Starting phenix.real_space_refine
on Thu Jun  5 09:32:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yht_39300/06_2025/8yht_39300.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yht_39300/06_2025/8yht_39300.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.88
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yht_39300/06_2025/8yht_39300.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yht_39300/06_2025/8yht_39300.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yht_39300/06_2025/8yht_39300.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yht_39300/06_2025/8yht_39300.cif"
  }
  resolution = 2.88
  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=   0.022
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      20      5.16       5
     C    3724      2.51       5
     N     972      2.21       5
     O    1129      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 5845
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 5323
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 663, 5323
          Classifications: {'peptide': 663}
          Link IDs: {'PTRANS': 26, 'TRANS': 636}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 326
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 40, 326
          Classifications: {'peptide': 40}
          Link IDs: {'PTRANS': 1, 'TRANS': 38}
    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: 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: "E"
      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: "F"
      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: "A"
      Number of atoms: 84
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 84
          Unusual residues: {'NAG': 6}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 6
  Time building chain proxies: 4.34, per 1000 atoms: 0.74
  Number of scatterers: 5845
  At special positions: 0
  Unit cell: (52.456, 102.92, 111.552, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      20     16.00
     O    1129      8.00
     N     972      7.00
     C    3724      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  28 " - pdb=" SG  CYS A  37 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  95 " - pdb=" SG  CYS A 122 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 649 " - pdb=" SG  CYS A 677 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 651 " - pdb=" SG  CYS A 696 " 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 "
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
    NAG-ASN
      " NAG A 801 " - " ASN A  52 "
      " NAG A 802 " - " ASN A  57 "
      " NAG A 803 " - " ASN A 124 "
      " NAG A 804 " - " ASN A 252 "
      " NAG A 805 " - " ASN A 275 "
      " NAG A 806 " - " ASN A 291 "
      " NAG C   1 " - " ASN A 247 "
      " NAG D   1 " - " ASN A 265 "
      " NAG E   1 " - " ASN A 398 "
      " NAG F   1 " - " ASN A 413 "
  Time building additional restraints: 1.36
  Conformation dependent library (CDL) restraints added in 769.4 milliseconds
  

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1354

  Finding SS restraints...
    Secondary structure from input PDB file:
      13 helices and 6 sheets defined
      15.6% alpha, 5.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.52
  Creating SS restraints...
    Processing helix  chain 'A' and resid 69 through 73
      removed outlier: 3.681A  pdb=" N   ARG A  73 " --> pdb=" O   ASN A  70 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 91 through 96
    Processing helix  chain 'A' and resid 188 through 195
      removed outlier: 4.612A  pdb=" N   ILE A 193 " --> pdb=" O   GLU A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 237 through 245
    Processing helix  chain 'A' and resid 269 through 273
      removed outlier: 3.850A  pdb=" N   TRP A 273 " --> pdb=" O   GLY A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 314 through 319
      removed outlier: 4.166A  pdb=" N   LEU A 318 " --> pdb=" O   SER A 315 " (cutoff:3.500A)
      removed outlier: 4.181A  pdb=" N   HIS A 319 " --> pdb=" O   HIS A 316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 397 through 405
      removed outlier: 3.591A  pdb=" N   THR A 400 " --> pdb=" O   THR A 397 " (cutoff:3.500A)
      removed outlier: 4.159A  pdb=" N   PHE A 401 " --> pdb=" O   ASN A 398 " (cutoff:3.500A)
      removed outlier: 5.386A  pdb=" N   VAL A 402 " --> pdb=" O   GLU A 399 " (cutoff:3.500A)
      removed outlier: 4.858A  pdb=" N   SER A 403 " --> pdb=" O   THR A 400 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 542 through 546
      removed outlier: 3.726A  pdb=" N   TRP A 546 " --> pdb=" O   ALA A 543 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 655 through 662
    Processing helix  chain 'A' and resid 680 through 684
      removed outlier: 3.569A  pdb=" N   TYR A 683 " --> pdb=" O   PRO A 680 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   HIS A 684 " --> pdb=" O   PRO A 681 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 680 through 684'
    Processing helix  chain 'A' and resid 687 through 691
    Processing helix  chain 'B' and resid 2 through 21
      removed outlier: 3.713A  pdb=" N   LEU B  11 " --> pdb=" O   VAL B   7 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 22 through 40
    Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30
      removed outlier: 4.413A  pdb=" N   THR A  29 " --> pdb=" O   ASP A  36 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 81
      removed outlier: 6.629A  pdb=" N   LEU A 104 " --> pdb=" O   HIS A 129 " (cutoff:3.500A)
      removed outlier: 7.622A  pdb=" N   LEU A 128 " --> pdb=" O   ASP A 153 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 333 through 335
      removed outlier: 6.879A  pdb=" N   ILE A 310 " --> pdb=" O   THR A 334 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   LYS A 345 " --> pdb=" O   GLN A 311 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   LEU A 313 " --> pdb=" O   LYS A 345 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 395 through 396
    Processing sheet with id=AA5, first strand: chain 'A' and resid 411 through 412
      removed outlier: 3.699A  pdb=" N   MET A 486 " --> pdb=" O   ILE A 461 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   SER A 514 " --> pdb=" O   LEU A 487 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 444 through 446
      removed outlier: 6.915A  pdb=" N   GLN A 445 " --> pdb=" O   GLN A 470 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   LYS A 493 " --> pdb=" O   LEU A 469 " (cutoff:3.500A)

    69 hydrogen bonds defined for protein.
    162 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.32

  Time building geometry restraints manager: 1.64 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1874
        1.34 -     1.46: 1285
        1.46 -     1.58: 2773
        1.58 -     1.70: 0
        1.70 -     1.82: 29
  Bond restraints: 5961
  Sorted by residual:
  bond pdb=" N   ASP A 292 "
       pdb=" CA  ASP A 292 "
    ideal  model  delta    sigma   weight residual
    1.457  1.487 -0.030 1.29e-02 6.01e+03 5.29e+00
  bond pdb=" N   PHE A 294 "
       pdb=" CA  PHE A 294 "
    ideal  model  delta    sigma   weight residual
    1.457  1.485 -0.028 1.29e-02 6.01e+03 4.62e+00
  bond pdb=" N   SER A 293 "
       pdb=" CA  SER A 293 "
    ideal  model  delta    sigma   weight residual
    1.454  1.480 -0.026 1.31e-02 5.83e+03 3.96e+00
  bond pdb=" CA  SER A 293 "
       pdb=" CB  SER A 293 "
    ideal  model  delta    sigma   weight residual
    1.534  1.503  0.031 1.60e-02 3.91e+03 3.88e+00
  bond pdb=" C1  NAG A 805 "
       pdb=" O5  NAG A 805 "
    ideal  model  delta    sigma   weight residual
    1.406  1.441 -0.035 2.00e-02 2.50e+03 3.06e+00
  ... (remaining 5956 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.57: 7741
        1.57 -     3.14: 291
        3.14 -     4.71: 43
        4.71 -     6.28: 9
        6.28 -     7.85: 1
  Bond angle restraints: 8085
  Sorted by residual:
  angle pdb=" N   ALA A 491 "
        pdb=" CA  ALA A 491 "
        pdb=" C   ALA A 491 "
      ideal   model   delta    sigma   weight residual
     108.63  103.06    5.57 1.60e+00 3.91e-01 1.21e+01
  angle pdb=" CA  SER A 293 "
        pdb=" C   SER A 293 "
        pdb=" O   SER A 293 "
      ideal   model   delta    sigma   weight residual
     121.68  117.84    3.84 1.18e+00 7.18e-01 1.06e+01
  angle pdb=" N   GLU B  15 "
        pdb=" CA  GLU B  15 "
        pdb=" CB  GLU B  15 "
      ideal   model   delta    sigma   weight residual
     110.16  114.68   -4.52 1.48e+00 4.57e-01 9.32e+00
  angle pdb=" CA  VAL A 144 "
        pdb=" C   VAL A 144 "
        pdb=" N   LYS A 145 "
      ideal   model   delta    sigma   weight residual
     116.60  120.92   -4.32 1.45e+00 4.76e-01 8.89e+00
  angle pdb=" C   PHE A 294 "
        pdb=" N   ALA A 295 "
        pdb=" CA  ALA A 295 "
      ideal   model   delta    sigma   weight residual
     120.99  115.82    5.17 1.86e+00 2.89e-01 7.72e+00
  ... (remaining 8080 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.41: 3453
       21.41 -    42.83: 290
       42.83 -    64.24: 32
       64.24 -    85.66: 8
       85.66 -   107.07: 8
  Dihedral angle restraints: 3791
    sinusoidal: 1721
      harmonic: 2070
  Sorted by residual:
  dihedral pdb=" CB  CYS A 651 "
           pdb=" SG  CYS A 651 "
           pdb=" SG  CYS A 696 "
           pdb=" CB  CYS A 696 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   12.59   80.41     1      1.00e+01 1.00e-02 8.00e+01
  dihedral pdb=" CB  CYS A 649 "
           pdb=" SG  CYS A 649 "
           pdb=" SG  CYS A 677 "
           pdb=" CB  CYS A 677 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   34.69   58.31     1      1.00e+01 1.00e-02 4.56e+01
  dihedral pdb=" CA  ASN A  61 "
           pdb=" C   ASN A  61 "
           pdb=" N   GLN A  62 "
           pdb=" CA  GLN A  62 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.29   22.71     0      5.00e+00 4.00e-02 2.06e+01
  ... (remaining 3788 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 634
       0.044 -    0.088: 275
       0.088 -    0.131: 59
       0.131 -    0.175: 6
       0.175 -    0.219: 2
  Chirality restraints: 976
  Sorted by residual:
  chirality pdb=" C1  NAG A 806 "
            pdb=" ND2 ASN A 291 "
            pdb=" C2  NAG A 806 "
            pdb=" O5  NAG A 806 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.18   -0.22 2.00e-01 2.50e+01 1.20e+00
  chirality pdb=" C1  NAG F   1 "
            pdb=" ND2 ASN A 413 "
            pdb=" C2  NAG F   1 "
            pdb=" O5  NAG F   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.22   -0.18 2.00e-01 2.50e+01 8.50e-01
  chirality pdb=" CB  ILE A 591 "
            pdb=" CA  ILE A 591 "
            pdb=" CG1 ILE A 591 "
            pdb=" CG2 ILE A 591 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.48    0.16 2.00e-01 2.50e+01 6.63e-01
  ... (remaining 973 not shown)

  Planarity restraints: 1024
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 668 "   -0.028 5.00e-02 4.00e+02   4.26e-02 2.91e+00
        pdb=" N   PRO A 669 "    0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO A 669 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 669 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 291 "    0.008 2.00e-02 2.50e+03   1.68e-02 2.81e+00
        pdb=" C   ASN A 291 "   -0.029 2.00e-02 2.50e+03
        pdb=" O   ASN A 291 "    0.011 2.00e-02 2.50e+03
        pdb=" N   ASP A 292 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 631 "    0.026 5.00e-02 4.00e+02   3.98e-02 2.53e+00
        pdb=" N   PRO A 632 "   -0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO A 632 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 632 "    0.022 5.00e-02 4.00e+02
  ... (remaining 1021 not shown)

  Histogram of nonbonded interaction distances:
        2.00 -     2.58: 52
        2.58 -     3.16: 4839
        3.16 -     3.74: 8712
        3.74 -     4.32: 12137
        4.32 -     4.90: 19597
  Nonbonded interactions: 45337
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS A 416 "
            pdb=" OE2 GLU B  19 "
     model   vdw
     1.995 3.120
  nonbonded pdb=" O   GLU A 363 "
            pdb=" OG  SER A 389 "
     model   vdw
     2.211 3.040
  nonbonded pdb=" OG  SER A 387 "
            pdb=" OG1 THR A 415 "
     model   vdw
     2.270 3.040
  nonbonded pdb=" O   ASP A 648 "
            pdb=" OG  SER A 653 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" NZ  LYS A 201 "
            pdb=" OE2 GLU A 203 "
     model   vdw
     2.285 3.120
  ... (remaining 45332 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
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

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:             7.700
  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:             0.000
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     16.730
  Find NCS groups from input model:        0.220
  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:13.460
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.480
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6217
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      :  0.004   0.036   5979  Z= 0.195
  Angle     :  0.708   7.848   8135  Z= 0.361
  Chirality :  0.047   0.219    976
  Planarity :  0.004   0.043   1014
  Dihedral  : 15.457 107.071   2425
  Min Nonbonded Distance : 1.995

Molprobity Statistics.
  All-atom Clashscore : 11.47
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 12.05 %
    Favored  : 87.80 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  :  0.31 %
    Favored  : 99.23 %
  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: -3.01 (0.32), residues: 697
  helix: -0.67 (0.62), residues: 75
  sheet: -4.11 (0.49), residues: 74
  loop : -2.04 (0.27), residues: 548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 546 
 HIS   0.003   0.001   HIS A 108 
 PHE   0.009   0.001   PHE A 119 
 TYR   0.020   0.002   TYR B   6 
 ARG   0.002   0.000   ARG A 689 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00291 (   10)
  link_NAG-ASN         : angle       1.78916 (   30)
  link_BETA1-4         : bond        0.00333 (    4)
  link_BETA1-4         : angle       0.89383 (   12)
  hydrogen bonds       : bond        0.23794 (   69)
  hydrogen bonds       : angle       6.97953 (  162)
  SS BOND              : bond        0.00200 (    4)
  SS BOND              : angle       1.10141 (    8)
  covalent geometry    : bond        0.00398 ( 5961)
  covalent geometry    : angle       0.69978 ( 8085)

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

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

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 157
  time to evaluate  : 0.639 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 3
  outliers final: 0
  residues processed: 160
  average time/residue: 0.8814
  time to fit residues: 149.9910
Evaluate side-chains
  68 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.765 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 59 optimal weight:    4.9990
   chunk 53 optimal weight:    4.9990
   chunk 29 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 54 optimal weight:    0.8980
   chunk 21 optimal weight:    0.7980
   chunk 33 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A 107 GLN
A 109 ASN
A 169 GLN
** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 361 ASN
A 365 ASN
A 538 GLN
A 541 ASN
A 550 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4776 r_free = 0.4776 target = 0.145757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4408 r_free = 0.4408 target = 0.118025 restraints weight = 14172.403|
|-----------------------------------------------------------------------------|
r_work (start): 0.4367 rms_B_bonded: 5.55
r_work (final): 0.4367
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6600
moved from start:          0.2689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5979  Z= 0.158
  Angle     :  0.780  10.170   8135  Z= 0.373
  Chirality :  0.050   0.501    976
  Planarity :  0.004   0.047   1014
  Dihedral  : 10.089  83.964   1032
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 12.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.91 %
    Favored  : 88.09 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 14.75 %
    Favored  : 81.57 %
  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: -2.91 (0.31), residues: 697
  helix: -0.58 (0.60), residues: 69
  sheet: -4.11 (0.45), residues: 80
  loop : -1.91 (0.27), residues: 548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 546 
 HIS   0.003   0.001   HIS A 108 
 PHE   0.013   0.001   PHE A 574 
 TYR   0.019   0.002   TYR A 307 
 ARG   0.004   0.000   ARG A 394 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01208 (   10)
  link_NAG-ASN         : angle       2.58664 (   30)
  link_BETA1-4         : bond        0.00515 (    4)
  link_BETA1-4         : angle       1.38717 (   12)
  hydrogen bonds       : bond        0.05814 (   69)
  hydrogen bonds       : angle       6.08982 (  162)
  SS BOND              : bond        0.00263 (    4)
  SS BOND              : angle       1.65503 (    8)
  covalent geometry    : bond        0.00364 ( 5961)
  covalent geometry    : angle       0.76279 ( 8085)

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

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

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 80
  time to evaluate  : 0.731 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8050 (mm)
REVERT: A  245 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8269 (mm)
REVERT: A  328 ASN cc_start: 0.7196 (OUTLIER) cc_final: 0.6681 (t0)
REVERT: A  330 LYS cc_start: 0.7709 (tttm) cc_final: 0.7182 (tttp)
REVERT: A  347 ASP cc_start: 0.6061 (m-30) cc_final: 0.5629 (m-30)
REVERT: A  361 ASN cc_start: 0.7199 (OUTLIER) cc_final: 0.6335 (t0)
REVERT: A  363 GLU cc_start: 0.6705 (tp30) cc_final: 0.5736 (tp30)
REVERT: A  440 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7995 (mp)
REVERT: A  525 MET cc_start: 0.4672 (OUTLIER) cc_final: 0.3780 (mpt)
REVERT: A  585 LEU cc_start: 0.7928 (mt) cc_final: 0.7626 (mm)
REVERT: A  613 LYS cc_start: 0.8571 (mttt) cc_final: 0.8128 (mmmt)
REVERT: B   27 ARG cc_start: 0.9334 (mmp80) cc_final: 0.9037 (mmp80)
  outliers start: 24
  outliers final: 8
  residues processed: 96
  average time/residue: 0.8928
  time to fit residues: 92.3315
Evaluate side-chains
  80 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 66
  time to evaluate  : 0.876 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  328 ASN
Chi-restraints excluded: chain A residue  361 ASN
Chi-restraints excluded: chain A residue  370 ILE
Chi-restraints excluded: chain A residue  389 SER
Chi-restraints excluded: chain A residue  413 ASN
Chi-restraints excluded: chain A residue  440 LEU
Chi-restraints excluded: chain A residue  525 MET
Chi-restraints excluded: chain A residue  555 ILE
Chi-restraints excluded: chain A residue  667 ASN
Chi-restraints excluded: chain B residue   30 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 39 optimal weight:    3.9990
   chunk 61 optimal weight:    4.9990
   chunk 60 optimal weight:    0.7980
   chunk 1 optimal weight:    8.9990
   chunk 47 optimal weight:    5.9990
   chunk 28 optimal weight:    0.5980
   chunk 14 optimal weight:    7.9990
   chunk 30 optimal weight:    0.8980
   chunk 3 optimal weight:    3.9990
   chunk 50 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   overall best weight:    1.8584

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

Flipped N/Q/H residues before XYZ refinement:
A  61 ASN
** A 232 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 = 0.4731 r_free = 0.4731 target = 0.142343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4361 r_free = 0.4361 target = 0.115052 restraints weight = 14234.743|
|-----------------------------------------------------------------------------|
r_work (start): 0.4310 rms_B_bonded: 5.42
r_work (final): 0.4310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6733
moved from start:          0.3220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   5979  Z= 0.193
  Angle     :  0.795   7.946   8135  Z= 0.379
  Chirality :  0.050   0.468    976
  Planarity :  0.004   0.052   1014
  Dihedral  :  8.635  63.676   1032
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 13.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.34 %
    Favored  : 87.66 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 19.05 %
    Favored  : 77.11 %
  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: -2.86 (0.31), residues: 697
  helix: -0.59 (0.59), residues: 69
  sheet: -4.13 (0.45), residues: 75
  loop : -1.89 (0.27), residues: 553

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 452 
 HIS   0.004   0.001   HIS A 108 
 PHE   0.014   0.002   PHE A 119 
 TYR   0.016   0.002   TYR B   6 
 ARG   0.004   0.000   ARG A 394 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00861 (   10)
  link_NAG-ASN         : angle       2.28716 (   30)
  link_BETA1-4         : bond        0.00495 (    4)
  link_BETA1-4         : angle       1.37848 (   12)
  hydrogen bonds       : bond        0.05801 (   69)
  hydrogen bonds       : angle       5.88834 (  162)
  SS BOND              : bond        0.00284 (    4)
  SS BOND              : angle       1.01888 (    8)
  covalent geometry    : bond        0.00451 ( 5961)
  covalent geometry    : angle       0.78240 ( 8085)

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

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

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 69
  time to evaluate  : 0.668 
Fit side-chains
   revert: symmetry clash
REVERT: A   61 ASN cc_start: 0.7897 (m-40) cc_final: 0.7497 (t0)
REVERT: A   94 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8055 (mm)
REVERT: A  203 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7283 (mp0)
REVERT: A  330 LYS cc_start: 0.7794 (tttm) cc_final: 0.7302 (tttp)
REVERT: A  347 ASP cc_start: 0.6369 (m-30) cc_final: 0.5951 (m-30)
REVERT: A  361 ASN cc_start: 0.7384 (OUTLIER) cc_final: 0.6594 (t0)
REVERT: A  363 GLU cc_start: 0.6931 (tp30) cc_final: 0.5986 (tp30)
REVERT: A  525 MET cc_start: 0.4954 (OUTLIER) cc_final: 0.3766 (mpt)
REVERT: A  575 ASP cc_start: 0.7469 (m-30) cc_final: 0.7141 (m-30)
REVERT: A  585 LEU cc_start: 0.8119 (mt) cc_final: 0.7878 (mm)
REVERT: A  613 LYS cc_start: 0.8648 (mttt) cc_final: 0.8271 (mmmt)
REVERT: B    8 LYS cc_start: 0.9168 (mtmm) cc_final: 0.8920 (ptpt)
REVERT: B   27 ARG cc_start: 0.9320 (mmp80) cc_final: 0.9048 (mmp80)
REVERT: B   31 GLU cc_start: 0.8917 (mm-30) cc_final: 0.8705 (mm-30)
  outliers start: 25
  outliers final: 11
  residues processed: 85
  average time/residue: 0.8423
  time to fit residues: 76.9757
Evaluate side-chains
  79 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 64
  time to evaluate  : 0.655 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 THR
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue  122 CYS
Chi-restraints excluded: chain A residue  203 GLU
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  361 ASN
Chi-restraints excluded: chain A residue  370 ILE
Chi-restraints excluded: chain A residue  389 SER
Chi-restraints excluded: chain A residue  413 ASN
Chi-restraints excluded: chain A residue  486 MET
Chi-restraints excluded: chain A residue  510 ILE
Chi-restraints excluded: chain A residue  525 MET
Chi-restraints excluded: chain A residue  555 ILE
Chi-restraints excluded: chain A residue  570 GLU
Chi-restraints excluded: chain B residue   30 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 45 optimal weight:    0.5980
   chunk 43 optimal weight:    0.8980
   chunk 50 optimal weight:    2.9990
   chunk 11 optimal weight:    9.9990
   chunk 42 optimal weight:    0.9990
   chunk 56 optimal weight:    0.0010
   chunk 63 optimal weight:    1.9990
   chunk 57 optimal weight:    5.9990
   chunk 36 optimal weight:    0.9990
   chunk 68 optimal weight:    1.9990
   chunk 60 optimal weight:    0.6980
   overall best weight:    0.6388

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

Flipped N/Q/H residues before XYZ refinement:
A  96 GLN
A 133 ASN
** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 361 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4768 r_free = 0.4768 target = 0.145021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4419 r_free = 0.4419 target = 0.118140 restraints weight = 14352.005|
|-----------------------------------------------------------------------------|
r_work (start): 0.4374 rms_B_bonded: 5.48
r_work (final): 0.4374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6663
moved from start:          0.3545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5979  Z= 0.122
  Angle     :  0.760  18.196   8135  Z= 0.347
  Chirality :  0.047   0.417    976
  Planarity :  0.004   0.049   1014
  Dihedral  :  7.433  53.906   1032
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 10.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.33 %
    Favored  : 89.67 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 19.97 %
    Favored  : 76.34 %
  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: -2.85 (0.31), residues: 697
  helix: -0.49 (0.59), residues: 70
  sheet: -4.05 (0.47), residues: 75
  loop : -1.92 (0.27), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 452 
 HIS   0.002   0.000   HIS A 129 
 PHE   0.012   0.001   PHE A 119 
 TYR   0.014   0.002   TYR B   5 
 ARG   0.004   0.000   ARG A 394 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00706 (   10)
  link_NAG-ASN         : angle       2.07397 (   30)
  link_BETA1-4         : bond        0.00464 (    4)
  link_BETA1-4         : angle       1.56073 (   12)
  hydrogen bonds       : bond        0.04662 (   69)
  hydrogen bonds       : angle       5.51612 (  162)
  SS BOND              : bond        0.00674 (    4)
  SS BOND              : angle       1.38214 (    8)
  covalent geometry    : bond        0.00279 ( 5961)
  covalent geometry    : angle       0.74814 ( 8085)

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

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

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 69
  time to evaluate  : 0.713 
Fit side-chains
   revert: symmetry clash
REVERT: A  203 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7339 (mp0)
REVERT: A  330 LYS cc_start: 0.7729 (tttm) cc_final: 0.7411 (ttmp)
REVERT: A  347 ASP cc_start: 0.6374 (m-30) cc_final: 0.5906 (m-30)
REVERT: A  363 GLU cc_start: 0.6717 (tp30) cc_final: 0.5902 (tp30)
REVERT: A  525 MET cc_start: 0.4959 (OUTLIER) cc_final: 0.4102 (mpt)
REVERT: A  575 ASP cc_start: 0.7494 (m-30) cc_final: 0.7144 (m-30)
REVERT: A  613 LYS cc_start: 0.8386 (mttt) cc_final: 0.8025 (mmmt)
REVERT: B    8 LYS cc_start: 0.9189 (mtmm) cc_final: 0.8944 (mtmm)
REVERT: B   27 ARG cc_start: 0.9313 (mmp80) cc_final: 0.9010 (mmp80)
  outliers start: 24
  outliers final: 7
  residues processed: 85
  average time/residue: 0.8480
  time to fit residues: 77.4386
Evaluate side-chains
  66 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 57
  time to evaluate  : 0.593 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 THR
Chi-restraints excluded: chain A residue  203 GLU
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  370 ILE
Chi-restraints excluded: chain A residue  389 SER
Chi-restraints excluded: chain A residue  510 ILE
Chi-restraints excluded: chain A residue  525 MET
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  555 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 52 optimal weight:    0.5980
   chunk 35 optimal weight:    1.9990
   chunk 38 optimal weight:    0.5980
   chunk 43 optimal weight:    1.9990
   chunk 33 optimal weight:    0.6980
   chunk 54 optimal weight:    1.9990
   chunk 50 optimal weight:    4.9990
   chunk 49 optimal weight:    2.9990
   chunk 8 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 51 optimal weight:    1.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
** A 207 ASN ** 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 = 0.4740 r_free = 0.4740 target = 0.142957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4384 r_free = 0.4384 target = 0.116317 restraints weight = 14503.455|
|-----------------------------------------------------------------------------|
r_work (start): 0.4337 rms_B_bonded: 5.47
r_work (final): 0.4337
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6726
moved from start:          0.3811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   5979  Z= 0.148
  Angle     :  0.756   9.592   8135  Z= 0.353
  Chirality :  0.049   0.548    976
  Planarity :  0.004   0.050   1014
  Dihedral  :  7.129  54.084   1032
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 11.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.62 %
    Favored  : 88.38 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 22.12 %
    Favored  : 74.04 %
  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: -2.84 (0.31), residues: 697
  helix: -0.38 (0.59), residues: 69
  sheet: -4.05 (0.47), residues: 75
  loop : -1.92 (0.27), residues: 553

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 452 
 HIS   0.003   0.000   HIS A 108 
 PHE   0.010   0.001   PHE A  71 
 TYR   0.026   0.002   TYR B   6 
 ARG   0.003   0.000   ARG A 394 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00872 (   10)
  link_NAG-ASN         : angle       2.35329 (   30)
  link_BETA1-4         : bond        0.00421 (    4)
  link_BETA1-4         : angle       1.72731 (   12)
  hydrogen bonds       : bond        0.05032 (   69)
  hydrogen bonds       : angle       5.37824 (  162)
  SS BOND              : bond        0.00341 (    4)
  SS BOND              : angle       1.29818 (    8)
  covalent geometry    : bond        0.00349 ( 5961)
  covalent geometry    : angle       0.74078 ( 8085)

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

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

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 64
  time to evaluate  : 0.714 
Fit side-chains
REVERT: A  203 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7433 (mp0)
REVERT: A  330 LYS cc_start: 0.7692 (tttm) cc_final: 0.7254 (tttp)
REVERT: A  347 ASP cc_start: 0.6517 (m-30) cc_final: 0.6062 (m-30)
REVERT: A  361 ASN cc_start: 0.7354 (OUTLIER) cc_final: 0.6612 (t0)
REVERT: A  525 MET cc_start: 0.5146 (OUTLIER) cc_final: 0.4208 (mpt)
REVERT: A  575 ASP cc_start: 0.7564 (m-30) cc_final: 0.7227 (m-30)
REVERT: A  613 LYS cc_start: 0.8430 (mttt) cc_final: 0.8227 (mppt)
REVERT: B    8 LYS cc_start: 0.9199 (mtmm) cc_final: 0.8982 (mtmm)
REVERT: B   12 ARG cc_start: 0.8575 (ptt180) cc_final: 0.8052 (ptm160)
REVERT: B   15 GLU cc_start: 0.8944 (mm-30) cc_final: 0.8692 (mm-30)
REVERT: B   27 ARG cc_start: 0.9304 (mmp80) cc_final: 0.8952 (mmp80)
  outliers start: 25
  outliers final: 9
  residues processed: 83
  average time/residue: 0.7589
  time to fit residues: 67.8243
Evaluate side-chains
  71 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 59
  time to evaluate  : 0.662 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 THR
Chi-restraints excluded: chain A residue  203 GLU
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  361 ASN
Chi-restraints excluded: chain A residue  370 ILE
Chi-restraints excluded: chain A residue  389 SER
Chi-restraints excluded: chain A residue  448 THR
Chi-restraints excluded: chain A residue  510 ILE
Chi-restraints excluded: chain A residue  525 MET
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  555 ILE
Chi-restraints excluded: chain B residue   30 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 43 optimal weight:    5.9990
   chunk 3 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 49 optimal weight:    4.9990
   chunk 13 optimal weight:   10.0000
   chunk 32 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9990
   chunk 67 optimal weight:    0.8980
   chunk 6 optimal weight:    6.9990
   chunk 47 optimal weight:    0.7980
   chunk 52 optimal weight:    4.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
** A 207 ASN ** 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 = 0.4724 r_free = 0.4724 target = 0.141532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4368 r_free = 0.4368 target = 0.115207 restraints weight = 14619.083|
|-----------------------------------------------------------------------------|
r_work (start): 0.4314 rms_B_bonded: 5.46
r_work (final): 0.4314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6763
moved from start:          0.4074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   5979  Z= 0.154
  Angle     :  0.785  10.238   8135  Z= 0.360
  Chirality :  0.051   0.659    976
  Planarity :  0.004   0.049   1014
  Dihedral  :  6.904  54.052   1032
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 11.64
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 11.62 %
    Favored  : 88.24 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 23.50 %
    Favored  : 72.96 %
  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: -2.83 (0.31), residues: 697
  helix: -0.36 (0.59), residues: 69
  sheet: -3.97 (0.49), residues: 75
  loop : -1.93 (0.27), residues: 553

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 452 
 HIS   0.003   0.000   HIS A 108 
 PHE   0.015   0.001   PHE A 119 
 TYR   0.028   0.002   TYR B   6 
 ARG   0.003   0.000   ARG A 394 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00611 (   10)
  link_NAG-ASN         : angle       2.51450 (   30)
  link_BETA1-4         : bond        0.00332 (    4)
  link_BETA1-4         : angle       1.76365 (   12)
  hydrogen bonds       : bond        0.05103 (   69)
  hydrogen bonds       : angle       5.32906 (  162)
  SS BOND              : bond        0.00339 (    4)
  SS BOND              : angle       1.03891 (    8)
  covalent geometry    : bond        0.00364 ( 5961)
  covalent geometry    : angle       0.76876 ( 8085)

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

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

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 63
  time to evaluate  : 0.651 
Fit side-chains
REVERT: A  330 LYS cc_start: 0.7696 (tttm) cc_final: 0.7216 (tppt)
REVERT: A  347 ASP cc_start: 0.6674 (m-30) cc_final: 0.6209 (m-30)
REVERT: A  361 ASN cc_start: 0.7305 (OUTLIER) cc_final: 0.6575 (t0)
REVERT: A  525 MET cc_start: 0.5311 (OUTLIER) cc_final: 0.4352 (mpt)
REVERT: A  575 ASP cc_start: 0.7628 (m-30) cc_final: 0.7358 (m-30)
REVERT: A  613 LYS cc_start: 0.8466 (mttt) cc_final: 0.8240 (mppt)
REVERT: B   12 ARG cc_start: 0.8603 (ptt180) cc_final: 0.8100 (ptm160)
REVERT: B   27 ARG cc_start: 0.9312 (mmp80) cc_final: 0.8985 (mmp80)
REVERT: B   31 GLU cc_start: 0.8968 (mm-30) cc_final: 0.8755 (mm-30)
  outliers start: 23
  outliers final: 11
  residues processed: 81
  average time/residue: 0.7295
  time to fit residues: 63.8589
Evaluate side-chains
  70 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 57
  time to evaluate  : 0.614 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 THR
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  361 ASN
Chi-restraints excluded: chain A residue  367 ILE
Chi-restraints excluded: chain A residue  370 ILE
Chi-restraints excluded: chain A residue  389 SER
Chi-restraints excluded: chain A residue  448 THR
Chi-restraints excluded: chain A residue  510 ILE
Chi-restraints excluded: chain A residue  525 MET
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  555 ILE
Chi-restraints excluded: chain B residue   30 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 61 optimal weight:    2.9990
   chunk 33 optimal weight:    0.1980
   chunk 4 optimal weight:    7.9990
   chunk 21 optimal weight:    8.9990
   chunk 31 optimal weight:    1.9990
   chunk 67 optimal weight:    0.6980
   chunk 10 optimal weight:    0.0670
   chunk 9 optimal weight:    9.9990
   chunk 20 optimal weight:    3.9990
   chunk 52 optimal weight:    3.9990
   chunk 49 optimal weight:    2.9990
   overall best weight:    1.1922

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

Flipped N/Q/H residues before XYZ refinement:
** A 207 ASN ** 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 = 0.4714 r_free = 0.4714 target = 0.140857 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4356 r_free = 0.4356 target = 0.114209 restraints weight = 14397.526|
|-----------------------------------------------------------------------------|
r_work (start): 0.4311 rms_B_bonded: 5.40
r_work (final): 0.4311
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6769
moved from start:          0.4249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5979  Z= 0.148
  Angle     :  0.775  11.419   8135  Z= 0.356
  Chirality :  0.051   0.632    976
  Planarity :  0.004   0.049   1014
  Dihedral  :  6.744  54.043   1032
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 11.90
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 11.33 %
    Favored  : 88.52 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 23.96 %
    Favored  : 71.74 %
  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: -2.95 (0.31), residues: 697
  helix: -0.62 (0.56), residues: 75
  sheet: -3.93 (0.49), residues: 75
  loop : -2.02 (0.26), residues: 547

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 452 
 HIS   0.003   0.000   HIS A 108 
 PHE   0.009   0.001   PHE A  71 
 TYR   0.030   0.002   TYR B   6 
 ARG   0.003   0.000   ARG A 394 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00759 (   10)
  link_NAG-ASN         : angle       2.56599 (   30)
  link_BETA1-4         : bond        0.00418 (    4)
  link_BETA1-4         : angle       1.68291 (   12)
  hydrogen bonds       : bond        0.04969 (   69)
  hydrogen bonds       : angle       5.29370 (  162)
  SS BOND              : bond        0.00329 (    4)
  SS BOND              : angle       0.93832 (    8)
  covalent geometry    : bond        0.00348 ( 5961)
  covalent geometry    : angle       0.75767 ( 8085)

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

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

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 63
  time to evaluate  : 0.649 
Fit side-chains
   revert: symmetry clash
REVERT: A  203 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7742 (mp0)
REVERT: A  313 LEU cc_start: 0.7007 (tp) cc_final: 0.6786 (tt)
REVERT: A  330 LYS cc_start: 0.7693 (tttm) cc_final: 0.7210 (tppt)
REVERT: A  347 ASP cc_start: 0.6699 (m-30) cc_final: 0.6202 (m-30)
REVERT: A  361 ASN cc_start: 0.7334 (OUTLIER) cc_final: 0.6585 (t0)
REVERT: A  525 MET cc_start: 0.5408 (OUTLIER) cc_final: 0.4450 (mpt)
REVERT: A  575 ASP cc_start: 0.7604 (m-30) cc_final: 0.7320 (m-30)
REVERT: A  613 LYS cc_start: 0.8480 (mttt) cc_final: 0.8219 (mppt)
REVERT: B    4 GLU cc_start: 0.8721 (mp0) cc_final: 0.8493 (mp0)
REVERT: B    8 LYS cc_start: 0.9228 (mtmm) cc_final: 0.8915 (pttm)
REVERT: B   27 ARG cc_start: 0.9308 (mmp80) cc_final: 0.8965 (mmp80)
  outliers start: 28
  outliers final: 14
  residues processed: 83
  average time/residue: 0.7862
  time to fit residues: 70.3609
Evaluate side-chains
  78 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 61
  time to evaluate  : 0.677 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 THR
Chi-restraints excluded: chain A residue   86 THR
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  203 GLU
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  361 ASN
Chi-restraints excluded: chain A residue  370 ILE
Chi-restraints excluded: chain A residue  389 SER
Chi-restraints excluded: chain A residue  448 THR
Chi-restraints excluded: chain A residue  510 ILE
Chi-restraints excluded: chain A residue  525 MET
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  546 TRP
Chi-restraints excluded: chain A residue  555 ILE
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  615 LEU
Chi-restraints excluded: chain A residue  667 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 58 optimal weight:    8.9990
   chunk 10 optimal weight:    9.9990
   chunk 6 optimal weight:    4.9990
   chunk 26 optimal weight:   10.0000
   chunk 44 optimal weight:    5.9990
   chunk 22 optimal weight:    1.9990
   chunk 68 optimal weight:    5.9990
   chunk 48 optimal weight:    0.8980
   chunk 60 optimal weight:    1.9990
   chunk 1 optimal weight:    9.9990
   chunk 25 optimal weight:    0.8980
   overall best weight:    2.1586

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

Flipped N/Q/H residues before XYZ refinement:
** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 259 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 = 0.4679 r_free = 0.4679 target = 0.138032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4313 r_free = 0.4313 target = 0.111354 restraints weight = 14701.851|
|-----------------------------------------------------------------------------|
r_work (start): 0.4253 rms_B_bonded: 5.40
r_work (final): 0.4253
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6859
moved from start:          0.4513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   5979  Z= 0.211
  Angle     :  0.851  11.439   8135  Z= 0.394
  Chirality :  0.055   0.823    976
  Planarity :  0.004   0.050   1014
  Dihedral  :  6.823  54.168   1032
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 14.98
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 13.77 %
    Favored  : 86.08 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 24.27 %
    Favored  : 70.97 %
  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: -3.08 (0.30), residues: 697
  helix: -0.76 (0.55), residues: 75
  sheet: -4.22 (0.50), residues: 66
  loop : -2.13 (0.26), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 452 
 HIS   0.005   0.001   HIS A 108 
 PHE   0.016   0.001   PHE A 119 
 TYR   0.031   0.003   TYR B   6 
 ARG   0.004   0.000   ARG B  12 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00848 (   10)
  link_NAG-ASN         : angle       3.08003 (   30)
  link_BETA1-4         : bond        0.00285 (    4)
  link_BETA1-4         : angle       1.66141 (   12)
  hydrogen bonds       : bond        0.05684 (   69)
  hydrogen bonds       : angle       5.52060 (  162)
  SS BOND              : bond        0.00428 (    4)
  SS BOND              : angle       1.06285 (    8)
  covalent geometry    : bond        0.00496 ( 5961)
  covalent geometry    : angle       0.82962 ( 8085)

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

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

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 64
  time to evaluate  : 0.781 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  143 PHE cc_start: 0.8484 (p90) cc_final: 0.7760 (p90)
REVERT: A  203 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7139 (mp0)
REVERT: A  330 LYS cc_start: 0.7672 (tttm) cc_final: 0.7216 (tppt)
REVERT: A  347 ASP cc_start: 0.6852 (m-30) cc_final: 0.6426 (m-30)
REVERT: A  525 MET cc_start: 0.5570 (OUTLIER) cc_final: 0.4573 (mpt)
REVERT: A  575 ASP cc_start: 0.7668 (m-30) cc_final: 0.7402 (m-30)
REVERT: A  613 LYS cc_start: 0.8633 (mttt) cc_final: 0.8319 (mppt)
REVERT: B    3 MET cc_start: 0.9155 (mpp) cc_final: 0.8510 (mpp)
REVERT: B    8 LYS cc_start: 0.9208 (mtmm) cc_final: 0.8993 (pttm)
REVERT: B   19 GLU cc_start: 0.8886 (tm-30) cc_final: 0.8403 (OUTLIER)
  outliers start: 31
  outliers final: 16
  residues processed: 89
  average time/residue: 0.7270
  time to fit residues: 70.2292
Evaluate side-chains
  75 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 58
  time to evaluate  : 0.629 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 THR
Chi-restraints excluded: chain A residue   61 ASN
Chi-restraints excluded: chain A residue   86 THR
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  203 GLU
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  370 ILE
Chi-restraints excluded: chain A residue  389 SER
Chi-restraints excluded: chain A residue  448 THR
Chi-restraints excluded: chain A residue  510 ILE
Chi-restraints excluded: chain A residue  525 MET
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  546 TRP
Chi-restraints excluded: chain A residue  555 ILE
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  667 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 57 optimal weight:    0.6980
   chunk 64 optimal weight:    7.9990
   chunk 6 optimal weight:    2.9990
   chunk 15 optimal weight:    6.9990
   chunk 54 optimal weight:    0.6980
   chunk 44 optimal weight:    4.9990
   chunk 62 optimal weight:    2.9990
   chunk 61 optimal weight:    4.9990
   chunk 37 optimal weight:    3.9990
   chunk 24 optimal weight:    6.9990
   chunk 55 optimal weight:    2.9990
   overall best weight:    2.0786

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

Flipped N/Q/H residues before XYZ refinement:
** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 259 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 = 0.4675 r_free = 0.4675 target = 0.137699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4313 r_free = 0.4313 target = 0.111053 restraints weight = 14475.646|
|-----------------------------------------------------------------------------|
r_work (start): 0.4258 rms_B_bonded: 5.32
r_work (final): 0.4258
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6856
moved from start:          0.4710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058   5979  Z= 0.206
  Angle     :  0.879  13.888   8135  Z= 0.407
  Chirality :  0.055   0.780    976
  Planarity :  0.004   0.050   1014
  Dihedral  :  6.936  53.829   1032
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 15.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.77 %
    Favored  : 86.23 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 25.81 %
    Favored  : 69.59 %
  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: -3.17 (0.30), residues: 697
  helix: -0.88 (0.55), residues: 75
  sheet: -4.39 (0.55), residues: 54
  loop : -2.24 (0.25), residues: 568

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 452 
 HIS   0.005   0.001   HIS A 108 
 PHE   0.011   0.001   PHE A 557 
 TYR   0.030   0.003   TYR B   6 
 ARG   0.003   0.000   ARG A 394 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00837 (   10)
  link_NAG-ASN         : angle       3.71825 (   30)
  link_BETA1-4         : bond        0.00343 (    4)
  link_BETA1-4         : angle       1.58484 (   12)
  hydrogen bonds       : bond        0.05805 (   69)
  hydrogen bonds       : angle       5.59496 (  162)
  SS BOND              : bond        0.00436 (    4)
  SS BOND              : angle       1.02986 (    8)
  covalent geometry    : bond        0.00487 ( 5961)
  covalent geometry    : angle       0.84973 ( 8085)

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

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

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 57
  time to evaluate  : 0.698 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  143 PHE cc_start: 0.8521 (p90) cc_final: 0.7766 (p90)
REVERT: A  203 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7871 (mp0)
REVERT: A  330 LYS cc_start: 0.7692 (tttm) cc_final: 0.7271 (tppt)
REVERT: A  347 ASP cc_start: 0.6846 (m-30) cc_final: 0.6367 (m-30)
REVERT: A  525 MET cc_start: 0.5677 (OUTLIER) cc_final: 0.4684 (mpt)
REVERT: A  575 ASP cc_start: 0.7707 (m-30) cc_final: 0.7439 (m-30)
REVERT: A  585 LEU cc_start: 0.7913 (mt) cc_final: 0.7689 (mm)
REVERT: A  613 LYS cc_start: 0.8667 (mttt) cc_final: 0.8276 (mmmt)
REVERT: B    3 MET cc_start: 0.9065 (mpp) cc_final: 0.8527 (mpp)
REVERT: B    4 GLU cc_start: 0.8726 (mp0) cc_final: 0.8511 (mp0)
REVERT: B    8 LYS cc_start: 0.9182 (mtmm) cc_final: 0.8886 (pttm)
  outliers start: 30
  outliers final: 18
  residues processed: 80
  average time/residue: 0.8147
  time to fit residues: 70.6306
Evaluate side-chains
  74 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 54
  time to evaluate  : 0.698 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 THR
Chi-restraints excluded: chain A residue   61 ASN
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue   86 THR
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  203 GLU
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  370 ILE
Chi-restraints excluded: chain A residue  389 SER
Chi-restraints excluded: chain A residue  448 THR
Chi-restraints excluded: chain A residue  510 ILE
Chi-restraints excluded: chain A residue  521 ILE
Chi-restraints excluded: chain A residue  525 MET
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  546 TRP
Chi-restraints excluded: chain A residue  555 ILE
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  667 ASN
Chi-restraints excluded: chain B residue    7 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 63 optimal weight:    1.9990
   chunk 4 optimal weight:    7.9990
   chunk 69 optimal weight:    6.9990
   chunk 1 optimal weight:   10.0000
   chunk 56 optimal weight:    4.9990
   chunk 59 optimal weight:    0.9980
   chunk 27 optimal weight:    2.9990
   chunk 11 optimal weight:    6.9990
   chunk 54 optimal weight:    0.6980
   chunk 31 optimal weight:    0.7980
   chunk 50 optimal weight:    3.9990
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
A 172 ASN
** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 259 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 = 0.4692 r_free = 0.4692 target = 0.138805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4338 r_free = 0.4338 target = 0.112451 restraints weight = 14530.711|
|-----------------------------------------------------------------------------|
r_work (start): 0.4289 rms_B_bonded: 5.38
r_work (final): 0.4289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6824
moved from start:          0.4896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   5979  Z= 0.168
  Angle     :  0.850  13.104   8135  Z= 0.391
  Chirality :  0.052   0.701    976
  Planarity :  0.004   0.050   1014
  Dihedral  :  6.754  53.904   1032
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 14.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.48 %
    Favored  : 87.52 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 27.19 %
    Favored  : 69.59 %
  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: -3.09 (0.30), residues: 697
  helix: -0.81 (0.56), residues: 75
  sheet: -4.58 (0.61), residues: 39
  loop : -2.25 (0.25), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 546 
 HIS   0.003   0.001   HIS A 108 
 PHE   0.019   0.001   PHE A 119 
 TYR   0.028   0.002   TYR B   6 
 ARG   0.003   0.000   ARG A 394 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00848 (   10)
  link_NAG-ASN         : angle       3.54505 (   30)
  link_BETA1-4         : bond        0.00468 (    4)
  link_BETA1-4         : angle       1.40504 (   12)
  hydrogen bonds       : bond        0.05487 (   69)
  hydrogen bonds       : angle       5.59247 (  162)
  SS BOND              : bond        0.00372 (    4)
  SS BOND              : angle       0.90187 (    8)
  covalent geometry    : bond        0.00400 ( 5961)
  covalent geometry    : angle       0.82230 ( 8085)

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

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

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 59
  time to evaluate  : 0.609 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  143 PHE cc_start: 0.8570 (p90) cc_final: 0.7804 (p90)
REVERT: A  330 LYS cc_start: 0.7756 (tttm) cc_final: 0.7276 (tppt)
REVERT: A  347 ASP cc_start: 0.6792 (m-30) cc_final: 0.6294 (m-30)
REVERT: A  525 MET cc_start: 0.5625 (OUTLIER) cc_final: 0.4797 (mpt)
REVERT: A  575 ASP cc_start: 0.7720 (m-30) cc_final: 0.7433 (m-30)
REVERT: A  585 LEU cc_start: 0.7919 (mt) cc_final: 0.7700 (mm)
REVERT: A  613 LYS cc_start: 0.8591 (mttt) cc_final: 0.8221 (mmmt)
REVERT: B    3 MET cc_start: 0.9127 (mpp) cc_final: 0.8560 (mpp)
REVERT: B    4 GLU cc_start: 0.8736 (mp0) cc_final: 0.8490 (mp0)
REVERT: B    5 TYR cc_start: 0.8284 (t80) cc_final: 0.7964 (t80)
REVERT: B    6 TYR cc_start: 0.8547 (t80) cc_final: 0.8311 (t80)
REVERT: B    8 LYS cc_start: 0.9163 (mtmm) cc_final: 0.8886 (pttm)
  outliers start: 21
  outliers final: 17
  residues processed: 76
  average time/residue: 0.7617
  time to fit residues: 62.3185
Evaluate side-chains
  75 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 57
  time to evaluate  : 0.579 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 THR
Chi-restraints excluded: chain A residue   61 ASN
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue   86 THR
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  370 ILE
Chi-restraints excluded: chain A residue  389 SER
Chi-restraints excluded: chain A residue  448 THR
Chi-restraints excluded: chain A residue  510 ILE
Chi-restraints excluded: chain A residue  521 ILE
Chi-restraints excluded: chain A residue  525 MET
Chi-restraints excluded: chain A residue  546 TRP
Chi-restraints excluded: chain A residue  555 ILE
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  615 LEU
Chi-restraints excluded: chain A residue  667 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 38 optimal weight:    0.4980
   chunk 69 optimal weight:    4.9990
   chunk 64 optimal weight:    7.9990
   chunk 57 optimal weight:    5.9990
   chunk 54 optimal weight:    0.0040
   chunk 55 optimal weight:    1.9990
   chunk 45 optimal weight:    0.7980
   chunk 16 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 5 optimal weight:    0.6980
   chunk 49 optimal weight:    4.9990
   overall best weight:    0.7994

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

Flipped N/Q/H residues before XYZ refinement:
** A 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 361 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4718 r_free = 0.4718 target = 0.140647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4374 r_free = 0.4374 target = 0.114560 restraints weight = 14512.787|
|-----------------------------------------------------------------------------|
r_work (start): 0.4332 rms_B_bonded: 5.40
r_work (final): 0.4332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6771
moved from start:          0.4977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   5979  Z= 0.130
  Angle     :  0.808  13.575   8135  Z= 0.370
  Chirality :  0.051   0.659    976
  Planarity :  0.004   0.049   1014
  Dihedral  :  6.553  53.928   1032
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 11.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.05 %
    Favored  : 88.95 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 27.19 %
    Favored  : 68.97 %
  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: -2.97 (0.30), residues: 697
  helix: -0.74 (0.56), residues: 75
  sheet: -3.94 (0.60), residues: 51
  loop : -2.15 (0.25), residues: 571

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 546 
 HIS   0.003   0.000   HIS A 129 
 PHE   0.014   0.001   PHE A 217 
 TYR   0.022   0.002   TYR B   6 
 ARG   0.003   0.000   ARG A 394 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00855 (   10)
  link_NAG-ASN         : angle       3.56614 (   30)
  link_BETA1-4         : bond        0.00423 (    4)
  link_BETA1-4         : angle       1.33009 (   12)
  hydrogen bonds       : bond        0.04958 (   69)
  hydrogen bonds       : angle       5.44280 (  162)
  SS BOND              : bond        0.00289 (    4)
  SS BOND              : angle       0.75018 (    8)
  covalent geometry    : bond        0.00304 ( 5961)
  covalent geometry    : angle       0.77866 ( 8085)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4284.94 seconds
wall clock time: 75 minutes 52.01 seconds (4552.01 seconds total)