Starting phenix.real_space_refine
on Tue Jun 10 11:12:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wdy_37467/06_2025/8wdy_37467.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wdy_37467/06_2025/8wdy_37467.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.69
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wdy_37467/06_2025/8wdy_37467.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wdy_37467/06_2025/8wdy_37467.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wdy_37467/06_2025/8wdy_37467.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wdy_37467/06_2025/8wdy_37467.cif"
  }
  resolution = 2.69
  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=   0.001 sd=   0.027
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 6322 atoms to isotropic.
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      37      5.16       5
     C    4188      2.51       5
     N    1073      2.21       5
     O    1249      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 6548
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 4862
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 596, 4862
          Classifications: {'peptide': 596}
          Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568}
    Chain: "B"
      Number of atoms: 1549
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 195, 1549
          Classifications: {'peptide': 195}
          Link IDs: {'PTRANS': 12, 'TRANS': 182}
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 38
          Unusual residues: {'FUC': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 57
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 57
          Unusual residues: {' ZN': 1, 'NAG': 4}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          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: 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: 5.00, per 1000 atoms: 0.76
  Number of scatterers: 6548
  At special positions: 0
  Unit cell: (74.8, 85.85, 124.95, 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      37     16.00
     O    1249      8.00
     N    1073      7.00
     C    4188      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 133 " - pdb=" SG  CYS A 141 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A 344 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 530 " - pdb=" SG  CYS A 542 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 391 " - pdb=" SG  CYS B 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 488 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
    BETA1-6
      " NAG D   1 " - " FUC D   3 "
       ~> Even though FUC is an alpha isomer, a beta linkage is required...
    NAG-ASN
      " NAG A 901 " - " ASN A  53 "
      " NAG A 902 " - " ASN A  90 "
      " NAG A 903 " - " ASN A 322 "
      " NAG A 904 " - " ASN A 432 "
      " NAG B 601 " - " ASN B 343 "
      " NAG C   1 " - " ASN A 103 "
      " NAG D   1 " - " ASN A 546 "
  Time building additional restraints: 1.90
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 905 "
        pdb="ZN    ZN A 905 " - pdb=" NE2 HIS A 378 "
        pdb="ZN    ZN A 905 " - pdb=" NE2 HIS A 374 "


  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1490

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 6 sheets defined
      53.2% alpha, 6.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.64
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 53
      removed outlier: 3.527A  pdb=" N   GLN A  24 " --> pdb=" O   THR A  20 " (cutoff:3.500A)
      removed outlier: 4.208A  pdb=" N   HIS A  34 " --> pdb=" O   ASP A  30 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   GLU A  35 " --> pdb=" O   LYS A  31 " (cutoff:3.500A)
      removed outlier: 4.814A  pdb=" N   GLU A  37 " --> pdb=" O   ASN A  33 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ASP A  38 " --> pdb=" O   HIS A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 79
      removed outlier: 3.567A  pdb=" N   ASP A  67 " --> pdb=" O   ASN A  63 " (cutoff:3.500A)
      removed outlier: 4.157A  pdb=" N   LYS A  68 " --> pdb=" O   ASN A  64 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   TRP A  69 " --> pdb=" O   ALA A  65 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   SER A  70 " --> pdb=" O   GLY A  66 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 101
      removed outlier: 4.200A  pdb=" N   GLN A  96 " --> pdb=" O   THR A  92 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   LEU A  97 " --> pdb=" O   VAL A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 103 through 108
      removed outlier: 4.026A  pdb=" N   VAL A 107 " --> pdb=" O   GLY A 104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 129
    Processing helix  chain 'A' and resid 149 through 154
    Processing helix  chain 'A' and resid 157 through 172
      removed outlier: 3.510A  pdb=" N   ARG A 161 " --> pdb=" O   ASP A 157 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   ARG A 169 " --> pdb=" O   TRP A 165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 173 through 175
      No H-bonds generated for 'chain 'A' and resid 173 through 175'
    Processing helix  chain 'A' and resid 176 through 194
      removed outlier: 3.671A  pdb=" N   GLU A 182 " --> pdb=" O   PRO A 178 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 205
    Processing helix  chain 'A' and resid 206 through 208
      No H-bonds generated for 'chain 'A' and resid 206 through 208'
    Processing helix  chain 'A' and resid 218 through 249
      removed outlier: 4.009A  pdb=" N   LEU A 222 " --> pdb=" O   SER A 218 " (cutoff:3.500A)
      removed outlier: 4.497A  pdb=" N   ILE A 223 " --> pdb=" O   ARG A 219 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   GLU A 224 " --> pdb=" O   GLY A 220 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   GLU A 232 " --> pdb=" O   HIS A 228 " (cutoff:3.500A)
      Proline residue:  A 235  - end of helix
    Processing helix  chain 'A' and resid 275 through 279
    Processing helix  chain 'A' and resid 293 through 300
    Processing helix  chain 'A' and resid 303 through 317
    Processing helix  chain 'A' and resid 324 through 331
      removed outlier: 3.795A  pdb=" N   TRP A 328 " --> pdb=" O   THR A 324 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   GLU A 329 " --> pdb=" O   GLN A 325 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   SER A 331 " --> pdb=" O   PHE A 327 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 385
      removed outlier: 3.608A  pdb=" N   HIS A 373 " --> pdb=" O   PHE A 369 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   TYR A 385 " --> pdb=" O   TYR A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 393
    Processing helix  chain 'A' and resid 400 through 411
      removed outlier: 3.887A  pdb=" N   SER A 411 " --> pdb=" O   ILE A 407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 421
    Processing helix  chain 'A' and resid 433 through 447
      removed outlier: 3.742A  pdb=" N   THR A 445 " --> pdb=" O   LYS A 441 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 449 through 466
    Processing helix  chain 'A' and resid 472 through 484
    Processing helix  chain 'A' and resid 499 through 502
    Processing helix  chain 'A' and resid 503 through 508
    Processing helix  chain 'A' and resid 512 through 533
      removed outlier: 4.503A  pdb=" N   TYR A 516 " --> pdb=" O   PHE A 512 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   PHE A 523 " --> pdb=" O   THR A 519 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   GLN A 524 " --> pdb=" O   LEU A 520 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 542
      removed outlier: 3.577A  pdb=" N   CYS A 542 " --> pdb=" O   LEU A 539 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 547 through 559
      removed outlier: 3.537A  pdb=" N   LEU A 554 " --> pdb=" O   ALA A 550 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   MET A 557 " --> pdb=" O   LYS A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 575
      removed outlier: 3.741A  pdb=" N   VAL A 573 " --> pdb=" O   ALA A 569 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 581 through 588
    Processing helix  chain 'A' and resid 588 through 599
    Processing helix  chain 'B' and resid 349 through 353
      removed outlier: 3.787A  pdb=" N   TRP B 353 " --> pdb=" O   VAL B 350 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 364 through 369
      removed outlier: 3.652A  pdb=" N   LEU B 368 " --> pdb=" O   ASP B 364 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   TYR B 369 " --> pdb=" O   TYR B 365 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 364 through 369'
    Processing helix  chain 'B' and resid 384 through 388
      removed outlier: 3.859A  pdb=" N   ASN B 388 " --> pdb=" O   THR B 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 405 through 410
      removed outlier: 5.012A  pdb=" N   SER B 408 " --> pdb=" O   ASN B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 416 through 422
    Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133
    Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263
      removed outlier: 6.251A  pdb=" N   LEU A 262 " --> pdb=" O   VAL A 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 352
      removed outlier: 6.116A  pdb=" N   ASP A 355 " --> pdb=" O   LEU A 351 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 358
      removed outlier: 3.896A  pdb=" N   ASN B 354 " --> pdb=" O   SER B 399 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   SER B 399 " --> pdb=" O   ASN B 354 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ASN B 394 " --> pdb=" O   GLU B 516 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 452 through 454
    Processing sheet with id=AA6, first strand: chain 'B' and resid 473 through 474

    278 hydrogen bonds defined for protein.
    789 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: 2.02

  Time building geometry restraints manager: 2.28 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 2059
        1.34 -     1.47: 1746
        1.47 -     1.59: 2868
        1.59 -     1.72: 0
        1.72 -     1.85: 58
  Bond restraints: 6731
  Sorted by residual:
  bond pdb=" CE1 HIS A  34 "
       pdb=" NE2 HIS A  34 "
    ideal  model  delta    sigma   weight residual
    1.321  1.360 -0.039 1.00e-02 1.00e+04 1.55e+01
  bond pdb=" C   HIS A  34 "
       pdb=" N   GLU A  35 "
    ideal  model  delta    sigma   weight residual
    1.334  1.288  0.046 1.20e-02 6.94e+03 1.50e+01
  bond pdb=" C1  NAG A 901 "
       pdb=" O5  NAG A 901 "
    ideal  model  delta    sigma   weight residual
    1.406  1.476 -0.070 2.00e-02 2.50e+03 1.22e+01
  bond pdb=" CE1 HIS A 401 "
       pdb=" NE2 HIS A 401 "
    ideal  model  delta    sigma   weight residual
    1.321  1.355 -0.034 1.00e-02 1.00e+04 1.15e+01
  bond pdb=" N   HIS A  34 "
       pdb=" CA  HIS A  34 "
    ideal  model  delta    sigma   weight residual
    1.457  1.497 -0.040 1.17e-02 7.31e+03 1.14e+01
  ... (remaining 6726 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.35: 8940
        2.35 -     4.70: 182
        4.70 -     7.06: 25
        7.06 -     9.41: 4
        9.41 -    11.76: 1
  Bond angle restraints: 9152
  Sorted by residual:
  angle pdb=" N   HIS A  34 "
        pdb=" CA  HIS A  34 "
        pdb=" C   HIS A  34 "
      ideal   model   delta    sigma   weight residual
     112.72  100.96   11.76 1.28e+00 6.10e-01 8.44e+01
  angle pdb=" C   HIS A  34 "
        pdb=" N   GLU A  35 "
        pdb=" CA  GLU A  35 "
      ideal   model   delta    sigma   weight residual
     120.79  129.77   -8.98 1.39e+00 5.18e-01 4.18e+01
  angle pdb=" N   THR A  92 "
        pdb=" CA  THR A  92 "
        pdb=" C   THR A  92 "
      ideal   model   delta    sigma   weight residual
     113.41  106.00    7.41 1.22e+00 6.72e-01 3.69e+01
  angle pdb=" O   ASN A  33 "
        pdb=" C   ASN A  33 "
        pdb=" N   HIS A  34 "
      ideal   model   delta    sigma   weight residual
     122.59  115.99    6.60 1.33e+00 5.65e-01 2.46e+01
  angle pdb=" N   GLU A  87 "
        pdb=" CA  GLU A  87 "
        pdb=" C   GLU A  87 "
      ideal   model   delta    sigma   weight residual
     113.50  107.53    5.97 1.23e+00 6.61e-01 2.35e+01
  ... (remaining 9147 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.77: 3860
       24.77 -    49.53: 195
       49.53 -    74.30: 29
       74.30 -    99.06: 11
       99.06 -   123.83: 1
  Dihedral angle restraints: 4096
    sinusoidal: 1774
      harmonic: 2322
  Sorted by residual:
  dihedral pdb=" CB  CYS A 133 "
           pdb=" SG  CYS A 133 "
           pdb=" SG  CYS A 141 "
           pdb=" CB  CYS A 141 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   27.76   65.24     1      1.00e+01 1.00e-02 5.58e+01
  dihedral pdb=" CA  GLU A 145 "
           pdb=" C   GLU A 145 "
           pdb=" N   PRO A 146 "
           pdb=" CA  PRO A 146 "
      ideal   model   delta  harmonic     sigma   weight residual
       0.00  -28.16   28.16     0      5.00e+00 4.00e-02 3.17e+01
  dihedral pdb=" C2  NAG A 901 "
           pdb=" C1  NAG A 901 "
           pdb=" O5  NAG A 901 "
           pdb=" C5  NAG A 901 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -62.96   60.87 -123.83     1      3.00e+01 1.11e-03 1.66e+01
  ... (remaining 4093 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 832
       0.060 -    0.119: 136
       0.119 -    0.178: 13
       0.178 -    0.238: 5
       0.238 -    0.297: 1
  Chirality restraints: 987
  Sorted by residual:
  chirality pdb=" CA  HIS A  34 "
            pdb=" N   HIS A  34 "
            pdb=" C   HIS A  34 "
            pdb=" CB  HIS A  34 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.81   -0.30 2.00e-01 2.50e+01 2.21e+00
  chirality pdb=" CA  TYR B 501 "
            pdb=" N   TYR B 501 "
            pdb=" C   TYR B 501 "
            pdb=" CB  TYR B 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.11e+00
  chirality pdb=" CA  TYR B 453 "
            pdb=" N   TYR B 453 "
            pdb=" C   TYR B 453 "
            pdb=" CB  TYR B 453 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 1.03e+00
  ... (remaining 984 not shown)

  Planarity restraints: 1180
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS A  34 "    0.042 2.00e-02 2.50e+03   9.01e-02 8.11e+01
        pdb=" C   HIS A  34 "   -0.156 2.00e-02 2.50e+03
        pdb=" O   HIS A  34 "    0.059 2.00e-02 2.50e+03
        pdb=" N   GLU A  35 "    0.054 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B 484 "    0.018 2.00e-02 2.50e+03   3.66e-02 1.34e+01
        pdb=" C   ALA B 484 "   -0.063 2.00e-02 2.50e+03
        pdb=" O   ALA B 484 "    0.024 2.00e-02 2.50e+03
        pdb=" N   GLY B 485 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A  85 "   -0.017 2.00e-02 2.50e+03   3.44e-02 1.18e+01
        pdb=" C   LEU A  85 "    0.059 2.00e-02 2.50e+03
        pdb=" O   LEU A  85 "   -0.023 2.00e-02 2.50e+03
        pdb=" N   GLN A  86 "   -0.020 2.00e-02 2.50e+03
  ... (remaining 1177 not shown)

  Histogram of nonbonded interaction distances:
        2.00 -     2.58: 42
        2.58 -     3.16: 5172
        3.16 -     3.74: 9722
        3.74 -     4.32: 13544
        4.32 -     4.90: 22870
  Nonbonded interactions: 51350
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 402 "
            pdb="ZN    ZN A 905 "
     model   vdw
     2.000 2.230
  nonbonded pdb=" O   ALA A 501 "
            pdb=" OG  SER A 507 "
     model   vdw
     2.173 3.040
  nonbonded pdb=" OG  SER A 425 "
            pdb=" OD1 ASP A 427 "
     model   vdw
     2.186 3.040
  nonbonded pdb=" NE2 GLN A  42 "
            pdb=" NH2 ARG B 498 "
     model   vdw
     2.234 3.200
  nonbonded pdb=" OG1 THR A  20 "
            pdb=" OE1 GLU A  23 "
     model   vdw
     2.269 3.040
  ... (remaining 51345 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 individual isotropic
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:             14.400
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.090
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     23.540
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:14.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   53.350
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7557
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.204   6750  Z= 0.285
  Angle     :  0.770  11.760   9196  Z= 0.479
  Chirality :  0.047   0.297    987
  Planarity :  0.005   0.090   1173
  Dihedral  : 14.720 123.825   2585
  Min Nonbonded Distance : 2.000

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.81 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  :  0.87 %
    Favored  : 97.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  0.26 (0.31), residues: 787
  helix:  1.05 (0.28), residues: 383
  sheet:  1.83 (0.79), residues: 44
  loop : -1.02 (0.34), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 477 
 HIS   0.005   0.001   HIS A 374 
 PHE   0.035   0.001   PHE A 592 
 TYR   0.044   0.001   TYR B 453 
 ARG   0.002   0.000   ARG B 355 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00403 (    7)
  link_NAG-ASN         : angle       2.30085 (   21)
  link_BETA1-4         : bond        0.00430 (    2)
  link_BETA1-4         : angle       0.78761 (    6)
  hydrogen bonds       : bond        0.16713 (  278)
  hydrogen bonds       : angle       6.07163 (  789)
  link_BETA1-6         : bond        0.00395 (    1)
  link_BETA1-6         : angle       1.33646 (    3)
  metal coordination   : bond        0.20327 (    2)
  SS BOND              : bond        0.00562 (    7)
  SS BOND              : angle       1.26862 (   14)
  covalent geometry    : bond        0.00415 ( 6731)
  covalent geometry    : angle       0.76156 ( 9152)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 188
  time to evaluate  : 1.172 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  455 MET cc_start: 0.7107 (tmm) cc_final: 0.6699 (tmm)
REVERT: B  406 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7314 (mt-10)
REVERT: B  509 ARG cc_start: 0.8448 (mtt180) cc_final: 0.8230 (mtt-85)
  outliers start: 10
  outliers final: 3
  residues processed: 191
  average time/residue: 1.1065
  time to fit residues: 222.3254
Evaluate side-chains
  166 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 163
  time to evaluate  : 0.756 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 ILE
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain B residue  494 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    2.9990
   chunk 59 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 39 optimal weight:    0.8980
   chunk 31 optimal weight:    0.4980
   chunk 61 optimal weight:    0.5980
   chunk 23 optimal weight:    0.7980
   chunk 37 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 70 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A  42 GLN
A  61 ASN
A  64 ASN
A 598 GLN
B 437 ASN
B 487 ASN
B 506 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.132244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.114734 restraints weight = 8962.519|
|-----------------------------------------------------------------------------|
r_work (start): 0.3536 rms_B_bonded: 1.94
r_work: 0.3430 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3293 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7982
moved from start:          0.1241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6750  Z= 0.154
  Angle     :  0.566  10.868   9196  Z= 0.283
  Chirality :  0.043   0.234    987
  Planarity :  0.004   0.051   1173
  Dihedral  :  8.564 108.731   1070
  Min Nonbonded Distance : 2.041

Molprobity Statistics.
  All-atom Clashscore : 3.44
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.05 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 10.97 %
    Favored  : 87.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  0.44 (0.31), residues: 787
  helix:  1.30 (0.28), residues: 377
  sheet:  1.72 (0.75), residues: 44
  loop : -0.97 (0.34), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 436 
 HIS   0.004   0.001   HIS A 374 
 PHE   0.014   0.001   PHE A 400 
 TYR   0.017   0.001   TYR A 202 
 ARG   0.002   0.000   ARG A 460 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00649 (    7)
  link_NAG-ASN         : angle       2.34419 (   21)
  link_BETA1-4         : bond        0.00490 (    2)
  link_BETA1-4         : angle       0.95940 (    6)
  hydrogen bonds       : bond        0.04759 (  278)
  hydrogen bonds       : angle       4.46918 (  789)
  link_BETA1-6         : bond        0.00305 (    1)
  link_BETA1-6         : angle       1.26053 (    3)
  metal coordination   : bond        0.00569 (    2)
  SS BOND              : bond        0.00610 (    7)
  SS BOND              : angle       1.25552 (   14)
  covalent geometry    : bond        0.00348 ( 6731)
  covalent geometry    : angle       0.55273 ( 9152)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 167
  time to evaluate  : 0.679 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 GLU cc_start: 0.6845 (mp0) cc_final: 0.6457 (mp0)
REVERT: A  364 VAL cc_start: 0.8332 (m) cc_final: 0.8109 (t)
REVERT: A  431 ASP cc_start: 0.7621 (p0) cc_final: 0.7409 (p0)
REVERT: A  455 MET cc_start: 0.7656 (tmm) cc_final: 0.7307 (tmm)
REVERT: A  496 THR cc_start: 0.8794 (m) cc_final: 0.8556 (t)
REVERT: B  343 ASN cc_start: 0.7730 (t0) cc_final: 0.7379 (t0)
  outliers start: 10
  outliers final: 3
  residues processed: 172
  average time/residue: 1.0973
  time to fit residues: 198.7470
Evaluate side-chains
  166 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 163
  time to evaluate  : 0.682 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 THR
Chi-restraints excluded: chain A residue  128 SER
Chi-restraints excluded: chain A residue  212 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 26 optimal weight:    0.9990
   chunk 46 optimal weight:    0.6980
   chunk 64 optimal weight:    4.9990
   chunk 25 optimal weight:    0.5980
   chunk 9 optimal weight:    4.9990
   chunk 27 optimal weight:    0.0970
   chunk 21 optimal weight:    1.9990
   chunk 76 optimal weight:    0.5980
   chunk 67 optimal weight:    0.4980
   chunk 45 optimal weight:    0.7980
   chunk 65 optimal weight:    0.9980
   overall best weight:    0.4978

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

Flipped N/Q/H residues before XYZ refinement:
A 598 GLN
B 409 GLN
B 506 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.132268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.115070 restraints weight = 9104.964|
|-----------------------------------------------------------------------------|
r_work (start): 0.3543 rms_B_bonded: 1.91
r_work: 0.3436 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3298 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7976
moved from start:          0.1441

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6750  Z= 0.116
  Angle     :  0.518   7.970   9196  Z= 0.256
  Chirality :  0.041   0.215    987
  Planarity :  0.004   0.039   1173
  Dihedral  :  7.702 105.278   1065
  Min Nonbonded Distance : 2.031

Molprobity Statistics.
  All-atom Clashscore : 3.13
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.18 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 13.13 %
    Favored  : 84.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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 (0.31), residues: 787
  helix:  1.45 (0.28), residues: 378
  sheet:  1.33 (0.75), residues: 44
  loop : -0.87 (0.34), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 436 
 HIS   0.004   0.001   HIS A 241 
 PHE   0.008   0.001   PHE A 400 
 TYR   0.015   0.001   TYR A 202 
 ARG   0.002   0.000   ARG A 169 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00532 (    7)
  link_NAG-ASN         : angle       2.13147 (   21)
  link_BETA1-4         : bond        0.00386 (    2)
  link_BETA1-4         : angle       0.92621 (    6)
  hydrogen bonds       : bond        0.04161 (  278)
  hydrogen bonds       : angle       4.14551 (  789)
  link_BETA1-6         : bond        0.00389 (    1)
  link_BETA1-6         : angle       1.10844 (    3)
  metal coordination   : bond        0.00346 (    2)
  SS BOND              : bond        0.00576 (    7)
  SS BOND              : angle       1.21113 (   14)
  covalent geometry    : bond        0.00257 ( 6731)
  covalent geometry    : angle       0.50627 ( 9152)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 164
  time to evaluate  : 0.688 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  364 VAL cc_start: 0.8276 (OUTLIER) cc_final: 0.8067 (t)
REVERT: A  455 MET cc_start: 0.7629 (tmm) cc_final: 0.7283 (tmm)
REVERT: B  343 ASN cc_start: 0.7675 (t0) cc_final: 0.7288 (t0)
  outliers start: 13
  outliers final: 7
  residues processed: 166
  average time/residue: 1.1507
  time to fit residues: 201.2489
Evaluate side-chains
  168 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 160
  time to evaluate  : 0.748 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 THR
Chi-restraints excluded: chain A residue   64 ASN
Chi-restraints excluded: chain A residue  128 SER
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  212 VAL
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  536 GLU
Chi-restraints excluded: chain B residue  500 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 21 optimal weight:    0.3980
   chunk 0 optimal weight:    4.9990
   chunk 62 optimal weight:    2.9990
   chunk 2 optimal weight:    0.5980
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
A 598 GLN
B 409 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.129686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.112156 restraints weight = 9121.269|
|-----------------------------------------------------------------------------|
r_work (start): 0.3499 rms_B_bonded: 1.94
r_work: 0.3392 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3252 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.3252
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8034
moved from start:          0.1784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   6750  Z= 0.215
  Angle     :  0.590   9.684   9196  Z= 0.293
  Chirality :  0.045   0.225    987
  Planarity :  0.004   0.040   1173
  Dihedral  :  7.355  96.590   1065
  Min Nonbonded Distance : 1.966

Molprobity Statistics.
  All-atom Clashscore : 3.13
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.94 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 13.71 %
    Favored  : 83.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  0.44 (0.31), residues: 787
  helix:  1.39 (0.28), residues: 371
  sheet:  1.13 (0.74), residues: 44
  loop : -0.96 (0.34), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 168 
 HIS   0.006   0.001   HIS A 241 
 PHE   0.015   0.002   PHE A 400 
 TYR   0.015   0.002   TYR A 385 
 ARG   0.002   0.000   ARG A 192 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00508 (    7)
  link_NAG-ASN         : angle       2.22853 (   21)
  link_BETA1-4         : bond        0.00398 (    2)
  link_BETA1-4         : angle       0.92776 (    6)
  hydrogen bonds       : bond        0.05321 (  278)
  hydrogen bonds       : angle       4.17266 (  789)
  link_BETA1-6         : bond        0.00487 (    1)
  link_BETA1-6         : angle       1.11112 (    3)
  metal coordination   : bond        0.00916 (    2)
  SS BOND              : bond        0.00673 (    7)
  SS BOND              : angle       1.29209 (   14)
  covalent geometry    : bond        0.00504 ( 6731)
  covalent geometry    : angle       0.57908 ( 9152)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 166
  time to evaluate  : 0.722 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  189 GLU cc_start: 0.7954 (tp30) cc_final: 0.7648 (tp30)
REVERT: A  190 MET cc_start: 0.8381 (tmm) cc_final: 0.8110 (ttp)
REVERT: A  364 VAL cc_start: 0.8375 (OUTLIER) cc_final: 0.8168 (t)
REVERT: A  455 MET cc_start: 0.7817 (tmm) cc_final: 0.7348 (tmm)
REVERT: A  564 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7559 (mp0)
REVERT: B  343 ASN cc_start: 0.7701 (t0) cc_final: 0.7256 (t0)
  outliers start: 16
  outliers final: 10
  residues processed: 171
  average time/residue: 1.0966
  time to fit residues: 197.6916
Evaluate side-chains
  174 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 162
  time to evaluate  : 0.717 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 THR
Chi-restraints excluded: chain A residue  128 SER
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  212 VAL
Chi-restraints excluded: chain A residue  329 GLU
Chi-restraints excluded: chain A residue  332 MET
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  458 LYS
Chi-restraints excluded: chain A residue  536 GLU
Chi-restraints excluded: chain A residue  564 GLU
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  500 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 44 optimal weight:    0.0670
   chunk 64 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   chunk 72 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   chunk 54 optimal weight:    0.3980
   chunk 20 optimal weight:    3.9990
   chunk 59 optimal weight:    3.9990
   overall best weight:    0.8920

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

Flipped N/Q/H residues before XYZ refinement:
A 102 GLN
A 598 GLN
B 370 ASN
B 409 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.130294 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.112824 restraints weight = 9069.632|
|-----------------------------------------------------------------------------|
r_work (start): 0.3505 rms_B_bonded: 1.93
r_work: 0.3401 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3262 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8018
moved from start:          0.1872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6750  Z= 0.167
  Angle     :  0.559   9.269   9196  Z= 0.276
  Chirality :  0.044   0.240    987
  Planarity :  0.004   0.039   1173
  Dihedral  :  6.961  87.924   1065
  Min Nonbonded Distance : 1.994

Molprobity Statistics.
  All-atom Clashscore : 3.52
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.80 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 15.01 %
    Favored  : 82.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  0.51 (0.31), residues: 787
  helix:  1.46 (0.28), residues: 371
  sheet:  0.96 (0.74), residues: 44
  loop : -0.91 (0.34), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 168 
 HIS   0.006   0.001   HIS A 241 
 PHE   0.008   0.001   PHE A 400 
 TYR   0.015   0.001   TYR A 202 
 ARG   0.002   0.000   ARG A 192 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00534 (    7)
  link_NAG-ASN         : angle       2.30396 (   21)
  link_BETA1-4         : bond        0.00403 (    2)
  link_BETA1-4         : angle       0.94745 (    6)
  hydrogen bonds       : bond        0.04777 (  278)
  hydrogen bonds       : angle       4.10997 (  789)
  link_BETA1-6         : bond        0.00435 (    1)
  link_BETA1-6         : angle       1.15988 (    3)
  metal coordination   : bond        0.00621 (    2)
  SS BOND              : bond        0.00623 (    7)
  SS BOND              : angle       1.24354 (   14)
  covalent geometry    : bond        0.00386 ( 6731)
  covalent geometry    : angle       0.54585 ( 9152)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 161
  time to evaluate  : 0.743 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 GLU cc_start: 0.6961 (mp0) cc_final: 0.6504 (mp0)
REVERT: A  189 GLU cc_start: 0.7960 (tp30) cc_final: 0.7643 (tp30)
REVERT: A  190 MET cc_start: 0.8382 (tmm) cc_final: 0.8109 (ttp)
REVERT: A  364 VAL cc_start: 0.8320 (OUTLIER) cc_final: 0.8113 (t)
REVERT: A  455 MET cc_start: 0.7748 (tmm) cc_final: 0.7201 (tmm)
REVERT: A  564 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7565 (mp0)
REVERT: B  343 ASN cc_start: 0.7682 (t0) cc_final: 0.7233 (t0)
  outliers start: 15
  outliers final: 8
  residues processed: 166
  average time/residue: 1.0986
  time to fit residues: 192.0090
Evaluate side-chains
  169 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 159
  time to evaluate  : 0.680 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 THR
Chi-restraints excluded: chain A residue  128 SER
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  212 VAL
Chi-restraints excluded: chain A residue  332 MET
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  458 LYS
Chi-restraints excluded: chain A residue  564 GLU
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  500 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 43 optimal weight:    0.6980
   chunk 25 optimal weight:    0.8980
   chunk 57 optimal weight:    0.8980
   chunk 35 optimal weight:    0.9990
   chunk 46 optimal weight:    0.7980
   chunk 68 optimal weight:    0.9990
   chunk 59 optimal weight:    0.9980
   chunk 48 optimal weight:    0.5980
   chunk 45 optimal weight:    0.7980
   chunk 1 optimal weight:    1.9990
   chunk 6 optimal weight:    0.7980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A  42 GLN
A 598 GLN
B 409 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.130766 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.113317 restraints weight = 9034.060|
|-----------------------------------------------------------------------------|
r_work (start): 0.3519 rms_B_bonded: 1.93
r_work: 0.3411 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3270 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8017
moved from start:          0.1977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6750  Z= 0.146
  Angle     :  0.551   9.519   9196  Z= 0.271
  Chirality :  0.043   0.246    987
  Planarity :  0.004   0.038   1173
  Dihedral  :  6.602  77.891   1065
  Min Nonbonded Distance : 2.008

Molprobity Statistics.
  All-atom Clashscore : 3.44
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.80 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 15.01 %
    Favored  : 82.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  0.54 (0.31), residues: 787
  helix:  1.48 (0.28), residues: 373
  sheet:  0.79 (0.74), residues: 44
  loop : -0.87 (0.34), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  69 
 HIS   0.005   0.001   HIS A 241 
 PHE   0.008   0.001   PHE A 603 
 TYR   0.013   0.001   TYR A 497 
 ARG   0.001   0.000   ARG A 460 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00535 (    7)
  link_NAG-ASN         : angle       2.38646 (   21)
  link_BETA1-4         : bond        0.00393 (    2)
  link_BETA1-4         : angle       0.97295 (    6)
  hydrogen bonds       : bond        0.04502 (  278)
  hydrogen bonds       : angle       4.05709 (  789)
  link_BETA1-6         : bond        0.00388 (    1)
  link_BETA1-6         : angle       1.16601 (    3)
  metal coordination   : bond        0.00519 (    2)
  SS BOND              : bond        0.00602 (    7)
  SS BOND              : angle       1.18751 (   14)
  covalent geometry    : bond        0.00336 ( 6731)
  covalent geometry    : angle       0.53776 ( 9152)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 160
  time to evaluate  : 0.685 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 GLU cc_start: 0.6960 (mp0) cc_final: 0.6592 (mp0)
REVERT: A  189 GLU cc_start: 0.7975 (tp30) cc_final: 0.7698 (tp30)
REVERT: A  190 MET cc_start: 0.8375 (tmm) cc_final: 0.8119 (ttp)
REVERT: A  364 VAL cc_start: 0.8312 (OUTLIER) cc_final: 0.8111 (t)
REVERT: A  455 MET cc_start: 0.7720 (tmm) cc_final: 0.7304 (tmm)
REVERT: A  564 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7537 (mp0)
REVERT: B  355 ARG cc_start: 0.8250 (ttt90) cc_final: 0.7977 (ttt180)
  outliers start: 15
  outliers final: 11
  residues processed: 164
  average time/residue: 1.1336
  time to fit residues: 195.5611
Evaluate side-chains
  168 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 155
  time to evaluate  : 0.710 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 THR
Chi-restraints excluded: chain A residue  128 SER
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  212 VAL
Chi-restraints excluded: chain A residue  332 MET
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  458 LYS
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  536 GLU
Chi-restraints excluded: chain A residue  564 GLU
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  500 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 74 optimal weight:    2.9990
   chunk 25 optimal weight:    0.4980
   chunk 69 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 32 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9980
   chunk 43 optimal weight:    0.2980
   chunk 70 optimal weight:    0.5980
   chunk 47 optimal weight:    0.9990
   chunk 58 optimal weight:    0.9990
   chunk 75 optimal weight:    0.7980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 598 GLN
B 409 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.131280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.113894 restraints weight = 9002.781|
|-----------------------------------------------------------------------------|
r_work (start): 0.3519 rms_B_bonded: 1.92
r_work: 0.3415 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3277 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8001
moved from start:          0.2034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6750  Z= 0.129
  Angle     :  0.560  10.751   9196  Z= 0.270
  Chirality :  0.042   0.207    987
  Planarity :  0.004   0.038   1173
  Dihedral  :  6.251  67.621   1065
  Min Nonbonded Distance : 2.019

Molprobity Statistics.
  All-atom Clashscore : 3.60
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.41 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 15.44 %
    Favored  : 82.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  0.63 (0.31), residues: 787
  helix:  1.62 (0.28), residues: 367
  sheet:  0.73 (0.74), residues: 44
  loop : -0.84 (0.34), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  69 
 HIS   0.005   0.001   HIS A 374 
 PHE   0.011   0.001   PHE A 315 
 TYR   0.013   0.001   TYR A 202 
 ARG   0.001   0.000   ARG A 169 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00446 (    7)
  link_NAG-ASN         : angle       2.48025 (   21)
  link_BETA1-4         : bond        0.00395 (    2)
  link_BETA1-4         : angle       0.95000 (    6)
  hydrogen bonds       : bond        0.04258 (  278)
  hydrogen bonds       : angle       4.01360 (  789)
  link_BETA1-6         : bond        0.00398 (    1)
  link_BETA1-6         : angle       1.19437 (    3)
  metal coordination   : bond        0.00546 (    2)
  SS BOND              : bond        0.00563 (    7)
  SS BOND              : angle       1.15806 (   14)
  covalent geometry    : bond        0.00294 ( 6731)
  covalent geometry    : angle       0.54589 ( 9152)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 155
  time to evaluate  : 0.730 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 GLU cc_start: 0.6999 (mp0) cc_final: 0.6726 (mp0)
REVERT: A  189 GLU cc_start: 0.7961 (tp30) cc_final: 0.7702 (tp30)
REVERT: A  190 MET cc_start: 0.8364 (tmm) cc_final: 0.8109 (ttp)
REVERT: A  364 VAL cc_start: 0.8299 (OUTLIER) cc_final: 0.8099 (t)
REVERT: A  455 MET cc_start: 0.7691 (tmm) cc_final: 0.7280 (tmm)
REVERT: A  564 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7521 (mp0)
REVERT: B  343 ASN cc_start: 0.7731 (t0) cc_final: 0.7488 (t0)
REVERT: B  355 ARG cc_start: 0.8243 (ttt90) cc_final: 0.7962 (ttt180)
  outliers start: 13
  outliers final: 8
  residues processed: 158
  average time/residue: 1.1450
  time to fit residues: 190.1648
Evaluate side-chains
  163 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 153
  time to evaluate  : 0.756 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 THR
Chi-restraints excluded: chain A residue  128 SER
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  212 VAL
Chi-restraints excluded: chain A residue  332 MET
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  458 LYS
Chi-restraints excluded: chain A residue  536 GLU
Chi-restraints excluded: chain A residue  564 GLU
Chi-restraints excluded: chain B residue  500 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 44 optimal weight:    0.9980
   chunk 65 optimal weight:    2.9990
   chunk 35 optimal weight:    0.6980
   chunk 76 optimal weight:    1.9990
   chunk 53 optimal weight:    0.5980
   chunk 40 optimal weight:    0.3980
   chunk 46 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 9 optimal weight:    4.9990
   chunk 17 optimal weight:    0.8980
   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 598 GLN
B 409 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.131011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.113696 restraints weight = 9078.203|
|-----------------------------------------------------------------------------|
r_work (start): 0.3520 rms_B_bonded: 1.93
r_work: 0.3411 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3270 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8014
moved from start:          0.2119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6750  Z= 0.144
  Angle     :  0.558   9.048   9196  Z= 0.273
  Chirality :  0.042   0.228    987
  Planarity :  0.004   0.038   1173
  Dihedral  :  5.946  54.070   1065
  Min Nonbonded Distance : 2.008

Molprobity Statistics.
  All-atom Clashscore : 3.52
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.92 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 15.30 %
    Favored  : 82.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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 (0.31), residues: 787
  helix:  1.60 (0.28), residues: 367
  sheet:  0.69 (0.73), residues: 44
  loop : -0.84 (0.34), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  69 
 HIS   0.005   0.001   HIS A 241 
 PHE   0.008   0.001   PHE A  72 
 TYR   0.012   0.001   TYR A 202 
 ARG   0.001   0.000   ARG B 452 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00461 (    7)
  link_NAG-ASN         : angle       2.60401 (   21)
  link_BETA1-4         : bond        0.00383 (    2)
  link_BETA1-4         : angle       0.96806 (    6)
  hydrogen bonds       : bond        0.04422 (  278)
  hydrogen bonds       : angle       4.04095 (  789)
  link_BETA1-6         : bond        0.00419 (    1)
  link_BETA1-6         : angle       1.17039 (    3)
  metal coordination   : bond        0.00543 (    2)
  SS BOND              : bond        0.00571 (    7)
  SS BOND              : angle       1.15972 (   14)
  covalent geometry    : bond        0.00333 ( 6731)
  covalent geometry    : angle       0.54273 ( 9152)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 157
  time to evaluate  : 0.691 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 GLU cc_start: 0.7002 (mp0) cc_final: 0.6779 (mp0)
REVERT: A  162 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8377 (tt)
REVERT: A  189 GLU cc_start: 0.7962 (tp30) cc_final: 0.7718 (tp30)
REVERT: A  190 MET cc_start: 0.8372 (tmm) cc_final: 0.8124 (ttp)
REVERT: A  227 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7624 (mt-10)
REVERT: A  455 MET cc_start: 0.7722 (tmm) cc_final: 0.7307 (tmm)
REVERT: A  564 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7526 (mp0)
REVERT: B  343 ASN cc_start: 0.7750 (t0) cc_final: 0.7499 (t0)
REVERT: B  355 ARG cc_start: 0.8247 (ttt90) cc_final: 0.7984 (ttt180)
  outliers start: 17
  outliers final: 12
  residues processed: 164
  average time/residue: 1.1274
  time to fit residues: 194.4663
Evaluate side-chains
  171 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 156
  time to evaluate  : 0.669 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 THR
Chi-restraints excluded: chain A residue  128 SER
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  212 VAL
Chi-restraints excluded: chain A residue  227 GLU
Chi-restraints excluded: chain A residue  332 MET
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  458 LYS
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  536 GLU
Chi-restraints excluded: chain A residue  564 GLU
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  494 SER
Chi-restraints excluded: chain B residue  500 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 30 optimal weight:    0.0000
   chunk 11 optimal weight:    0.9990
   chunk 32 optimal weight:    0.4980
   chunk 43 optimal weight:    0.3980
   chunk 37 optimal weight:    0.9980
   chunk 56 optimal weight:    0.7980
   chunk 23 optimal weight:    0.7980
   chunk 62 optimal weight:    9.9990
   chunk 44 optimal weight:    0.2980
   chunk 49 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9980
   overall best weight:    0.3984

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

Flipped N/Q/H residues before XYZ refinement:
A 598 GLN
B 409 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.131470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.113844 restraints weight = 9110.848|
|-----------------------------------------------------------------------------|
r_work (start): 0.3536 rms_B_bonded: 1.94
r_work: 0.3429 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3291 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
moved from start:          0.2150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   6750  Z= 0.109
  Angle     :  0.547   9.000   9196  Z= 0.264
  Chirality :  0.041   0.200    987
  Planarity :  0.004   0.037   1173
  Dihedral  :  5.649  52.995   1065
  Min Nonbonded Distance : 2.052

Molprobity Statistics.
  All-atom Clashscore : 3.52
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.80 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 15.58 %
    Favored  : 82.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  0.70 (0.31), residues: 787
  helix:  1.69 (0.28), residues: 367
  sheet:  0.59 (0.73), residues: 44
  loop : -0.80 (0.34), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  69 
 HIS   0.005   0.001   HIS A 374 
 PHE   0.010   0.001   PHE A 315 
 TYR   0.012   0.001   TYR A 202 
 ARG   0.001   0.000   ARG B 452 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00485 (    7)
  link_NAG-ASN         : angle       2.64283 (   21)
  link_BETA1-4         : bond        0.00401 (    2)
  link_BETA1-4         : angle       0.95948 (    6)
  hydrogen bonds       : bond        0.03857 (  278)
  hydrogen bonds       : angle       3.98370 (  789)
  link_BETA1-6         : bond        0.00373 (    1)
  link_BETA1-6         : angle       1.19399 (    3)
  metal coordination   : bond        0.00263 (    2)
  SS BOND              : bond        0.00487 (    7)
  SS BOND              : angle       1.12090 (   14)
  covalent geometry    : bond        0.00244 ( 6731)
  covalent geometry    : angle       0.53092 ( 9152)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 155
  time to evaluate  : 0.768 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 SER cc_start: 0.8602 (t) cc_final: 0.8342 (m)
REVERT: A  162 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8362 (tt)
REVERT: A  190 MET cc_start: 0.8357 (tmm) cc_final: 0.8151 (ttp)
REVERT: A  227 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7620 (mt-10)
REVERT: A  455 MET cc_start: 0.7631 (tmm) cc_final: 0.7267 (tmm)
REVERT: B  343 ASN cc_start: 0.7710 (t0) cc_final: 0.7457 (t0)
  outliers start: 15
  outliers final: 11
  residues processed: 161
  average time/residue: 1.1681
  time to fit residues: 197.6090
Evaluate side-chains
  165 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 152
  time to evaluate  : 0.691 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 SER
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  212 VAL
Chi-restraints excluded: chain A residue  227 GLU
Chi-restraints excluded: chain A residue  332 MET
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  458 LYS
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  536 GLU
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  494 SER
Chi-restraints excluded: chain B residue  500 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 13 optimal weight:    0.7980
   chunk 58 optimal weight:    1.9990
   chunk 22 optimal weight:    0.4980
   chunk 66 optimal weight:    0.0770
   chunk 17 optimal weight:    0.9980
   chunk 63 optimal weight:    0.8980
   chunk 76 optimal weight:    0.7980
   chunk 26 optimal weight:    0.0870
   chunk 4 optimal weight:    3.9990
   chunk 69 optimal weight:    0.9990
   chunk 47 optimal weight:    0.1980
   overall best weight:    0.3316

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

Flipped N/Q/H residues before XYZ refinement:
A  61 ASN
A 102 GLN
A 598 GLN
B 409 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.132595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.115310 restraints weight = 9175.582|
|-----------------------------------------------------------------------------|
r_work (start): 0.3545 rms_B_bonded: 1.94
r_work: 0.3436 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3295 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7984
moved from start:          0.2210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   6750  Z= 0.105
  Angle     :  0.550   9.364   9196  Z= 0.269
  Chirality :  0.041   0.195    987
  Planarity :  0.004   0.036   1173
  Dihedral  :  5.464  53.047   1065
  Min Nonbonded Distance : 2.062

Molprobity Statistics.
  All-atom Clashscore : 3.21
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.80 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 16.74 %
    Favored  : 81.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  0.74 (0.32), residues: 787
  helix:  1.74 (0.28), residues: 368
  sheet:  0.56 (0.72), residues: 44
  loop : -0.80 (0.34), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  69 
 HIS   0.004   0.001   HIS A 374 
 PHE   0.009   0.001   PHE A 315 
 TYR   0.012   0.001   TYR A 202 
 ARG   0.001   0.000   ARG A 177 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00482 (    7)
  link_NAG-ASN         : angle       2.57840 (   21)
  link_BETA1-4         : bond        0.00397 (    2)
  link_BETA1-4         : angle       0.96595 (    6)
  hydrogen bonds       : bond        0.03685 (  278)
  hydrogen bonds       : angle       3.95332 (  789)
  link_BETA1-6         : bond        0.00426 (    1)
  link_BETA1-6         : angle       1.20627 (    3)
  metal coordination   : bond        0.00216 (    2)
  SS BOND              : bond        0.00494 (    7)
  SS BOND              : angle       1.10566 (   14)
  covalent geometry    : bond        0.00234 ( 6731)
  covalent geometry    : angle       0.53463 ( 9152)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 153
  time to evaluate  : 0.681 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 SER cc_start: 0.8603 (t) cc_final: 0.8348 (m)
REVERT: A  190 MET cc_start: 0.8305 (tmm) cc_final: 0.8031 (ttp)
REVERT: A  227 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7592 (mt-10)
REVERT: A  455 MET cc_start: 0.7612 (tmm) cc_final: 0.7259 (tmm)
REVERT: A  564 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7513 (mp0)
REVERT: B  343 ASN cc_start: 0.7714 (t0) cc_final: 0.7452 (t0)
REVERT: B  506 GLN cc_start: 0.8561 (mt0) cc_final: 0.8278 (mt0)
  outliers start: 13
  outliers final: 9
  residues processed: 158
  average time/residue: 1.1745
  time to fit residues: 195.2811
Evaluate side-chains
  164 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 153
  time to evaluate  : 0.741 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 SER
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  212 VAL
Chi-restraints excluded: chain A residue  227 GLU
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  458 LYS
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  564 GLU
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  494 SER
Chi-restraints excluded: chain B residue  500 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 21 optimal weight:    0.9980
   chunk 51 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 26 optimal weight:    0.0670
   chunk 16 optimal weight:    0.7980
   chunk 30 optimal weight:    0.0870
   chunk 15 optimal weight:    0.7980
   chunk 57 optimal weight:    0.9990
   chunk 49 optimal weight:    0.7980
   chunk 43 optimal weight:    0.5980
   chunk 31 optimal weight:    0.0970
   overall best weight:    0.3294

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

Flipped N/Q/H residues before XYZ refinement:
A  61 ASN
A 102 GLN
A 598 GLN
B 409 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.132935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.115707 restraints weight = 9204.686|
|-----------------------------------------------------------------------------|
r_work (start): 0.3549 rms_B_bonded: 1.94
r_work: 0.3441 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3302 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.3302
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7975
moved from start:          0.2240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   6750  Z= 0.105
  Angle     :  0.547  12.193   9196  Z= 0.265
  Chirality :  0.040   0.172    987
  Planarity :  0.004   0.036   1173
  Dihedral  :  5.301  53.020   1065
  Min Nonbonded Distance : 2.056

Molprobity Statistics.
  All-atom Clashscore : 3.68
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.41 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 17.03 %
    Favored  : 81.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  0.75 (0.32), residues: 787
  helix:  1.76 (0.28), residues: 368
  sheet:  0.52 (0.71), residues: 44
  loop : -0.80 (0.34), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 477 
 HIS   0.005   0.001   HIS A 374 
 PHE   0.012   0.001   PHE A 315 
 TYR   0.011   0.001   TYR A 202 
 ARG   0.001   0.000   ARG A 460 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00400 (    7)
  link_NAG-ASN         : angle       2.46624 (   21)
  link_BETA1-4         : bond        0.00422 (    2)
  link_BETA1-4         : angle       0.96586 (    6)
  hydrogen bonds       : bond        0.03604 (  278)
  hydrogen bonds       : angle       3.94798 (  789)
  link_BETA1-6         : bond        0.00385 (    1)
  link_BETA1-6         : angle       1.16641 (    3)
  metal coordination   : bond        0.00245 (    2)
  SS BOND              : bond        0.00483 (    7)
  SS BOND              : angle       1.10235 (   14)
  covalent geometry    : bond        0.00234 ( 6731)
  covalent geometry    : angle       0.53233 ( 9152)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6111.44 seconds
wall clock time: 104 minutes 36.83 seconds (6276.83 seconds total)