 347 through 350
    Processing sheet with id=AA3, first strand: chain 'A' and resid 27 through 30
      removed outlier: 3.939A  pdb=" N   ALA A  27 " --> pdb=" O   TRP A  64 " (cutoff:3.500A)
      removed outlier: 8.184A  pdb=" N   ASN A  61 " --> pdb=" O   TYR A 269 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   TYR A 269 " --> pdb=" O   ASN A  61 " (cutoff:3.500A)
      removed outlier: 4.155A  pdb=" N   LYS A 187 " --> pdb=" O   ILE A 210 " (cutoff:3.500A)
      removed outlier: 5.153A  pdb=" N   SER A 205 " --> pdb=" O   PRO A 225 " (cutoff:3.500A)
      removed outlier: 9.471A  pdb=" N   HIS A 207 " --> pdb=" O   LEU A 223 " (cutoff:3.500A)
      removed outlier: 9.229A  pdb=" N   LEU A 223 " --> pdb=" O   HIS A 207 " (cutoff:3.500A)
      removed outlier: 6.842A  pdb=" N   VAL A  36 " --> pdb=" O   LEU A 223 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 55
      removed outlier: 3.847A  pdb=" N   ASP A 287 " --> pdb=" O   LYS A 278 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 85
      removed outlier: 6.815A  pdb=" N   ARG A 237 " --> pdb=" O   PHE A 106 " (cutoff:3.500A)
      removed outlier: 4.571A  pdb=" N   PHE A 106 " --> pdb=" O   ARG A 237 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   GLN A 239 " --> pdb=" O   TRP A 104 " (cutoff:3.500A)
      removed outlier: 4.551A  pdb=" N   TRP A 104 " --> pdb=" O   GLN A 239 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   LEU A 241 " --> pdb=" O   ARG A 102 " (cutoff:3.500A)
      removed outlier: 5.748A  pdb=" N   ARG A 102 " --> pdb=" O   ASN A 121 " (cutoff:3.500A)
      removed outlier: 11.012A  pdb=" N   VAL A 126 " --> pdb=" O   GLU A 169 " (cutoff:3.500A)
      removed outlier: 9.667A  pdb=" N   GLU A 169 " --> pdb=" O   VAL A 126 " (cutoff:3.500A)
      removed outlier: 11.093A  pdb=" N   ILE A 128 " --> pdb=" O   THR A 167 " (cutoff:3.500A)
      removed outlier: 8.560A  pdb=" N   THR A 167 " --> pdb=" O   ILE A 128 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   VAL A 130 " --> pdb=" O   ASN A 165 " (cutoff:3.500A)
      removed outlier: 7.045A  pdb=" N   ASN A 165 " --> pdb=" O   VAL A 130 " (cutoff:3.500A)
      removed outlier: 6.449A  pdb=" N   GLU A 132 " --> pdb=" O   ALA A 163 " (cutoff:3.500A)
      removed outlier: 4.617A  pdb=" N   ALA A 163 " --> pdb=" O   GLU A 132 " (cutoff:3.500A)
      removed outlier: 6.423A  pdb=" N   GLN A 134 " --> pdb=" O   SER A 161 " (cutoff:3.500A)
      removed outlier: 6.944A  pdb=" N   VAL A 159 " --> pdb=" O   CYS A 136 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 142 through 143
      removed outlier: 5.622A  pdb=" N   LEU A 244 " --> pdb=" O   VAL A 143 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 313
    Processing sheet with id=AA8, first strand: chain 'A' and resid 324 through 328
      removed outlier: 3.898A  pdb=" N   GLU A 324 " --> pdb=" O   CYS A 538 " (cutoff:3.500A)
      removed outlier: 6.200A  pdb=" N   ILE A 584 " --> pdb=" O   SER A 555 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358
    Processing sheet with id=AB1, first strand: chain 'A' and resid 391 through 392
    Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474
    Processing sheet with id=AB4, first strand: chain 'A' and resid 664 through 667
      removed outlier: 6.534A  pdb=" N   ILE A 670 " --> pdb=" O   ILE A 666 " (cutoff:3.500A)

    416 hydrogen bonds defined for protein.
    1146 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: 2.77

  Time building geometry restraints manager: 2.69 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3104
        1.34 -     1.46: 2360
        1.46 -     1.58: 4545
        1.58 -     1.70: 0
        1.70 -     1.82: 74
  Bond restraints: 10083
  Sorted by residual:
  bond pdb=" N   CYS A 291 "
       pdb=" CA  CYS A 291 "
    ideal  model  delta    sigma   weight residual
    1.459  1.497 -0.039 1.24e-02 6.50e+03 9.76e+00
  bond pdb=" N   VAL A 320 "
       pdb=" CA  VAL A 320 "
    ideal  model  delta    sigma   weight residual
    1.459  1.497 -0.038 1.25e-02 6.40e+03 9.11e+00
  bond pdb=" N   ARG A 319 "
       pdb=" CA  ARG A 319 "
    ideal  model  delta    sigma   weight residual
    1.456  1.492 -0.037 1.22e-02 6.72e+03 9.01e+00
  bond pdb=" N   LYS A 529 "
       pdb=" CA  LYS A 529 "
    ideal  model  delta    sigma   weight residual
    1.454  1.488 -0.034 1.18e-02 7.18e+03 8.27e+00
  bond pdb=" N   ASP A 290 "
       pdb=" CA  ASP A 290 "
    ideal  model  delta    sigma   weight residual
    1.458  1.492 -0.034 1.24e-02 6.50e+03 7.73e+00
  ... (remaining 10078 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.31: 13281
        1.31 -     2.62: 313
        2.62 -     3.93: 102
        3.93 -     5.24: 9
        5.24 -     6.54: 3
  Bond angle restraints: 13708
  Sorted by residual:
  angle pdb=" CA  CYS A 291 "
        pdb=" C   CYS A 291 "
        pdb=" O   CYS A 291 "
      ideal   model   delta    sigma   weight residual
     120.55  116.78    3.77 1.07e+00 8.73e-01 1.24e+01
  angle pdb=" CA  PHE A 318 "
        pdb=" C   PHE A 318 "
        pdb=" O   PHE A 318 "
      ideal   model   delta    sigma   weight residual
     121.55  117.93    3.62 1.06e+00 8.90e-01 1.17e+01
  angle pdb=" CA  SER A 591 "
        pdb=" C   SER A 591 "
        pdb=" O   SER A 591 "
      ideal   model   delta    sigma   weight residual
     121.55  118.37    3.18 1.06e+00 8.90e-01 9.00e+00
  angle pdb=" CA  ILE A 332 "
        pdb=" C   ILE A 332 "
        pdb=" O   ILE A 332 "
      ideal   model   delta    sigma   weight residual
     121.09  117.94    3.15 1.06e+00 8.90e-01 8.82e+00
  angle pdb=" CA  ARG A 319 "
        pdb=" C   ARG A 319 "
        pdb=" O   ARG A 319 "
      ideal   model   delta    sigma   weight residual
     121.16  117.98    3.18 1.12e+00 7.97e-01 8.06e+00
  ... (remaining 13703 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.52: 5491
       17.52 -    35.04: 437
       35.04 -    52.57: 83
       52.57 -    70.09: 19
       70.09 -    87.61: 10
  Dihedral angle restraints: 6040
    sinusoidal: 2502
      harmonic: 3538
  Sorted by residual:
  dihedral pdb=" CB  CYS A 538 "
           pdb=" SG  CYS A 538 "
           pdb=" SG  CYS A 590 "
           pdb=" CB  CYS A 590 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -153.14   67.14     1      1.00e+01 1.00e-02 5.87e+01
  dihedral pdb=" CB  CYS D 133 "
           pdb=" SG  CYS D 133 "
           pdb=" SG  CYS D 141 "
           pdb=" CB  CYS D 141 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   32.40   60.60     1      1.00e+01 1.00e-02 4.89e+01
  dihedral pdb=" CB  CYS A 336 "
           pdb=" SG  CYS A 336 "
           pdb=" SG  CYS A 361 "
           pdb=" CB  CYS A 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -38.84  -47.16     1      1.00e+01 1.00e-02 3.07e+01
  ... (remaining 6037 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 1147
       0.044 -    0.087: 233
       0.087 -    0.131: 103
       0.131 -    0.174: 9
       0.174 -    0.218: 2
  Chirality restraints: 1494
  Sorted by residual:
  chirality pdb=" CA  ILE A 332 "
            pdb=" N   ILE A 332 "
            pdb=" C   ILE A 332 "
            pdb=" CB  ILE A 332 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.22 2.00e-01 2.50e+01 1.18e+00
  chirality pdb=" CA  VAL A 143 "
            pdb=" N   VAL A 143 "
            pdb=" C   VAL A 143 "
            pdb=" CB  VAL A 143 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.62   -0.18 2.00e-01 2.50e+01 7.70e-01
  chirality pdb=" CA  VAL A 320 "
            pdb=" N   VAL A 320 "
            pdb=" C   VAL A 320 "
            pdb=" CB  VAL A 320 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.61   -0.17 2.00e-01 2.50e+01 7.42e-01
  ... (remaining 1491 not shown)

  Planarity restraints: 1767
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU D  35 "    0.016 2.00e-02 2.50e+03   3.13e-02 9.82e+00
        pdb=" C   GLU D  35 "   -0.054 2.00e-02 2.50e+03
        pdb=" O   GLU D  35 "    0.020 2.00e-02 2.50e+03
        pdb=" N   ALA D  36 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 478 "    0.036 5.00e-02 4.00e+02   5.45e-02 4.75e+00
        pdb=" N   PRO A 479 "   -0.094 5.00e-02 4.00e+02
        pdb=" CA  PRO A 479 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 479 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 289 "   -0.011 2.00e-02 2.50e+03   2.13e-02 4.54e+00
        pdb=" C   VAL A 289 "    0.037 2.00e-02 2.50e+03
        pdb=" O   VAL A 289 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   ASP A 290 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 1764 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.68: 176
        2.68 -     3.24: 9263
        3.24 -     3.79: 14875
        3.79 -     4.35: 19540
        4.35 -     4.90: 32679
  Nonbonded interactions: 76533
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU D 402 "
            pdb="ZN    ZN D 901 "
     model   vdw
     2.131 2.230
  nonbonded pdb=" O   PRO A  85 "
            pdb=" OH  TYR A 269 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" O   ASN A  81 "
            pdb=" NE2 GLN A 239 "
     model   vdw
     2.292 3.120
  nonbonded pdb=" O   ASN A 439 "
            pdb=" OG  SER A 443 "
     model   vdw
     2.296 3.040
  nonbonded pdb=" O   ASN D  53 "
            pdb=" ND2 ASN D  58 "
     model   vdw
     2.334 3.120
  ... (remaining 76528 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:             393.830
  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:          0.370
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     25.440
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  422.820
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8321
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   0.039  10105  Z= 0.187
  Angle     :  0.524   6.545  13755  Z= 0.293
  Chirality :  0.043   0.218   1494
  Planarity :  0.003   0.054   1760
  Dihedral  : 13.309  87.611   3729
  Min Nonbonded Distance : 2.131

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  :  0.19 %
    Favored  : 99.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.67 (0.25), residues: 1196
  helix:  2.25 (0.28), residues: 388
  sheet:  0.80 (0.38), residues: 182
  loop : -0.87 (0.25), residues: 626

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 353 
 HIS   0.005   0.001   HIS A 146 
 PHE   0.010   0.001   PHE D 512 
 TYR   0.012   0.001   TYR A 265 
 ARG   0.002   0.000   ARG D 245 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00365 (    7)
  link_NAG-ASN         : angle       1.91630 (   21)
  hydrogen bonds       : bond        0.12487 (  416)
  hydrogen bonds       : angle       5.13874 ( 1146)
  metal coordination   : bond        0.00121 (    2)
  SS BOND              : bond        0.00983 (   13)
  SS BOND              : angle       1.26653 (   26)
  covalent geometry    : bond        0.00315 (10083)
  covalent geometry    : angle       0.51629 (13708)

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 65
  time to evaluate  : 1.136 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  190 MET cc_start: 0.9308 (ttp) cc_final: 0.9053 (tmm)
REVERT: D  270 MET cc_start: 0.8684 (tpp) cc_final: 0.8244 (tpp)
REVERT: A  177 MET cc_start: 0.4589 (ttm) cc_final: 0.4307 (mtm)
  outliers start: 5
  outliers final: 3
  residues processed: 70
  average time/residue: 0.2335
  time to fit residues: 23.8090
Evaluate side-chains
  41 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 38
  time to evaluate  : 1.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  146 HIS
Chi-restraints excluded: chain A residue  319 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 101 optimal weight:    3.9990
   chunk 90 optimal weight:    0.9980
   chunk 50 optimal weight:    0.8980
   chunk 31 optimal weight:    0.0980
   chunk 61 optimal weight:    0.3980
   chunk 48 optimal weight:    1.9990
   chunk 94 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9990
   chunk 57 optimal weight:    4.9990
   chunk 70 optimal weight:    9.9990
   chunk 108 optimal weight:    0.9980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
D 101 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.076012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.049745 restraints weight = 45103.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.048838 restraints weight = 31627.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.049236 restraints weight = 25922.724|
|-----------------------------------------------------------------------------|
r_work (final): 0.2958
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8272
moved from start:          0.1082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10105  Z= 0.117
  Angle     :  0.513  10.602  13755  Z= 0.259
  Chirality :  0.042   0.169   1494
  Planarity :  0.004   0.057   1760
  Dihedral  :  6.176  59.544   1463
  Min Nonbonded Distance : 2.110

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  :  4.31 %
    Favored  : 94.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.59 (0.25), residues: 1196
  helix:  2.15 (0.27), residues: 384
  sheet:  0.92 (0.39), residues: 161
  loop : -0.88 (0.24), residues: 651

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 436 
 HIS   0.003   0.001   HIS D 378 
 PHE   0.008   0.001   PHE D 369 
 TYR   0.011   0.001   TYR A 612 
 ARG   0.005   0.000   ARG A 646 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00412 (    7)
  link_NAG-ASN         : angle       2.03092 (   21)
  hydrogen bonds       : bond        0.03808 (  416)
  hydrogen bonds       : angle       4.51889 ( 1146)
  metal coordination   : bond        0.00087 (    2)
  SS BOND              : bond        0.00176 (   13)
  SS BOND              : angle       0.58931 (   26)
  covalent geometry    : bond        0.00251 (10083)
  covalent geometry    : angle       0.50726 (13708)

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 39
  time to evaluate  : 1.167 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  190 MET cc_start: 0.9399 (ttp) cc_final: 0.8978 (tmm)
REVERT: D  270 MET cc_start: 0.8513 (tpp) cc_final: 0.8001 (tpp)
REVERT: D  303 ASP cc_start: 0.6900 (p0) cc_final: 0.6698 (p0)
REVERT: D  332 MET cc_start: 0.8317 (ppp) cc_final: 0.8107 (tmm)
REVERT: A  258 TRP cc_start: 0.5135 (p-90) cc_final: 0.4905 (p-90)
REVERT: A  266 TYR cc_start: 0.9239 (OUTLIER) cc_final: 0.8254 (m-80)
  outliers start: 8
  outliers final: 4
  residues processed: 47
  average time/residue: 0.2240
  time to fit residues: 16.0560
Evaluate side-chains
  38 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 33
  time to evaluate  : 1.047 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  146 HIS
Chi-restraints excluded: chain A residue  266 TYR
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  320 VAL
Chi-restraints excluded: chain A residue  646 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 117 optimal weight:   10.0000
   chunk 43 optimal weight:    0.7980
   chunk 113 optimal weight:    3.9990
   chunk 33 optimal weight:    0.8980
   chunk 98 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9990
   chunk 2 optimal weight:    0.5980
   chunk 21 optimal weight:    0.7980
   chunk 68 optimal weight:    0.0000
   chunk 20 optimal weight:    0.8980
   overall best weight:    0.6184

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

Flipped N/Q/H residues before XYZ refinement:
D  98 GLN
A 146 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.075828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.049495 restraints weight = 45864.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.048586 restraints weight = 29340.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.048889 restraints weight = 25184.651|
|-----------------------------------------------------------------------------|
r_work (final): 0.2942
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8298
moved from start:          0.1297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  10105  Z= 0.104
  Angle     :  0.484   7.372  13755  Z= 0.244
  Chirality :  0.041   0.179   1494
  Planarity :  0.003   0.050   1760
  Dihedral  :  5.438  55.170   1458
  Min Nonbonded Distance : 2.119

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  :  6.09 %
    Favored  : 93.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.62 (0.25), residues: 1196
  helix:  2.18 (0.27), residues: 385
  sheet:  0.91 (0.40), residues: 159
  loop : -0.84 (0.24), residues: 652

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 436 
 HIS   0.003   0.001   HIS D 378 
 PHE   0.010   0.001   PHE D 230 
 TYR   0.015   0.001   TYR A 612 
 ARG   0.005   0.000   ARG A 646 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00311 (    7)
  link_NAG-ASN         : angle       2.12589 (   21)
  hydrogen bonds       : bond        0.03481 (  416)
  hydrogen bonds       : angle       4.35394 ( 1146)
  metal coordination   : bond        0.00090 (    2)
  SS BOND              : bond        0.00158 (   13)
  SS BOND              : angle       0.48009 (   26)
  covalent geometry    : bond        0.00231 (10083)
  covalent geometry    : angle       0.47725 (13708)

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 33
  time to evaluate  : 1.288 
Fit side-chains
   revert: symmetry clash
REVERT: D  152 MET cc_start: 0.8872 (tpp) cc_final: 0.8506 (tpt)
REVERT: D  190 MET cc_start: 0.9393 (ttp) cc_final: 0.8976 (tmm)
REVERT: D  249 MET cc_start: 0.8161 (mmt) cc_final: 0.7946 (mmt)
REVERT: D  270 MET cc_start: 0.8490 (tpp) cc_final: 0.7924 (tpp)
REVERT: D  303 ASP cc_start: 0.6964 (p0) cc_final: 0.6694 (p0)
REVERT: A  258 TRP cc_start: 0.5148 (p-90) cc_final: 0.4825 (p-90)
REVERT: A  266 TYR cc_start: 0.9312 (OUTLIER) cc_final: 0.8525 (m-80)
  outliers start: 8
  outliers final: 3
  residues processed: 40
  average time/residue: 0.2171
  time to fit residues: 13.8345
Evaluate side-chains
  36 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 32
  time to evaluate  : 1.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  339 VAL
Chi-restraints excluded: chain A residue  146 HIS
Chi-restraints excluded: chain A residue  266 TYR
Chi-restraints excluded: chain A residue  277 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 39 optimal weight:    3.9990
   chunk 41 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9980
   chunk 111 optimal weight:    4.9990
   chunk 55 optimal weight:    0.0970
   chunk 3 optimal weight:    0.8980
   chunk 70 optimal weight:    9.9990
   chunk 100 optimal weight:    0.0370
   chunk 117 optimal weight:   10.0000
   chunk 69 optimal weight:    3.9990
   chunk 99 optimal weight:    0.1980
   overall best weight:    0.4456

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.076066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.049831 restraints weight = 45278.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.049065 restraints weight = 28237.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.049154 restraints weight = 25273.281|
|-----------------------------------------------------------------------------|
r_work (final): 0.2948
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8291
moved from start:          0.1500

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  10105  Z= 0.089
  Angle     :  0.464   7.671  13755  Z= 0.233
  Chirality :  0.041   0.186   1494
  Planarity :  0.003   0.035   1760
  Dihedral  :  5.054  54.926   1458
  Min Nonbonded Distance : 2.137

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  :  7.77 %
    Favored  : 91.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.67 (0.25), residues: 1196
  helix:  2.20 (0.27), residues: 385
  sheet:  1.04 (0.40), residues: 154
  loop : -0.82 (0.25), residues: 657

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 436 
 HIS   0.002   0.000   HIS D  34 
 PHE   0.011   0.001   PHE D 230 
 TYR   0.016   0.001   TYR A 612 
 ARG   0.003   0.000   ARG A 646 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00318 (    7)
  link_NAG-ASN         : angle       2.18094 (   21)
  hydrogen bonds       : bond        0.03171 (  416)
  hydrogen bonds       : angle       4.22190 ( 1146)
  metal coordination   : bond        0.00069 (    2)
  SS BOND              : bond        0.00124 (   13)
  SS BOND              : angle       0.42699 (   26)
  covalent geometry    : bond        0.00194 (10083)
  covalent geometry    : angle       0.45630 (13708)

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 34
  time to evaluate  : 1.048 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  152 MET cc_start: 0.8921 (tpp) cc_final: 0.8544 (tpt)
REVERT: D  190 MET cc_start: 0.9392 (ttp) cc_final: 0.8977 (tmm)
REVERT: D  270 MET cc_start: 0.8463 (tpp) cc_final: 0.7892 (tpp)
REVERT: D  303 ASP cc_start: 0.7152 (p0) cc_final: 0.6899 (p0)
REVERT: D  332 MET cc_start: 0.8158 (ppp) cc_final: 0.7859 (tmm)
REVERT: D  360 MET cc_start: 0.8332 (mtm) cc_final: 0.8083 (ttp)
REVERT: A  266 TYR cc_start: 0.9309 (OUTLIER) cc_final: 0.8553 (m-80)
  outliers start: 7
  outliers final: 3
  residues processed: 41
  average time/residue: 0.2098
  time to fit residues: 13.4621
Evaluate side-chains
  37 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 33
  time to evaluate  : 1.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  339 VAL
Chi-restraints excluded: chain D residue  364 VAL
Chi-restraints excluded: chain A residue  146 HIS
Chi-restraints excluded: chain A residue  266 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 98 optimal weight:    0.8980
   chunk 61 optimal weight:    7.9990
   chunk 42 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9990
   chunk 0 optimal weight:    5.9990
   chunk 60 optimal weight:   10.0000
   chunk 39 optimal weight:    1.9990
   chunk 77 optimal weight:    0.4980
   chunk 75 optimal weight:    3.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.075242 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 83)----------------|
| r_work = 0.2896 r_free = 0.2896 target = 0.045001 restraints weight = 45460.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.046504 restraints weight = 26189.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.047478 restraints weight = 18868.563|
|-----------------------------------------------------------------------------|
r_work (final): 0.2921
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8385
moved from start:          0.1626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10105  Z= 0.143
  Angle     :  0.489   7.935  13755  Z= 0.248
  Chirality :  0.041   0.174   1494
  Planarity :  0.003   0.034   1760
  Dihedral  :  5.041  56.118   1458
  Min Nonbonded Distance : 2.070

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  :  8.15 %
    Favored  : 91.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.68 (0.25), residues: 1196
  helix:  2.10 (0.27), residues: 391
  sheet:  1.14 (0.40), residues: 151
  loop : -0.79 (0.25), residues: 654

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 258 
 HIS   0.004   0.001   HIS D 378 
 PHE   0.010   0.001   PHE D 369 
 TYR   0.015   0.001   TYR A 453 
 ARG   0.003   0.000   ARG A 646 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00267 (    7)
  link_NAG-ASN         : angle       2.21284 (   21)
  hydrogen bonds       : bond        0.03474 (  416)
  hydrogen bonds       : angle       4.27314 ( 1146)
  metal coordination   : bond        0.00081 (    2)
  SS BOND              : bond        0.00165 (   13)
  SS BOND              : angle       0.55396 (   26)
  covalent geometry    : bond        0.00322 (10083)
  covalent geometry    : angle       0.48107 (13708)

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 33
  time to evaluate  : 1.168 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  152 MET cc_start: 0.8939 (tpp) cc_final: 0.8570 (tpt)
REVERT: D  190 MET cc_start: 0.9220 (ttp) cc_final: 0.8824 (tmm)
REVERT: D  248 LEU cc_start: 0.9197 (tp) cc_final: 0.8988 (tp)
REVERT: D  270 MET cc_start: 0.8493 (tpp) cc_final: 0.7927 (tpp)
REVERT: D  303 ASP cc_start: 0.6926 (p0) cc_final: 0.6624 (p0)
REVERT: D  332 MET cc_start: 0.8075 (ppp) cc_final: 0.7826 (tmm)
REVERT: D  360 MET cc_start: 0.8350 (mtm) cc_final: 0.8134 (ttp)
REVERT: A  177 MET cc_start: 0.4104 (mtp) cc_final: 0.3622 (mtp)
REVERT: A  266 TYR cc_start: 0.9595 (OUTLIER) cc_final: 0.8913 (m-80)
  outliers start: 8
  outliers final: 4
  residues processed: 41
  average time/residue: 0.2560
  time to fit residues: 16.1253
Evaluate side-chains
  37 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 32
  time to evaluate  : 1.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  339 VAL
Chi-restraints excluded: chain D residue  401 HIS
Chi-restraints excluded: chain A residue  146 HIS
Chi-restraints excluded: chain A residue  266 TYR
Chi-restraints excluded: chain A residue  277 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 48 optimal weight:    0.7980
   chunk 27 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9980
   chunk 8 optimal weight:    2.9990
   chunk 77 optimal weight:    0.9980
   chunk 76 optimal weight:    5.9990
   chunk 66 optimal weight:    9.9990
   chunk 25 optimal weight:    0.9990
   chunk 114 optimal weight:    0.4980
   chunk 50 optimal weight:    0.9980
   chunk 65 optimal weight:    0.0970
   overall best weight:    0.6778

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

Flipped N/Q/H residues before XYZ refinement:
** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.075563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.049481 restraints weight = 45104.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.048746 restraints weight = 31725.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.048906 restraints weight = 24810.184|
|-----------------------------------------------------------------------------|
r_work (final): 0.2945
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8285
moved from start:          0.1744

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  10105  Z= 0.104
  Angle     :  0.473   8.949  13755  Z= 0.237
  Chirality :  0.040   0.180   1494
  Planarity :  0.003   0.034   1760
  Dihedral  :  4.933  55.687   1458
  Min Nonbonded Distance : 2.127

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  :  9.08 %
    Favored  : 90.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.71 (0.25), residues: 1196
  helix:  2.12 (0.27), residues: 391
  sheet:  1.15 (0.40), residues: 154
  loop : -0.78 (0.25), residues: 651

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 436 
 HIS   0.002   0.000   HIS D 378 
 PHE   0.009   0.001   PHE D 369 
 TYR   0.014   0.001   TYR A 612 
 ARG   0.002   0.000   ARG A 646 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00309 (    7)
  link_NAG-ASN         : angle       2.22219 (   21)
  hydrogen bonds       : bond        0.03230 (  416)
  hydrogen bonds       : angle       4.17959 ( 1146)
  metal coordination   : bond        0.00089 (    2)
  SS BOND              : bond        0.00136 (   13)
  SS BOND              : angle       0.45276 (   26)
  covalent geometry    : bond        0.00234 (10083)
  covalent geometry    : angle       0.46562 (13708)

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 32
  time to evaluate  : 1.170 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  152 MET cc_start: 0.8954 (tpp) cc_final: 0.8567 (tpt)
REVERT: D  190 MET cc_start: 0.9381 (ttp) cc_final: 0.9127 (tmm)
REVERT: D  248 LEU cc_start: 0.9264 (tp) cc_final: 0.9017 (tp)
REVERT: D  270 MET cc_start: 0.8450 (tpp) cc_final: 0.7922 (tpp)
REVERT: D  332 MET cc_start: 0.8076 (ppp) cc_final: 0.7873 (tmm)
REVERT: D  360 MET cc_start: 0.8458 (mtm) cc_final: 0.8034 (ttp)
REVERT: D  375 GLU cc_start: 0.8776 (mm-30) cc_final: 0.8307 (mp0)
REVERT: A  177 MET cc_start: 0.1218 (mtp) cc_final: 0.0982 (mtp)
REVERT: A  266 TYR cc_start: 0.9145 (OUTLIER) cc_final: 0.8353 (m-80)
  outliers start: 6
  outliers final: 4
  residues processed: 38
  average time/residue: 0.2339
  time to fit residues: 14.3048
Evaluate side-chains
  37 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 32
  time to evaluate  : 1.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  339 VAL
Chi-restraints excluded: chain D residue  401 HIS
Chi-restraints excluded: chain A residue  146 HIS
Chi-restraints excluded: chain A residue  266 TYR
Chi-restraints excluded: chain A residue  277 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 74 optimal weight:   20.0000
   chunk 98 optimal weight:    2.9990
   chunk 39 optimal weight:    0.0970
   chunk 18 optimal weight:    4.9990
   chunk 86 optimal weight:    7.9990
   chunk 88 optimal weight:    3.9990
   chunk 58 optimal weight:   50.0000
   chunk 85 optimal weight:    1.9990
   chunk 49 optimal weight:    0.3980
   chunk 111 optimal weight:    7.9990
   chunk 15 optimal weight:    0.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
D 340 GLN
** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.074571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.045411 restraints weight = 46035.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.047466 restraints weight = 28552.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.046872 restraints weight = 17174.708|
|-----------------------------------------------------------------------------|
r_work (final): 0.2863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8398
moved from start:          0.1878

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  10105  Z= 0.170
  Angle     :  0.513   9.904  13755  Z= 0.260
  Chirality :  0.041   0.176   1494
  Planarity :  0.003   0.034   1760
  Dihedral  :  5.053  56.906   1458
  Min Nonbonded Distance : 2.058

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  :  9.08 %
    Favored  : 89.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.62 (0.25), residues: 1196
  helix:  2.00 (0.27), residues: 390
  sheet:  1.17 (0.41), residues: 152
  loop : -0.80 (0.25), residues: 654

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 258 
 HIS   0.003   0.001   HIS D 378 
 PHE   0.011   0.001   PHE D 369 
 TYR   0.018   0.001   TYR D 207 
 ARG   0.004   0.000   ARG A 454 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00272 (    7)
  link_NAG-ASN         : angle       2.27710 (   21)
  hydrogen bonds       : bond        0.03706 (  416)
  hydrogen bonds       : angle       4.30810 ( 1146)
  metal coordination   : bond        0.00216 (    2)
  SS BOND              : bond        0.00185 (   13)
  SS BOND              : angle       0.62483 (   26)
  covalent geometry    : bond        0.00382 (10083)
  covalent geometry    : angle       0.50493 (13708)

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 32
  time to evaluate  : 1.400 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  152 MET cc_start: 0.8964 (tpp) cc_final: 0.8565 (tpt)
REVERT: D  190 MET cc_start: 0.9406 (ttp) cc_final: 0.8978 (tmm)
REVERT: D  248 LEU cc_start: 0.9322 (tp) cc_final: 0.9097 (tp)
REVERT: D  270 MET cc_start: 0.8565 (tpp) cc_final: 0.7922 (tpp)
REVERT: D  332 MET cc_start: 0.8138 (ppp) cc_final: 0.7919 (tmm)
REVERT: D  366 MET cc_start: 0.7833 (tmm) cc_final: 0.7594 (tmm)
REVERT: D  375 GLU cc_start: 0.8886 (mm-30) cc_final: 0.8359 (mp0)
REVERT: A  177 MET cc_start: 0.2224 (mtp) cc_final: 0.1913 (mtp)
REVERT: A  266 TYR cc_start: 0.9394 (OUTLIER) cc_final: 0.8632 (m-80)
  outliers start: 11
  outliers final: 6
  residues processed: 42
  average time/residue: 0.4427
  time to fit residues: 26.4203
Evaluate side-chains
  39 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 32
  time to evaluate  : 1.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  339 VAL
Chi-restraints excluded: chain D residue  401 HIS
Chi-restraints excluded: chain D residue  475 LYS
Chi-restraints excluded: chain A residue  146 HIS
Chi-restraints excluded: chain A residue  266 TYR
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  478 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 100 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 115 optimal weight:    5.9990
   chunk 11 optimal weight:    0.0470
   chunk 107 optimal weight:    1.9990
   chunk 35 optimal weight:    0.6980
   chunk 80 optimal weight:    2.9990
   chunk 66 optimal weight:    6.9990
   chunk 43 optimal weight:    0.5980
   chunk 27 optimal weight:    3.9990
   chunk 47 optimal weight:    0.0770
   overall best weight:    0.6838

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

Flipped N/Q/H residues before XYZ refinement:
** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.075218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.049087 restraints weight = 45722.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.048271 restraints weight = 33224.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.048482 restraints weight = 25474.716|
|-----------------------------------------------------------------------------|
r_work (final): 0.2931
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8303
moved from start:          0.1923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  10105  Z= 0.105
  Angle     :  0.477   9.690  13755  Z= 0.239
  Chirality :  0.040   0.178   1494
  Planarity :  0.003   0.034   1760
  Dihedral  :  4.952  56.065   1458
  Min Nonbonded Distance : 2.141

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  :  9.64 %
    Favored  : 89.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.67 (0.25), residues: 1196
  helix:  2.07 (0.27), residues: 391
  sheet:  1.15 (0.40), residues: 152
  loop : -0.77 (0.25), residues: 653

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 436 
 HIS   0.003   0.000   HIS D 378 
 PHE   0.009   0.001   PHE D 369 
 TYR   0.012   0.001   TYR D  50 
 ARG   0.002   0.000   ARG A 646 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00318 (    7)
  link_NAG-ASN         : angle       2.26446 (   21)
  hydrogen bonds       : bond        0.03297 (  416)
  hydrogen bonds       : angle       4.17517 ( 1146)
  metal coordination   : bond        0.00100 (    2)
  SS BOND              : bond        0.00129 (   13)
  SS BOND              : angle       0.46648 (   26)
  covalent geometry    : bond        0.00239 (10083)
  covalent geometry    : angle       0.46903 (13708)

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 32
  time to evaluate  : 1.168 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  152 MET cc_start: 0.8964 (tpp) cc_final: 0.8592 (tpt)
REVERT: D  190 MET cc_start: 0.9390 (ttp) cc_final: 0.9159 (tmm)
REVERT: D  248 LEU cc_start: 0.9279 (tp) cc_final: 0.9072 (tp)
REVERT: D  270 MET cc_start: 0.8418 (tpp) cc_final: 0.7855 (tpp)
REVERT: D  366 MET cc_start: 0.7684 (tmm) cc_final: 0.7482 (tmm)
REVERT: D  375 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8312 (mp0)
REVERT: D  474 MET cc_start: 0.8701 (mmp) cc_final: 0.8482 (mmm)
REVERT: A  266 TYR cc_start: 0.9151 (OUTLIER) cc_final: 0.8337 (m-80)
  outliers start: 9
  outliers final: 6
  residues processed: 41
  average time/residue: 0.2472
  time to fit residues: 16.3508
Evaluate side-chains
  38 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 31
  time to evaluate  : 1.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  339 VAL
Chi-restraints excluded: chain D residue  391 LEU
Chi-restraints excluded: chain D residue  401 HIS
Chi-restraints excluded: chain A residue  146 HIS
Chi-restraints excluded: chain A residue  266 TYR
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  478 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 95 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9990
   chunk 63 optimal weight:    9.9990
   chunk 114 optimal weight:    0.1980
   chunk 112 optimal weight:    4.9990
   chunk 107 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   chunk 66 optimal weight:    6.9990
   chunk 97 optimal weight:    0.6980
   chunk 44 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9990
   overall best weight:    0.7786

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

Flipped N/Q/H residues before XYZ refinement:
** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.075007 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.046011 restraints weight = 45681.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.048009 restraints weight = 28557.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.047523 restraints weight = 17129.803|
|-----------------------------------------------------------------------------|
r_work (final): 0.2888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8369
moved from start:          0.2010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10105  Z= 0.116
  Angle     :  0.488  10.408  13755  Z= 0.244
  Chirality :  0.040   0.174   1494
  Planarity :  0.003   0.033   1760
  Dihedral  :  4.932  55.961   1458
  Min Nonbonded Distance : 2.128

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  :  9.55 %
    Favored  : 89.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.64 (0.25), residues: 1196
  helix:  2.04 (0.27), residues: 391
  sheet:  1.07 (0.40), residues: 155
  loop : -0.78 (0.25), residues: 650

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 436 
 HIS   0.003   0.000   HIS D 378 
 PHE   0.009   0.001   PHE D 369 
 TYR   0.014   0.001   TYR A 612 
 ARG   0.002   0.000   ARG A 646 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00296 (    7)
  link_NAG-ASN         : angle       2.25294 (   21)
  hydrogen bonds       : bond        0.03366 (  416)
  hydrogen bonds       : angle       4.17333 ( 1146)
  metal coordination   : bond        0.00136 (    2)
  SS BOND              : bond        0.00153 (   13)
  SS BOND              : angle       0.47473 (   26)
  covalent geometry    : bond        0.00262 (10083)
  covalent geometry    : angle       0.48024 (13708)

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 31
  time to evaluate  : 1.649 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  152 MET cc_start: 0.9024 (tpp) cc_final: 0.8659 (tpt)
REVERT: D  190 MET cc_start: 0.9393 (ttp) cc_final: 0.9157 (tmm)
REVERT: D  248 LEU cc_start: 0.9315 (tp) cc_final: 0.9111 (tp)
REVERT: D  270 MET cc_start: 0.8499 (tpp) cc_final: 0.7881 (tpp)
REVERT: D  366 MET cc_start: 0.7735 (tmm) cc_final: 0.7508 (tmm)
REVERT: D  375 GLU cc_start: 0.8803 (mm-30) cc_final: 0.8308 (mp0)
REVERT: A  177 MET cc_start: 0.1985 (mtp) cc_final: 0.1439 (mpp)
REVERT: A  266 TYR cc_start: 0.9338 (OUTLIER) cc_final: 0.8530 (m-80)
  outliers start: 10
  outliers final: 7
  residues processed: 39
  average time/residue: 0.2488
  time to fit residues: 15.3396
Evaluate side-chains
  39 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 31
  time to evaluate  : 1.607 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  339 VAL
Chi-restraints excluded: chain D residue  401 HIS
Chi-restraints excluded: chain D residue  475 LYS
Chi-restraints excluded: chain D residue  579 MET
Chi-restraints excluded: chain A residue  146 HIS
Chi-restraints excluded: chain A residue  266 TYR
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  478 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 109 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   chunk 87 optimal weight:    0.0980
   chunk 50 optimal weight:    0.8980
   chunk 83 optimal weight:    0.8980
   chunk 54 optimal weight:    0.9990
   chunk 40 optimal weight:    7.9990
   chunk 39 optimal weight:    0.8980
   chunk 4 optimal weight:    3.9990
   chunk 63 optimal weight:   10.0000
   chunk 72 optimal weight:    4.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.075099 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.046124 restraints weight = 45756.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.048102 restraints weight = 29117.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.047780 restraints weight = 17711.792|
|-----------------------------------------------------------------------------|
r_work (final): 0.2895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8378
moved from start:          0.2076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10105  Z= 0.112
  Angle     :  0.484  10.019  13755  Z= 0.240
  Chirality :  0.040   0.175   1494
  Planarity :  0.003   0.033   1760
  Dihedral  :  4.900  55.845   1458
  Min Nonbonded Distance : 2.128

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  :  9.83 %
    Favored  : 89.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.65 (0.25), residues: 1196
  helix:  2.05 (0.27), residues: 390
  sheet:  1.13 (0.40), residues: 152
  loop : -0.78 (0.25), residues: 654

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 436 
 HIS   0.003   0.000   HIS D 378 
 PHE   0.009   0.001   PHE D 369 
 TYR   0.014   0.001   TYR A 612 
 ARG   0.002   0.000   ARG A 454 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00299 (    7)
  link_NAG-ASN         : angle       2.23760 (   21)
  hydrogen bonds       : bond        0.03282 (  416)
  hydrogen bonds       : angle       4.16048 ( 1146)
  metal coordination   : bond        0.00111 (    2)
  SS BOND              : bond        0.00149 (   13)
  SS BOND              : angle       0.46278 (   26)
  covalent geometry    : bond        0.00254 (10083)
  covalent geometry    : angle       0.47649 (13708)

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

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

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2392 Ramachandran restraints generated.
    1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 31
  time to evaluate  : 1.293 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  152 MET cc_start: 0.9023 (tpp) cc_final: 0.8663 (tpt)
REVERT: D  190 MET cc_start: 0.9380 (ttp) cc_final: 0.9150 (tmm)
REVERT: D  248 LEU cc_start: 0.9296 (tp) cc_final: 0.9078 (tp)
REVERT: D  270 MET cc_start: 0.8528 (tpp) cc_final: 0.7899 (tpp)
REVERT: D  366 MET cc_start: 0.7655 (tmm) cc_final: 0.7437 (tmm)
REVERT: D  375 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8318 (mp0)
REVERT: A  177 MET cc_start: 0.2588 (mtp) cc_final: 0.1668 (mpp)
REVERT: A  266 TYR cc_start: 0.9374 (OUTLIER) cc_final: 0.8572 (m-80)
  outliers start: 8
  outliers final: 7
  residues processed: 38
  average time/residue: 0.2228
  time to fit residues: 13.5277
Evaluate side-chains
  39 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 31
  time to evaluate  : 1.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  339 VAL
Chi-restraints excluded: chain D residue  401 HIS
Chi-restraints excluded: chain D residue  475 LYS
Chi-restraints excluded: chain D residue  579 MET
Chi-restraints excluded: chain A residue  146 HIS
Chi-restraints excluded: chain A residue  266 TYR
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  478 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 20 optimal weight:    0.2980
   chunk 8 optimal weight:    0.8980
   chunk 54 optimal weight:    0.9990
   chunk 79 optimal weight:    8.9990
   chunk 34 optimal weight:    0.6980
   chunk 119 optimal weight:    2.9990
   chunk 98 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9980
   chunk 63 optimal weight:   10.0000
   chunk 104 optimal weight:    0.9980
   chunk 73 optimal weight:    0.0370
   overall best weight:    0.5858

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.075365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.046403 restraints weight = 45369.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.048491 restraints weight = 28974.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.048066 restraints weight = 17330.768|
|-----------------------------------------------------------------------------|
r_work (final): 0.2904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8368
moved from start:          0.2153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  10105  Z= 0.096
  Angle     :  0.474   9.723  13755  Z= 0.235
  Chirality :  0.040   0.175   1494
  Planarity :  0.003   0.033   1760
  Dihedral  :  4.821  55.304   1458
  Min Nonbonded Distance : 2.155

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  :  9.83 %
    Favored  : 89.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.65 (0.25), residues: 1196
  helix:  2.09 (0.27), residues: 388
  sheet:  1.03 (0.40), residues: 155
  loop : -0.78 (0.25), residues: 653

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 436 
 HIS   0.002   0.000   HIS D 378 
 PHE   0.008   0.001   PHE D 369 
 TYR   0.016   0.001   TYR A 612 
 ARG   0.001   0.000   ARG A 646 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00304 (    7)
  link_NAG-ASN         : angle       2.20233 (   21)
  hydrogen bonds       : bond        0.03075 (  416)
  hydrogen bonds       : angle       4.10666 ( 1146)
  metal coordination   : bond        0.00101 (    2)
  SS BOND              : bond        0.00139 (   13)
  SS BOND              : angle       0.43689 (   26)
  covalent geometry    : bond        0.00217 (10083)
  covalent geometry    : angle       0.46642 (13708)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3763.19 seconds
wall clock time: 67 minutes 59.12 seconds (4079.12 seconds total)