Starting phenix.real_space_refine
on Thu Jun  5 09:36:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bur_44917/06_2025/9bur_44917.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bur_44917/06_2025/9bur_44917.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.95
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bur_44917/06_2025/9bur_44917.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bur_44917/06_2025/9bur_44917.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bur_44917/06_2025/9bur_44917.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bur_44917/06_2025/9bur_44917.cif"
  }
  resolution = 2.95
  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=   0.087
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       1      5.49       5
     S      27      5.16       5
     C    3842      2.51       5
     N     977      2.21       5
     O    1030      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 56 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: 5877
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 5423
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 663, 5423
          Classifications: {'peptide': 663}
          Incomplete info: {'truncation_to_alanine': 19}
          Link IDs: {'PTRANS': 33, 'TRANS': 629}
          Chain breaks: 2
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 76
          Unresolved non-hydrogen angles: 96
          Unresolved non-hydrogen dihedrals: 59
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'GLN:plan1': 4, 'PHE:plan': 1, 'ARG:plan': 4, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 50
    Chain: "B"
      Number of atoms: 333
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 42, 333
          Classifications: {'peptide': 42}
          Link IDs: {'PTRANS': 4, 'TRANS': 37}
          Chain breaks: 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: "A"
      Number of atoms: 93
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 93
          Unusual residues: {'CLR': 1, 'NAG': 2, 'POV': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 19
          Unresolved non-hydrogen dihedrals: 21
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 4.53, per 1000 atoms: 0.77
  Number of scatterers: 5877
  At special positions: 0
  Unit cell: (86.32, 92.96, 102.92, 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)
     S      27     16.00
     P       1     15.00
     O    1030      8.00
     N     977      7.00
     C    3842      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  99 " - pdb=" SG  CYS A 450 " 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 d   1 " - " NAG d   2 "
    NAG-ASN
      " NAG A1201 " - " ASN A 550 "
      " NAG A1202 " - " ASN A 605 "
      " NAG d   1 " - " ASN A 570 "
  Time building additional restraints: 1.83
  Conformation dependent library (CDL) restraints added in 980.6 milliseconds
  

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1336

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 3 sheets defined
      52.3% alpha, 8.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.68
  Creating SS restraints...
    Processing helix  chain 'A' and resid 32 through 39
      removed outlier: 3.868A  pdb=" N   LYS A  36 " --> pdb=" O   SER A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 56
    Processing helix  chain 'A' and resid 61 through 77
      removed outlier: 3.619A  pdb=" N   PHE A  67 " --> pdb=" O   SER A  63 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   PHE A  69 " --> pdb=" O   ALA A  65 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   LEU A  74 " --> pdb=" O   LEU A  70 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 77 through 82
      removed outlier: 3.771A  pdb=" N   GLN A  81 " --> pdb=" O   LEU A  77 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 92
    Processing helix  chain 'A' and resid 111 through 132
      removed outlier: 3.825A  pdb=" N   LEU A 117 " --> pdb=" O   ASP A 113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 152
      removed outlier: 3.615A  pdb=" N   VAL A 140 " --> pdb=" O   ARG A 136 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   PHE A 142 " --> pdb=" O   SER A 138 " (cutoff:3.500A)
      Proline residue:  A 145  - end of helix
    Processing helix  chain 'A' and resid 153 through 157
      removed outlier: 3.650A  pdb=" N   TRP A 157 " --> pdb=" O   LYS A 154 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 160 through 171
      removed outlier: 3.639A  pdb=" N   GLY A 165 " --> pdb=" O   SER A 161 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 187
      removed outlier: 3.621A  pdb=" N   LEU A 185 " --> pdb=" O   SER A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 197 through 218
      removed outlier: 3.899A  pdb=" N   LEU A 203 " --> pdb=" O   ASN A 199 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   ALA A 214 " --> pdb=" O   VAL A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 220 through 225
      removed outlier: 3.603A  pdb=" N   GLU A 225 " --> pdb=" O   ALA A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 244
      removed outlier: 5.641A  pdb=" N   TRP A 236 " --> pdb=" O   SER A 233 " (cutoff:3.500A)
      removed outlier: 6.314A  pdb=" N   LEU A 237 " --> pdb=" O   ARG A 234 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   PHE A 238 " --> pdb=" O   HIS A 235 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   SER A 239 " --> pdb=" O   TRP A 236 " (cutoff:3.500A)
      Proline residue:  A 240  - end of helix
      removed outlier: 3.655A  pdb=" N   LEU A 244 " --> pdb=" O   PHE A 241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 254
      removed outlier: 3.808A  pdb=" N   LEU A 252 " --> pdb=" O   GLU A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 264
    Processing helix  chain 'A' and resid 275 through 294
      removed outlier: 3.614A  pdb=" N   HIS A 287 " --> pdb=" O   VAL A 283 " (cutoff:3.500A)
      removed outlier: 4.099A  pdb=" N   GLN A 292 " --> pdb=" O   CYS A 288 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   PHE A 294 " --> pdb=" O   ASN A 290 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 307
      removed outlier: 3.690A  pdb=" N   LEU A 304 " --> pdb=" O   SER A 300 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   SER A 307 " --> pdb=" O   MET A 303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 308 through 311
    Processing helix  chain 'A' and resid 316 through 321
    Processing helix  chain 'A' and resid 326 through 330
      removed outlier: 4.015A  pdb=" N   GLN A 329 " --> pdb=" O   ARG A 326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 357 through 362
    Processing helix  chain 'A' and resid 362 through 377
      removed outlier: 3.702A  pdb=" N   LEU A 368 " --> pdb=" O   ALA A 364 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   LEU A 375 " --> pdb=" O   LEU A 371 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 378 through 383
      removed outlier: 5.289A  pdb=" N   HIS A 381 " --> pdb=" O   PRO A 378 " (cutoff:3.500A)
      removed outlier: 4.515A  pdb=" N   PHE A 382 " --> pdb=" O   TYR A 379 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 440 through 455
    Processing helix  chain 'A' and resid 456 through 459
      removed outlier: 3.767A  pdb=" N   ASN A 459 " --> pdb=" O   PRO A 456 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 456 through 459'
    Processing helix  chain 'A' and resid 506 through 511
      removed outlier: 3.648A  pdb=" N   LEU A 509 " --> pdb=" O   LEU A 506 " (cutoff:3.500A)
      Proline residue:  A 511  - end of helix
    Processing helix  chain 'A' and resid 512 through 523
    Processing helix  chain 'A' and resid 605 through 612
    Processing helix  chain 'A' and resid 614 through 619
    Processing helix  chain 'A' and resid 654 through 669
      removed outlier: 4.008A  pdb=" N   THR A 658 " --> pdb=" O   PRO A 654 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ARG A 662 " --> pdb=" O   THR A 658 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   GLN A 667 " --> pdb=" O   GLN A 663 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   GLU A 668 " --> pdb=" O   GLN A 664 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 676 through 708
      removed outlier: 3.682A  pdb=" N   SER A 695 " --> pdb=" O   VAL A 691 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   PHE A 696 " --> pdb=" O   PHE A 692 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   THR A 699 " --> pdb=" O   SER A 695 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   LEU A 706 " --> pdb=" O   SER A 702 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   ILE A 707 " --> pdb=" O   LEU A 703 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 712 through 724
      removed outlier: 3.747A  pdb=" N   GLU A 719 " --> pdb=" O   GLN A 715 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 88 through 97
      removed outlier: 3.528A  pdb=" N   ARG B  94 " --> pdb=" O   GLN B  90 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   PHE B  96 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 479 through 480
      removed outlier: 6.404A  pdb=" N   TYR A 466 " --> pdb=" O   ILE A 413 " (cutoff:3.500A)
      removed outlier: 4.356A  pdb=" N   ILE A 413 " --> pdb=" O   TYR A 466 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   ASP A 468 " --> pdb=" O   VAL A 411 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   VAL A 411 " --> pdb=" O   ASP A 468 " (cutoff:3.500A)
      removed outlier: 6.724A  pdb=" N   TRP A 470 " --> pdb=" O   GLN A 409 " (cutoff:3.500A)
      removed outlier: 4.538A  pdb=" N   ILE A 413 " --> pdb=" O   LEU A 426 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   TYR A 425 " --> pdb=" O   VAL B  37 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 527 through 534
      removed outlier: 6.671A  pdb=" N   MET A 600 " --> pdb=" O   LEU A 555 " (cutoff:3.500A)
      removed outlier: 5.608A  pdb=" N   LEU A 555 " --> pdb=" O   MET A 600 " (cutoff:3.500A)
      removed outlier: 7.057A  pdb=" N   VAL A 602 " --> pdb=" O   ILE A 553 " (cutoff:3.500A)
      removed outlier: 5.719A  pdb=" N   ILE A 553 " --> pdb=" O   VAL A 602 " (cutoff:3.500A)
      removed outlier: 7.230A  pdb=" N   VAL A 604 " --> pdb=" O   THR A 551 " (cutoff:3.500A)
      removed outlier: 5.421A  pdb=" N   THR A 551 " --> pdb=" O   VAL A 604 " (cutoff:3.500A)
      removed outlier: 4.371A  pdb=" N   THR A 551 " --> pdb=" O   LEU A 581 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 539 through 543
      removed outlier: 3.628A  pdb=" N   VAL A 560 " --> pdb=" O   LEU A 573 " (cutoff:3.500A)

    228 hydrogen bonds defined for protein.
    651 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: 2.04

  Time building geometry restraints manager: 2.01 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 893
        1.31 -     1.43: 1774
        1.43 -     1.56: 3331
        1.56 -     1.68: 2
        1.68 -     1.81: 44
  Bond restraints: 6044
  Sorted by residual:
  bond pdb=" C29 POV A1204 "
       pdb="C210 POV A1204 "
    ideal  model  delta    sigma   weight residual
    1.333  1.529 -0.196 2.00e-02 2.50e+03 9.61e+01
  bond pdb=" C   VAL B  45 "
       pdb=" N   VAL B  46 "
    ideal  model  delta    sigma   weight residual
    1.333  1.406 -0.073 1.29e-02 6.01e+03 3.20e+01
  bond pdb=" N   ARG A 680 "
       pdb=" CA  ARG A 680 "
    ideal  model  delta    sigma   weight residual
    1.459  1.411  0.048 1.18e-02 7.18e+03 1.66e+01
  bond pdb=" C   ARG A 680 "
       pdb=" O   ARG A 680 "
    ideal  model  delta    sigma   weight residual
    1.236  1.195  0.042 1.16e-02 7.43e+03 1.30e+01
  bond pdb=" C31 POV A1204 "
       pdb=" O31 POV A1204 "
    ideal  model  delta    sigma   weight residual
    1.327  1.395 -0.068 2.00e-02 2.50e+03 1.14e+01
  ... (remaining 6039 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.18: 8146
        4.18 -     8.36: 54
        8.36 -    12.55: 5
       12.55 -    16.73: 2
       16.73 -    20.91: 1
  Bond angle restraints: 8208
  Sorted by residual:
  angle pdb=" N   ARG A 680 "
        pdb=" CA  ARG A 680 "
        pdb=" C   ARG A 680 "
      ideal   model   delta    sigma   weight residual
     111.03   99.41   11.62 1.11e+00 8.12e-01 1.10e+02
  angle pdb=" O13 POV A1204 "
        pdb=" P   POV A1204 "
        pdb=" O14 POV A1204 "
      ideal   model   delta    sigma   weight residual
     121.11  100.20   20.91 3.00e+00 1.11e-01 4.86e+01
  angle pdb=" N   PRO A 654 "
        pdb=" CA  PRO A 654 "
        pdb=" CB  PRO A 654 "
      ideal   model   delta    sigma   weight residual
     103.51  109.76   -6.25 9.60e-01 1.09e+00 4.24e+01
  angle pdb=" C28 POV A1204 "
        pdb=" C29 POV A1204 "
        pdb="C210 POV A1204 "
      ideal   model   delta    sigma   weight residual
     127.79  111.92   15.87 3.00e+00 1.11e-01 2.80e+01
  angle pdb=" N   GLN B  40 "
        pdb=" CA  GLN B  40 "
        pdb=" C   GLN B  40 "
      ideal   model   delta    sigma   weight residual
     114.75  108.62    6.13 1.26e+00 6.30e-01 2.37e+01
  ... (remaining 8203 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.29: 3225
       16.29 -    32.57: 327
       32.57 -    48.86: 75
       48.86 -    65.14: 21
       65.14 -    81.43: 5
  Dihedral angle restraints: 3653
    sinusoidal: 1581
      harmonic: 2072
  Sorted by residual:
  dihedral pdb=" CA  PRO A 324 "
           pdb=" C   PRO A 324 "
           pdb=" N   ARG A 325 "
           pdb=" CA  ARG A 325 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.99  -28.01     0      5.00e+00 4.00e-02 3.14e+01
  dihedral pdb=" CA  THR A 653 "
           pdb=" C   THR A 653 "
           pdb=" N   PRO A 654 "
           pdb=" CA  PRO A 654 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.90   25.10     0      5.00e+00 4.00e-02 2.52e+01
  dihedral pdb=" CA  GLY A 429 "
           pdb=" C   GLY A 429 "
           pdb=" N   VAL A 430 "
           pdb=" CA  VAL A 430 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.30  -24.70     0      5.00e+00 4.00e-02 2.44e+01
  ... (remaining 3650 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 626
       0.052 -    0.103: 213
       0.103 -    0.155: 43
       0.155 -    0.206: 12
       0.206 -    0.258: 2
  Chirality restraints: 896
  Sorted by residual:
  chirality pdb=" CA  PRO A 654 "
            pdb=" N   PRO A 654 "
            pdb=" C   PRO A 654 "
            pdb=" CB  PRO A 654 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.46    0.26 2.00e-01 2.50e+01 1.66e+00
  chirality pdb=" CA  ARG A 680 "
            pdb=" N   ARG A 680 "
            pdb=" C   ARG A 680 "
            pdb=" CB  ARG A 680 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.23 2.00e-01 2.50e+01 1.35e+00
  chirality pdb=" CB  VAL A 691 "
            pdb=" CA  VAL A 691 "
            pdb=" CG1 VAL A 691 "
            pdb=" CG2 VAL A 691 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.43   -0.20 2.00e-01 2.50e+01 9.83e-01
  ... (remaining 893 not shown)

  Planarity restraints: 1024
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C28 POV A1204 "   -0.087 2.00e-02 2.50e+03   8.73e-02 7.62e+01
        pdb=" C29 POV A1204 "    0.084 2.00e-02 2.50e+03
        pdb="C210 POV A1204 "    0.091 2.00e-02 2.50e+03
        pdb="C211 POV A1204 "   -0.088 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 307 "   -0.053 5.00e-02 4.00e+02   7.84e-02 9.84e+00
        pdb=" N   PRO A 308 "    0.136 5.00e-02 4.00e+02
        pdb=" CA  PRO A 308 "   -0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO A 308 "   -0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 679 "    0.015 2.00e-02 2.50e+03   3.10e-02 9.63e+00
        pdb=" C   GLU A 679 "   -0.054 2.00e-02 2.50e+03
        pdb=" O   GLU A 679 "    0.020 2.00e-02 2.50e+03
        pdb=" N   ARG A 680 "    0.018 2.00e-02 2.50e+03
  ... (remaining 1021 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1301
        2.77 -     3.30: 5017
        3.30 -     3.84: 9827
        3.84 -     4.37: 12261
        4.37 -     4.90: 20678
  Nonbonded interactions: 49084
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 586 "
            pdb=" O   LYS B  39 "
     model   vdw
     2.241 3.040
  nonbonded pdb=" O   SER A 228 "
            pdb=" NE2 HIS A 256 "
     model   vdw
     2.257 3.120
  nonbonded pdb=" O   SER A 695 "
            pdb=" OG1 THR A 699 "
     model   vdw
     2.288 3.040
  nonbonded pdb=" OE1 GLN A 206 "
            pdb=" OH  TYR A 370 "
     model   vdw
     2.297 3.040
  nonbonded pdb=" O   LEU A 280 "
            pdb=" OG  SER A 284 "
     model   vdw
     2.313 3.040
  ... (remaining 49079 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:             12.420
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     19.220
  Find NCS groups from input model:        0.050
  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:             0.000
  Load rotamer database and sin/cos tables:15.490
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   47.500
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8030
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      :  0.008   0.196   6049  Z= 0.364
  Angle     :  1.040  20.909   8222  Z= 0.556
  Chirality :  0.055   0.258    896
  Planarity :  0.009   0.087   1021
  Dihedral  : 14.369  81.429   2314
  Min Nonbonded Distance : 2.241

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  :  5.19 %
    Favored  : 94.48 %
  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: -4.84 (0.24), residues: 693
  helix: -4.48 (0.12), residues: 325
  sheet: -2.44 (0.50), residues: 76
  loop : -1.54 (0.32), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 198 
 HIS   0.010   0.002   HIS A 526 
 PHE   0.013   0.002   PHE A 382 
 TYR   0.031   0.003   TYR B  97 
 ARG   0.012   0.001   ARG A 683 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00157 (    3)
  link_NAG-ASN         : angle       2.04580 (    9)
  link_BETA1-4         : bond        0.00270 (    1)
  link_BETA1-4         : angle       2.42238 (    3)
  hydrogen bonds       : bond        0.28087 (  228)
  hydrogen bonds       : angle      11.03093 (  651)
  SS BOND              : bond        0.00501 (    1)
  SS BOND              : angle       1.24654 (    2)
  covalent geometry    : bond        0.00782 ( 6044)
  covalent geometry    : angle       1.03706 ( 8208)

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

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

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 104
  time to evaluate  : 0.625 
Fit side-chains
   revert: symmetry clash
REVERT: A  104 LEU cc_start: 0.8235 (mm) cc_final: 0.7939 (mm)
REVERT: A  422 GLU cc_start: 0.7388 (mt-10) cc_final: 0.7012 (mm-30)
REVERT: A  459 ASN cc_start: 0.8152 (m-40) cc_final: 0.7028 (t0)
REVERT: A  475 ASP cc_start: 0.8054 (m-30) cc_final: 0.7795 (m-30)
REVERT: A  517 GLN cc_start: 0.7565 (tp-100) cc_final: 0.7295 (tp-100)
REVERT: A  569 LYS cc_start: 0.8169 (ttpp) cc_final: 0.7720 (tppt)
REVERT: A  680 ARG cc_start: 0.6212 (mmm-85) cc_final: 0.5909 (mtt180)
REVERT: A  689 LEU cc_start: 0.7896 (tt) cc_final: 0.7302 (mp)
  outliers start: 2
  outliers final: 1
  residues processed: 106
  average time/residue: 1.5668
  time to fit residues: 173.3471
Evaluate side-chains
  71 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 70
  time to evaluate  : 0.629 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  602 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 59 optimal weight:    7.9990
   chunk 53 optimal weight:    3.9990
   chunk 29 optimal weight:    9.9990
   chunk 18 optimal weight:    0.5980
   chunk 35 optimal weight:    0.0970
   chunk 28 optimal weight:    0.7980
   chunk 54 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9980
   chunk 33 optimal weight:    0.5980
   chunk 40 optimal weight:    0.9980
   chunk 63 optimal weight:    0.9980
   overall best weight:    0.6178

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

Flipped N/Q/H residues before XYZ refinement:
A  81 GLN
A 235 HIS
A 292 GLN
A 354 GLN
A 404 HIS
A 408 HIS
A 409 GLN
A 440 HIS
** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 526 HIS
A 674 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.149979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.120477 restraints weight = 6648.023|
|-----------------------------------------------------------------------------|
r_work (start): 0.3184 rms_B_bonded: 1.53
r_work: 0.3074 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.2959 rms_B_bonded: 3.22 restraints_weight: 0.2500
r_work (final): 0.2959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8316
moved from start:          0.1805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6049  Z= 0.129
  Angle     :  0.558   6.311   8222  Z= 0.289
  Chirality :  0.040   0.150    896
  Planarity :  0.006   0.062   1021
  Dihedral  :  7.929  57.913    959
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 12.99 %
    Favored  : 85.23 %
  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: -3.27 (0.27), residues: 693
  helix: -2.82 (0.20), residues: 349
  sheet: -1.98 (0.55), residues: 72
  loop : -0.93 (0.36), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 198 
 HIS   0.005   0.001   HIS A 256 
 PHE   0.012   0.001   PHE A 286 
 TYR   0.016   0.001   TYR A 162 
 ARG   0.004   0.001   ARG A 683 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00248 (    3)
  link_NAG-ASN         : angle       0.86264 (    9)
  link_BETA1-4         : bond        0.00170 (    1)
  link_BETA1-4         : angle       1.10930 (    3)
  hydrogen bonds       : bond        0.03641 (  228)
  hydrogen bonds       : angle       5.44799 (  651)
  SS BOND              : bond        0.00252 (    1)
  SS BOND              : angle       0.57028 (    2)
  covalent geometry    : bond        0.00298 ( 6044)
  covalent geometry    : angle       0.55683 ( 8208)

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

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

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 78
  time to evaluate  : 0.738 
Fit side-chains
   revert: symmetry clash
REVERT: A  104 LEU cc_start: 0.8313 (mm) cc_final: 0.8020 (mm)
REVERT: A  422 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7275 (mm-30)
REVERT: A  459 ASN cc_start: 0.8369 (m-40) cc_final: 0.7281 (t0)
REVERT: A  475 ASP cc_start: 0.8372 (m-30) cc_final: 0.8152 (m-30)
REVERT: A  569 LYS cc_start: 0.8141 (ttpp) cc_final: 0.7679 (tppt)
REVERT: A  612 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.5953 (mp0)
REVERT: A  689 LEU cc_start: 0.8606 (tt) cc_final: 0.7919 (mp)
REVERT: A  713 LEU cc_start: 0.7742 (mt) cc_final: 0.7481 (mm)
  outliers start: 11
  outliers final: 3
  residues processed: 82
  average time/residue: 1.5791
  time to fit residues: 136.1112
Evaluate side-chains
  68 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 64
  time to evaluate  : 0.649 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  312 SER
Chi-restraints excluded: chain A residue  494 SER
Chi-restraints excluded: chain A residue  602 VAL
Chi-restraints excluded: chain A residue  612 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 32 optimal weight:    3.9990
   chunk 39 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 66 optimal weight:    0.0470
   chunk 41 optimal weight:    0.9990
   chunk 44 optimal weight:    2.9990
   chunk 20 optimal weight:    5.9990
   chunk 38 optimal weight:    0.9980
   chunk 40 optimal weight:    0.8980
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.9882

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

Flipped N/Q/H residues before XYZ refinement:
A 187 ASN
A 354 GLN
A 479 GLN
B  90 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.142275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.110915 restraints weight = 6844.191|
|-----------------------------------------------------------------------------|
r_work (start): 0.3134 rms_B_bonded: 1.61
r_work: 0.3022 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.2905 rms_B_bonded: 3.33 restraints_weight: 0.2500
r_work (final): 0.2905
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8332
moved from start:          0.2215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   6049  Z= 0.165
  Angle     :  0.555   7.708   8222  Z= 0.280
  Chirality :  0.041   0.159    896
  Planarity :  0.005   0.055   1021
  Dihedral  :  7.269  59.146    959
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 13.80 %
    Favored  : 83.60 %
  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: -1.91 (0.30), residues: 693
  helix: -1.59 (0.25), residues: 347
  sheet: -1.44 (0.56), residues: 68
  loop : -0.46 (0.38), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 198 
 HIS   0.005   0.001   HIS A 256 
 PHE   0.016   0.001   PHE A 286 
 TYR   0.015   0.001   TYR A 162 
 ARG   0.004   0.000   ARG A 108 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00312 (    3)
  link_NAG-ASN         : angle       1.05024 (    9)
  link_BETA1-4         : bond        0.00242 (    1)
  link_BETA1-4         : angle       1.52525 (    3)
  hydrogen bonds       : bond        0.03225 (  228)
  hydrogen bonds       : angle       4.74665 (  651)
  SS BOND              : bond        0.00278 (    1)
  SS BOND              : angle       0.43494 (    2)
  covalent geometry    : bond        0.00396 ( 6044)
  covalent geometry    : angle       0.55319 ( 8208)

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

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

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 70
  time to evaluate  : 0.589 
Fit side-chains
REVERT: A  104 LEU cc_start: 0.8334 (mm) cc_final: 0.8054 (mm)
REVERT: A  422 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7163 (mm-30)
REVERT: A  459 ASN cc_start: 0.8364 (m-40) cc_final: 0.7202 (t0)
REVERT: A  475 ASP cc_start: 0.8403 (m-30) cc_final: 0.8137 (m-30)
REVERT: A  554 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.7520 (tt0)
REVERT: A  569 LYS cc_start: 0.8143 (ttpp) cc_final: 0.7663 (tppt)
REVERT: B   44 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7611 (mt-10)
  outliers start: 16
  outliers final: 4
  residues processed: 80
  average time/residue: 1.1604
  time to fit residues: 97.5993
Evaluate side-chains
  69 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 64
  time to evaluate  : 0.678 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  233 SER
Chi-restraints excluded: chain A residue  494 SER
Chi-restraints excluded: chain A residue  554 GLN
Chi-restraints excluded: chain A residue  602 VAL
Chi-restraints excluded: chain A residue  708 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 66 optimal weight:    2.9990
   chunk 51 optimal weight:    5.9990
   chunk 50 optimal weight:    0.5980
   chunk 38 optimal weight:    3.9990
   chunk 0 optimal weight:    7.9990
   chunk 45 optimal weight:    0.0970
   chunk 8 optimal weight:    0.0870
   chunk 6 optimal weight:    0.9980
   chunk 34 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 20 optimal weight:    5.9990
   overall best weight:    0.7558

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

Flipped N/Q/H residues before XYZ refinement:
A 187 ASN
A 479 GLN
B  90 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.155982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.124425 restraints weight = 6823.588|
|-----------------------------------------------------------------------------|
r_work (start): 0.3139 rms_B_bonded: 1.64
r_work: 0.2997 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.2864 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.2864
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8270
moved from start:          0.2452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6049  Z= 0.132
  Angle     :  0.513   8.731   8222  Z= 0.258
  Chirality :  0.040   0.184    896
  Planarity :  0.004   0.051   1021
  Dihedral  :  6.909  60.552    959
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 15.26 %
    Favored  : 82.79 %
  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: -1.36 (0.31), residues: 693
  helix: -1.05 (0.26), residues: 350
  sheet: -1.23 (0.58), residues: 68
  loop : -0.31 (0.38), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 198 
 HIS   0.004   0.001   HIS A 256 
 PHE   0.015   0.001   PHE A 286 
 TYR   0.014   0.001   TYR A 162 
 ARG   0.003   0.000   ARG A 108 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00265 (    3)
  link_NAG-ASN         : angle       1.08652 (    9)
  link_BETA1-4         : bond        0.00325 (    1)
  link_BETA1-4         : angle       1.37967 (    3)
  hydrogen bonds       : bond        0.02819 (  228)
  hydrogen bonds       : angle       4.41766 (  651)
  SS BOND              : bond        0.00251 (    1)
  SS BOND              : angle       0.45190 (    2)
  covalent geometry    : bond        0.00316 ( 6044)
  covalent geometry    : angle       0.51149 ( 8208)

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

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

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 70
  time to evaluate  : 0.601 
Fit side-chains
REVERT: A   36 LYS cc_start: 0.7628 (ttpp) cc_final: 0.7191 (mttm)
REVERT: A  104 LEU cc_start: 0.8267 (mm) cc_final: 0.7989 (mm)
REVERT: A  422 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7046 (mm-30)
REVERT: A  459 ASN cc_start: 0.8372 (m-40) cc_final: 0.8169 (m-40)
REVERT: A  475 ASP cc_start: 0.8396 (m-30) cc_final: 0.8124 (m-30)
REVERT: A  554 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.7504 (tt0)
REVERT: A  569 LYS cc_start: 0.8040 (ttpp) cc_final: 0.7521 (tppt)
REVERT: A  575 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.7006 (mp0)
REVERT: A  680 ARG cc_start: 0.7436 (OUTLIER) cc_final: 0.6449 (mtp85)
  outliers start: 12
  outliers final: 7
  residues processed: 78
  average time/residue: 1.0677
  time to fit residues: 88.2478
Evaluate side-chains
  74 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 64
  time to evaluate  : 0.679 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue  233 SER
Chi-restraints excluded: chain A residue  494 SER
Chi-restraints excluded: chain A residue  554 GLN
Chi-restraints excluded: chain A residue  575 GLU
Chi-restraints excluded: chain A residue  602 VAL
Chi-restraints excluded: chain A residue  680 ARG
Chi-restraints excluded: chain A residue  708 LEU
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   86 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 54 optimal weight:    8.9990
   chunk 3 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   chunk 61 optimal weight:    4.9990
   chunk 24 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 57 optimal weight:    8.9990
   chunk 67 optimal weight:    0.8980
   chunk 1 optimal weight:    5.9990
   chunk 48 optimal weight:    0.9990
   chunk 52 optimal weight:    1.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
A 187 ASN
A 526 HIS
B  90 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.153079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.121876 restraints weight = 6764.409|
|-----------------------------------------------------------------------------|
r_work (start): 0.3097 rms_B_bonded: 1.61
r_work: 0.2958 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2825 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.2825
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8292
moved from start:          0.2573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060   6049  Z= 0.203
  Angle     :  0.578   9.109   8222  Z= 0.287
  Chirality :  0.043   0.179    896
  Planarity :  0.005   0.052   1021
  Dihedral  :  7.026  65.908    959
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 16.07 %
    Favored  : 81.33 %
  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: -1.12 (0.31), residues: 693
  helix: -0.88 (0.26), residues: 351
  sheet: -1.02 (0.57), residues: 72
  loop : -0.15 (0.39), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 198 
 HIS   0.005   0.001   HIS A 160 
 PHE   0.015   0.001   PHE A 286 
 TYR   0.016   0.002   TYR A 162 
 ARG   0.003   0.000   ARG A 108 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00287 (    3)
  link_NAG-ASN         : angle       1.35008 (    9)
  link_BETA1-4         : bond        0.00035 (    1)
  link_BETA1-4         : angle       1.66571 (    3)
  hydrogen bonds       : bond        0.03059 (  228)
  hydrogen bonds       : angle       4.41885 (  651)
  SS BOND              : bond        0.00300 (    1)
  SS BOND              : angle       0.44838 (    2)
  covalent geometry    : bond        0.00497 ( 6044)
  covalent geometry    : angle       0.57542 ( 8208)

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

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

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 68
  time to evaluate  : 0.664 
Fit side-chains
REVERT: A   36 LYS cc_start: 0.7623 (ttpp) cc_final: 0.7146 (mttm)
REVERT: A  104 LEU cc_start: 0.8279 (mm) cc_final: 0.7997 (mm)
REVERT: A  422 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7008 (mm-30)
REVERT: A  459 ASN cc_start: 0.8371 (m-40) cc_final: 0.8151 (m-40)
REVERT: A  475 ASP cc_start: 0.8455 (m-30) cc_final: 0.8196 (m-30)
REVERT: A  541 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7625 (tp30)
REVERT: A  554 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.7554 (tt0)
REVERT: A  569 LYS cc_start: 0.8055 (ttpp) cc_final: 0.7563 (tppt)
REVERT: A  575 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.7072 (mp0)
REVERT: B   44 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7447 (mt-10)
  outliers start: 16
  outliers final: 5
  residues processed: 78
  average time/residue: 1.1289
  time to fit residues: 92.7491
Evaluate side-chains
  71 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 63
  time to evaluate  : 0.592 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  233 SER
Chi-restraints excluded: chain A residue  494 SER
Chi-restraints excluded: chain A residue  541 GLU
Chi-restraints excluded: chain A residue  554 GLN
Chi-restraints excluded: chain A residue  575 GLU
Chi-restraints excluded: chain A residue  602 VAL
Chi-restraints excluded: chain A residue  713 LEU
Chi-restraints excluded: chain B residue   37 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 14 optimal weight:    0.6980
   chunk 52 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 59 optimal weight:   10.0000
   chunk 9 optimal weight:    0.5980
   chunk 40 optimal weight:    0.7980
   chunk 67 optimal weight:    3.9990
   chunk 58 optimal weight:    6.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
A 187 ASN
B  90 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.154194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.123191 restraints weight = 6653.016|
|-----------------------------------------------------------------------------|
r_work (start): 0.3117 rms_B_bonded: 1.60
r_work: 0.2979 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.2848 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.2848
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8294
moved from start:          0.2715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   6049  Z= 0.160
  Angle     :  0.531   8.850   8222  Z= 0.266
  Chirality :  0.041   0.168    896
  Planarity :  0.004   0.051   1021
  Dihedral  :  6.811  66.371    959
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 16.56 %
    Favored  : 81.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.84 (0.31), residues: 693
  helix: -0.61 (0.27), residues: 351
  sheet: -0.92 (0.57), residues: 72
  loop : -0.06 (0.39), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 198 
 HIS   0.005   0.001   HIS A 256 
 PHE   0.014   0.001   PHE A 286 
 TYR   0.015   0.001   TYR A 162 
 ARG   0.004   0.000   ARG A 108 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00296 (    3)
  link_NAG-ASN         : angle       1.23820 (    9)
  link_BETA1-4         : bond        0.00189 (    1)
  link_BETA1-4         : angle       1.53625 (    3)
  hydrogen bonds       : bond        0.02866 (  228)
  hydrogen bonds       : angle       4.27527 (  651)
  SS BOND              : bond        0.00282 (    1)
  SS BOND              : angle       0.42657 (    2)
  covalent geometry    : bond        0.00390 ( 6044)
  covalent geometry    : angle       0.52889 ( 8208)

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

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

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 66
  time to evaluate  : 0.730 
Fit side-chains
REVERT: A   36 LYS cc_start: 0.7635 (ttpp) cc_final: 0.7135 (mttm)
REVERT: A  104 LEU cc_start: 0.8330 (mm) cc_final: 0.8065 (mm)
REVERT: A  422 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7130 (mm-30)
REVERT: A  459 ASN cc_start: 0.8390 (m-40) cc_final: 0.8170 (m-40)
REVERT: A  475 ASP cc_start: 0.8430 (m-30) cc_final: 0.8167 (m-30)
REVERT: A  541 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7607 (tp30)
REVERT: A  554 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.7499 (tt0)
REVERT: A  569 LYS cc_start: 0.8040 (ttpp) cc_final: 0.7564 (tppt)
REVERT: A  575 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.7032 (mp0)
REVERT: A  680 ARG cc_start: 0.7462 (OUTLIER) cc_final: 0.6448 (mtp85)
REVERT: B   44 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7453 (mt-10)
  outliers start: 15
  outliers final: 7
  residues processed: 76
  average time/residue: 1.0903
  time to fit residues: 87.4438
Evaluate side-chains
  74 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 63
  time to evaluate  : 0.543 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  182 VAL
Chi-restraints excluded: chain A residue  233 SER
Chi-restraints excluded: chain A residue  494 SER
Chi-restraints excluded: chain A residue  541 GLU
Chi-restraints excluded: chain A residue  554 GLN
Chi-restraints excluded: chain A residue  575 GLU
Chi-restraints excluded: chain A residue  602 VAL
Chi-restraints excluded: chain A residue  680 ARG
Chi-restraints excluded: chain A residue  713 LEU
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   86 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 20 optimal weight:    5.9990
   chunk 55 optimal weight:    0.0970
   chunk 0 optimal weight:    7.9990
   chunk 14 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 63 optimal weight:    0.7980
   chunk 42 optimal weight:    0.8980
   chunk 49 optimal weight:    3.9990
   chunk 40 optimal weight:    0.6980
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
A 187 ASN
A 526 HIS
B  90 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.154565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.123191 restraints weight = 6752.268|
|-----------------------------------------------------------------------------|
r_work (start): 0.3117 rms_B_bonded: 1.65
r_work: 0.2976 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.2845 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.2845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8288
moved from start:          0.2805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   6049  Z= 0.147
  Angle     :  0.530   9.120   8222  Z= 0.263
  Chirality :  0.041   0.167    896
  Planarity :  0.004   0.051   1021
  Dihedral  :  6.687  66.729    959
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 16.88 %
    Favored  : 80.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.68 (0.32), residues: 693
  helix: -0.44 (0.28), residues: 351
  sheet: -1.07 (0.56), residues: 74
  loop :  0.04 (0.39), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 198 
 HIS   0.005   0.001   HIS A 256 
 PHE   0.014   0.001   PHE A 286 
 TYR   0.015   0.001   TYR A 285 
 ARG   0.003   0.000   ARG A 108 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00269 (    3)
  link_NAG-ASN         : angle       1.25237 (    9)
  link_BETA1-4         : bond        0.00243 (    1)
  link_BETA1-4         : angle       1.47095 (    3)
  hydrogen bonds       : bond        0.02811 (  228)
  hydrogen bonds       : angle       4.17447 (  651)
  SS BOND              : bond        0.00255 (    1)
  SS BOND              : angle       0.41497 (    2)
  covalent geometry    : bond        0.00358 ( 6044)
  covalent geometry    : angle       0.52854 ( 8208)

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

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

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 64
  time to evaluate  : 0.683 
Fit side-chains
REVERT: A   36 LYS cc_start: 0.7649 (ttpp) cc_final: 0.7160 (mttm)
REVERT: A  104 LEU cc_start: 0.8350 (mm) cc_final: 0.8105 (mm)
REVERT: A  422 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7058 (tp30)
REVERT: A  459 ASN cc_start: 0.8358 (m-40) cc_final: 0.8150 (m-40)
REVERT: A  475 ASP cc_start: 0.8394 (m-30) cc_final: 0.8141 (m-30)
REVERT: A  541 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7589 (tp30)
REVERT: A  554 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.7479 (tt0)
REVERT: A  569 LYS cc_start: 0.8007 (ttpp) cc_final: 0.7547 (tppt)
REVERT: A  575 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.6999 (mp0)
REVERT: A  680 ARG cc_start: 0.7457 (OUTLIER) cc_final: 0.6443 (mtp85)
  outliers start: 14
  outliers final: 7
  residues processed: 73
  average time/residue: 1.1120
  time to fit residues: 86.0451
Evaluate side-chains
  72 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 61
  time to evaluate  : 0.657 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  182 VAL
Chi-restraints excluded: chain A residue  233 SER
Chi-restraints excluded: chain A residue  494 SER
Chi-restraints excluded: chain A residue  520 LYS
Chi-restraints excluded: chain A residue  541 GLU
Chi-restraints excluded: chain A residue  554 GLN
Chi-restraints excluded: chain A residue  575 GLU
Chi-restraints excluded: chain A residue  602 VAL
Chi-restraints excluded: chain A residue  680 ARG
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   86 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 53 optimal weight:    2.9990
   chunk 32 optimal weight:    3.9990
   chunk 34 optimal weight:    0.8980
   chunk 20 optimal weight:    5.9990
   chunk 13 optimal weight:    0.9990
   chunk 63 optimal weight:    0.2980
   chunk 66 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9980
   chunk 39 optimal weight:    1.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
A 187 ASN
A 526 HIS
B  90 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.154928 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.123742 restraints weight = 6665.358|
|-----------------------------------------------------------------------------|
r_work (start): 0.3125 rms_B_bonded: 1.62
r_work: 0.2985 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.2853 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.2853
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8286
moved from start:          0.2888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6049  Z= 0.140
  Angle     :  0.518   8.117   8222  Z= 0.259
  Chirality :  0.041   0.166    896
  Planarity :  0.004   0.051   1021
  Dihedral  :  6.613  66.848    959
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 17.37 %
    Favored  : 80.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.58 (0.32), residues: 693
  helix: -0.34 (0.28), residues: 351
  sheet: -1.01 (0.56), residues: 74
  loop :  0.05 (0.39), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 198 
 HIS   0.005   0.001   HIS A 256 
 PHE   0.014   0.001   PHE A 286 
 TYR   0.014   0.001   TYR A 162 
 ARG   0.003   0.000   ARG A 108 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00263 (    3)
  link_NAG-ASN         : angle       1.23545 (    9)
  link_BETA1-4         : bond        0.00249 (    1)
  link_BETA1-4         : angle       1.43955 (    3)
  hydrogen bonds       : bond        0.02756 (  228)
  hydrogen bonds       : angle       4.11698 (  651)
  SS BOND              : bond        0.00261 (    1)
  SS BOND              : angle       0.41595 (    2)
  covalent geometry    : bond        0.00342 ( 6044)
  covalent geometry    : angle       0.51630 ( 8208)

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

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

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 62
  time to evaluate  : 0.797 
Fit side-chains
REVERT: A   36 LYS cc_start: 0.7676 (ttpp) cc_final: 0.7190 (mttm)
REVERT: A  104 LEU cc_start: 0.8357 (mm) cc_final: 0.8107 (mm)
REVERT: A  422 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7073 (tp30)
REVERT: A  459 ASN cc_start: 0.8358 (m-40) cc_final: 0.8153 (m-40)
REVERT: A  475 ASP cc_start: 0.8358 (m-30) cc_final: 0.8099 (m-30)
REVERT: A  541 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7572 (tp30)
REVERT: A  554 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.7465 (tt0)
REVERT: A  569 LYS cc_start: 0.7961 (ttpp) cc_final: 0.7466 (tppt)
REVERT: A  575 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.7007 (mp0)
REVERT: A  680 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.6457 (mtp85)
  outliers start: 14
  outliers final: 8
  residues processed: 72
  average time/residue: 1.2264
  time to fit residues: 93.5816
Evaluate side-chains
  73 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 61
  time to evaluate  : 0.602 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  182 VAL
Chi-restraints excluded: chain A residue  233 SER
Chi-restraints excluded: chain A residue  289 MET
Chi-restraints excluded: chain A residue  494 SER
Chi-restraints excluded: chain A residue  520 LYS
Chi-restraints excluded: chain A residue  541 GLU
Chi-restraints excluded: chain A residue  554 GLN
Chi-restraints excluded: chain A residue  575 GLU
Chi-restraints excluded: chain A residue  602 VAL
Chi-restraints excluded: chain A residue  680 ARG
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   86 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 6 optimal weight:    0.9980
   chunk 3 optimal weight:    0.7980
   chunk 15 optimal weight:    3.9990
   chunk 54 optimal weight:    1.9990
   chunk 44 optimal weight:    0.3980
   chunk 55 optimal weight:    0.0770
   chunk 28 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9980
   chunk 61 optimal weight:    0.7980
   chunk 25 optimal weight:    2.9990
   chunk 36 optimal weight:    4.9990
   overall best weight:    0.6138

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

Flipped N/Q/H residues before XYZ refinement:
A 187 ASN
A 526 HIS
B  90 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 = 0.156287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.125344 restraints weight = 6643.747|
|-----------------------------------------------------------------------------|
r_work (start): 0.3172 rms_B_bonded: 1.61
r_work: 0.3052 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.2929 rms_B_bonded: 3.42 restraints_weight: 0.2500
r_work (final): 0.2929
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8274
moved from start:          0.2958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6049  Z= 0.114
  Angle     :  0.502   8.116   8222  Z= 0.249
  Chirality :  0.040   0.157    896
  Planarity :  0.004   0.050   1021
  Dihedral  :  6.402  65.756    959
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 18.83 %
    Favored  : 79.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.30 (0.32), residues: 693
  helix: -0.02 (0.28), residues: 345
  sheet: -0.93 (0.57), residues: 74
  loop :  0.05 (0.38), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 315 
 HIS   0.004   0.001   HIS A 256 
 PHE   0.013   0.001   PHE A 286 
 TYR   0.014   0.001   TYR A 285 
 ARG   0.003   0.000   ARG A 108 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00260 (    3)
  link_NAG-ASN         : angle       1.17835 (    9)
  link_BETA1-4         : bond        0.00361 (    1)
  link_BETA1-4         : angle       1.34372 (    3)
  hydrogen bonds       : bond        0.02630 (  228)
  hydrogen bonds       : angle       4.01201 (  651)
  SS BOND              : bond        0.00225 (    1)
  SS BOND              : angle       0.39236 (    2)
  covalent geometry    : bond        0.00274 ( 6044)
  covalent geometry    : angle       0.49973 ( 8208)

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

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

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 66
  time to evaluate  : 0.686 
Fit side-chains
REVERT: A   36 LYS cc_start: 0.7709 (ttpp) cc_final: 0.7223 (mttm)
REVERT: A  104 LEU cc_start: 0.8419 (mm) cc_final: 0.8171 (mm)
REVERT: A  346 LYS cc_start: 0.8132 (mptt) cc_final: 0.7871 (pttt)
REVERT: A  422 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7159 (tp30)
REVERT: A  459 ASN cc_start: 0.8358 (m-40) cc_final: 0.8137 (m-40)
REVERT: A  475 ASP cc_start: 0.8275 (m-30) cc_final: 0.8021 (m-30)
REVERT: A  554 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.7483 (tt0)
REVERT: A  569 LYS cc_start: 0.8067 (ttpp) cc_final: 0.7601 (tppt)
REVERT: A  575 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.6966 (mp0)
REVERT: A  579 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.7464 (ttt)
REVERT: A  680 ARG cc_start: 0.7484 (OUTLIER) cc_final: 0.6481 (mtp85)
REVERT: B   95 ARG cc_start: 0.7940 (tpp-160) cc_final: 0.7448 (mtp180)
  outliers start: 10
  outliers final: 5
  residues processed: 73
  average time/residue: 1.0838
  time to fit residues: 83.8724
Evaluate side-chains
  71 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 62
  time to evaluate  : 0.639 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  233 SER
Chi-restraints excluded: chain A residue  494 SER
Chi-restraints excluded: chain A residue  520 LYS
Chi-restraints excluded: chain A residue  554 GLN
Chi-restraints excluded: chain A residue  575 GLU
Chi-restraints excluded: chain A residue  579 MET
Chi-restraints excluded: chain A residue  680 ARG
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   86 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 40 optimal weight:    0.5980
   chunk 31 optimal weight:    0.0870
   chunk 41 optimal weight:    0.8980
   chunk 2 optimal weight:    0.7980
   chunk 6 optimal weight:    0.1980
   chunk 8 optimal weight:    0.7980
   chunk 35 optimal weight:    2.9990
   chunk 49 optimal weight:    0.8980
   chunk 47 optimal weight:    0.7980
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.4958

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

Flipped N/Q/H residues before XYZ refinement:
A 526 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.157451 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.126470 restraints weight = 6708.623|
|-----------------------------------------------------------------------------|
r_work (start): 0.3166 rms_B_bonded: 1.63
r_work: 0.3026 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.2894 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.2894
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8254
moved from start:          0.3078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   6049  Z= 0.104
  Angle     :  0.490   7.978   8222  Z= 0.244
  Chirality :  0.039   0.152    896
  Planarity :  0.004   0.050   1021
  Dihedral  :  6.178  65.001    958
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 19.32 %
    Favored  : 79.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.08 (0.32), residues: 693
  helix:  0.21 (0.28), residues: 345
  sheet: -0.83 (0.57), residues: 74
  loop :  0.07 (0.38), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 257 
 HIS   0.004   0.001   HIS A 256 
 PHE   0.014   0.001   PHE A 286 
 TYR   0.014   0.001   TYR A 162 
 ARG   0.003   0.000   ARG A 108 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00262 (    3)
  link_NAG-ASN         : angle       1.10815 (    9)
  link_BETA1-4         : bond        0.00349 (    1)
  link_BETA1-4         : angle       1.25947 (    3)
  hydrogen bonds       : bond        0.02538 (  228)
  hydrogen bonds       : angle       3.92113 (  651)
  SS BOND              : bond        0.00228 (    1)
  SS BOND              : angle       0.38438 (    2)
  covalent geometry    : bond        0.00248 ( 6044)
  covalent geometry    : angle       0.48829 ( 8208)

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

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

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 66
  time to evaluate  : 0.597 
Fit side-chains
REVERT: A   36 LYS cc_start: 0.7728 (ttpp) cc_final: 0.7200 (mttm)
REVERT: A  104 LEU cc_start: 0.8378 (mm) cc_final: 0.8147 (mm)
REVERT: A  422 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7120 (tp30)
REVERT: A  459 ASN cc_start: 0.8359 (m-40) cc_final: 0.8133 (m-40)
REVERT: A  475 ASP cc_start: 0.8307 (m-30) cc_final: 0.8004 (m-30)
REVERT: A  554 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.7479 (tt0)
REVERT: A  569 LYS cc_start: 0.8057 (ttpp) cc_final: 0.7568 (tppt)
REVERT: A  575 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6906 (mp0)
REVERT: A  680 ARG cc_start: 0.7452 (OUTLIER) cc_final: 0.6460 (mtp85)
REVERT: B   95 ARG cc_start: 0.7958 (tpp-160) cc_final: 0.7409 (mtp180)
  outliers start: 10
  outliers final: 6
  residues processed: 74
  average time/residue: 1.1505
  time to fit residues: 89.5769
Evaluate side-chains
  71 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 62
  time to evaluate  : 0.610 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  182 VAL
Chi-restraints excluded: chain A residue  233 SER
Chi-restraints excluded: chain A residue  494 SER
Chi-restraints excluded: chain A residue  554 GLN
Chi-restraints excluded: chain A residue  575 GLU
Chi-restraints excluded: chain A residue  579 MET
Chi-restraints excluded: chain A residue  680 ARG
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   86 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 25 optimal weight:    0.7980
   chunk 60 optimal weight:    0.0770
   chunk 32 optimal weight:    0.9980
   chunk 53 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 64 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9990
   chunk 54 optimal weight:    3.9990
   chunk 30 optimal weight:    0.4980
   chunk 21 optimal weight:    5.9990
   overall best weight:    0.6740

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

Flipped N/Q/H residues before XYZ refinement:
A 354 GLN
A 517 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.156504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.125298 restraints weight = 6715.215|
|-----------------------------------------------------------------------------|
r_work (start): 0.3153 rms_B_bonded: 1.65
r_work: 0.3032 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.2908 rms_B_bonded: 3.49 restraints_weight: 0.2500
r_work (final): 0.2908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8263
moved from start:          0.3090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6049  Z= 0.122
  Angle     :  0.506   7.882   8222  Z= 0.251
  Chirality :  0.040   0.157    896
  Planarity :  0.004   0.050   1021
  Dihedral  :  6.205  65.781    958
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 19.64 %
    Favored  : 78.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.01 (0.32), residues: 693
  helix:  0.26 (0.28), residues: 346
  sheet: -0.71 (0.57), residues: 74
  loop :  0.10 (0.38), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 257 
 HIS   0.004   0.001   HIS A 256 
 PHE   0.014   0.001   PHE A 286 
 TYR   0.015   0.001   TYR A 285 
 ARG   0.003   0.000   ARG A 476 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00261 (    3)
  link_NAG-ASN         : angle       1.14936 (    9)
  link_BETA1-4         : bond        0.00319 (    1)
  link_BETA1-4         : angle       1.31556 (    3)
  hydrogen bonds       : bond        0.02626 (  228)
  hydrogen bonds       : angle       3.94448 (  651)
  SS BOND              : bond        0.00236 (    1)
  SS BOND              : angle       0.41378 (    2)
  covalent geometry    : bond        0.00295 ( 6044)
  covalent geometry    : angle       0.50436 ( 8208)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4848.94 seconds
wall clock time: 84 minutes 52.47 seconds (5092.47 seconds total)