Starting phenix.real_space_refine
on Fri Aug 22 19:40:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qey_18379/08_2025/8qey_18379.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qey_18379/08_2025/8qey_18379.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8qey_18379/08_2025/8qey_18379.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qey_18379/08_2025/8qey_18379.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qey_18379/08_2025/8qey_18379.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qey_18379/08_2025/8qey_18379.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      31      5.16       5
     C    4754      2.51       5
     N    1185      2.21       5
     O    1336      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7306
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 3462
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 449, 3462
          Classifications: {'peptide': 449}
          Link IDs: {'PTRANS': 22, 'TRANS': 426}
    Chain: "B"
      Number of atoms: 3650
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 469, 3650
          Classifications: {'peptide': 469}
          Link IDs: {'PTRANS': 22, 'TRANS': 446}
    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: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "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: "A"
      Number of atoms: 85
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 85
          Unusual residues: {'AJP': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 1.58, per 1000 atoms: 0.22
  Number of scatterers: 7306
  At special positions: 0
  Unit cell: (94.734, 83.931, 131.298, 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      31     16.00
     O    1336      8.00
     N    1185      7.00
     C    4754      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 154 " - pdb=" SG  CYS B 109 " 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 D   2 " - " BMA D   3 "
      " NAG E   1 " - " NAG E   2 "
    NAG-ASN
      " NAG B 601 " - " ASN B 264 "
      " NAG C   1 " - " ASN B 323 "
      " NAG D   1 " - " ASN B 280 "
      " NAG E   1 " - " ASN B 405 "
  Time building additional restraints: 0.43
  Conformation dependent library (CDL) restraints added in 389.5 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1674

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 4 sheets defined
      58.3% alpha, 4.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 41 through 54
      removed outlier: 3.616A  pdb=" N   ALA A  45 " --> pdb=" O   GLY A  41 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 56 through 69
      removed outlier: 4.019A  pdb=" N   ILE A  60 " --> pdb=" O   SER A  56 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   SER A  61 " --> pdb=" O   GLY A  57 " (cutoff:3.500A)
      Proline residue:  A  62  - end of helix
    Processing helix  chain 'A' and resid 74 through 99
      removed outlier: 3.638A  pdb=" N   GLY A  83 " --> pdb=" O   TRP A  79 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 106 through 113
      removed outlier: 4.332A  pdb=" N   VAL A 110 " --> pdb=" O   ASP A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 114 through 130
      removed outlier: 4.434A  pdb=" N   ALA A 118 " --> pdb=" O   PHE A 114 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   GLY A 119 " --> pdb=" O   GLY A 115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 148
    Processing helix  chain 'A' and resid 157 through 177
      removed outlier: 3.570A  pdb=" N   SER A 161 " --> pdb=" O   PRO A 157 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 210
      removed outlier: 4.048A  pdb=" N   PHE A 210 " --> pdb=" O   LEU A 206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 218 through 222
    Processing helix  chain 'A' and resid 230 through 245
      removed outlier: 3.713A  pdb=" N   GLN A 240 " --> pdb=" O   LEU A 236 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   GLY A 241 " --> pdb=" O   ALA A 237 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 257
      removed outlier: 3.652A  pdb=" N   THR A 255 " --> pdb=" O   LEU A 251 " (cutoff:3.500A)
      removed outlier: 4.324A  pdb=" N   GLU A 256 " --> pdb=" O   ASN A 252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 271
    Processing helix  chain 'A' and resid 272 through 290
      removed outlier: 3.670A  pdb=" N   ALA A 290 " --> pdb=" O   ALA A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 292 through 298
      removed outlier: 3.817A  pdb=" N   LEU A 296 " --> pdb=" O   SER A 292 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   LEU A 297 " --> pdb=" O   PRO A 293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 304 through 310
      removed outlier: 3.868A  pdb=" N   LEU A 310 " --> pdb=" O   PHE A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 348
      Proline residue:  A 319  - end of helix
      removed outlier: 3.535A  pdb=" N   GLU A 347 " --> pdb=" O   SER A 343 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   GLY A 348 " --> pdb=" O   GLY A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 381
      removed outlier: 3.637A  pdb=" N   LEU A 368 " --> pdb=" O   PRO A 364 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   LEU A 369 " --> pdb=" O   ILE A 365 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   VAL A 370 " --> pdb=" O   PRO A 366 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   ALA A 374 " --> pdb=" O   VAL A 370 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   THR A 375 " --> pdb=" O   CYS A 371 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   ILE A 378 " --> pdb=" O   ALA A 374 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 413
    Processing helix  chain 'A' and resid 425 through 442
    Processing helix  chain 'A' and resid 445 through 458
      removed outlier: 3.806A  pdb=" N   CYS A 449 " --> pdb=" O   GLU A 445 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   VAL A 451 " --> pdb=" O   MET A 447 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 458 through 469
      removed outlier: 4.156A  pdb=" N   ILE A 462 " --> pdb=" O   THR A 458 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 474 through 479
    Processing helix  chain 'A' and resid 482 through 487
      removed outlier: 4.287A  pdb=" N   TRP A 486 " --> pdb=" O   SER A 482 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 65 through 73
    Processing helix  chain 'B' and resid 74 through 105
    Processing helix  chain 'B' and resid 128 through 134
    Processing helix  chain 'B' and resid 139 through 145
      removed outlier: 4.105A  pdb=" N   LYS B 144 " --> pdb=" O   ALA B 141 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 146 through 153
    Processing helix  chain 'B' and resid 185 through 199
    Processing helix  chain 'B' and resid 221 through 240
      removed outlier: 4.169A  pdb=" N   VAL B 225 " --> pdb=" O   GLN B 221 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   LYS B 228 " --> pdb=" O   THR B 224 " (cutoff:3.500A)
      removed outlier: 4.224A  pdb=" N   VAL B 229 " --> pdb=" O   VAL B 225 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   GLU B 234 " --> pdb=" O   LYS B 230 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 254 through 270
    Processing helix  chain 'B' and resid 283 through 291
    Processing helix  chain 'B' and resid 310 through 326
    Processing helix  chain 'B' and resid 348 through 357
      removed outlier: 4.472A  pdb=" N   LEU B 354 " --> pdb=" O   ARG B 350 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 407 through 414
      removed outlier: 3.565A  pdb=" N   ASP B 414 " --> pdb=" O   GLY B 410 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 417 through 432
      removed outlier: 3.598A  pdb=" N   SER B 430 " --> pdb=" O   SER B 426 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   LYS B 431 " --> pdb=" O   ASP B 427 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   GLU B 432 " --> pdb=" O   GLN B 428 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 433 through 438
    Processing sheet with id=AA1, first strand: chain 'B' and resid 123 through 125
      removed outlier: 6.662A  pdb=" N   TRP B 332 " --> pdb=" O   VAL B 364 " (cutoff:3.500A)
      removed outlier: 8.668A  pdb=" N   SER B 366 " --> pdb=" O   TRP B 332 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 164 through 165
      removed outlier: 4.218A  pdb=" N   LYS B 165 " --> pdb=" O   ASP B 175 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ASP B 175 " --> pdb=" O   LYS B 165 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 205 through 206
      removed outlier: 7.050A  pdb=" N   LEU B 205 " --> pdb=" O   GLN B 245 " (cutoff:3.500A)
      removed outlier: 6.104A  pdb=" N   PHE B 244 " --> pdb=" O   ILE B 276 " (cutoff:3.500A)
      removed outlier: 7.693A  pdb=" N   GLY B 278 " --> pdb=" O   PHE B 244 " (cutoff:3.500A)
      removed outlier: 6.656A  pdb=" N   VAL B 246 " --> pdb=" O   GLY B 278 " (cutoff:3.500A)
      removed outlier: 6.148A  pdb=" N   ALA B 277 " --> pdb=" O   THR B 300 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'B' and resid 441 through 442
      removed outlier: 3.593A  pdb=" N   HIS B 441 " --> pdb=" O   ILE B 453 " (cutoff:3.500A)
      removed outlier: 6.259A  pdb=" N   ARG B 524 " --> pdb=" O   LEU B 494 " (cutoff:3.500A)
      removed outlier: 5.310A  pdb=" N   LEU B 494 " --> pdb=" O   ARG B 524 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   ALA B 492 " --> pdb=" O   LEU B 508 " (cutoff:3.500A)

    363 hydrogen bonds defined for protein.
    1068 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: 0.90

  Time building geometry restraints manager: 0.57 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1339
        1.33 -     1.45: 1942
        1.45 -     1.57: 4168
        1.57 -     1.69: 2
        1.69 -     1.82: 49
  Bond restraints: 7500
  Sorted by residual:
  bond pdb=" CB  PRO B 526 "
       pdb=" CG  PRO B 526 "
    ideal  model  delta    sigma   weight residual
    1.492  1.608 -0.116 5.00e-02 4.00e+02 5.35e+00
  bond pdb=" C65 AJP A 601 "
       pdb=" O64 AJP A 601 "
    ideal  model  delta    sigma   weight residual
    1.373  1.407 -0.034 2.00e-02 2.50e+03 2.95e+00
  bond pdb=" C1  BMA D   3 "
       pdb=" C2  BMA D   3 "
    ideal  model  delta    sigma   weight residual
    1.519  1.553 -0.034 2.00e-02 2.50e+03 2.81e+00
  bond pdb=" CB  PRO A 149 "
       pdb=" CG  PRO A 149 "
    ideal  model  delta    sigma   weight residual
    1.492  1.575 -0.083 5.00e-02 4.00e+02 2.75e+00
  bond pdb=" C1  NAG C   2 "
       pdb=" O5  NAG C   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.438 -0.032 2.00e-02 2.50e+03 2.50e+00
  ... (remaining 7495 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.64: 10103
        3.64 -     7.28: 105
        7.28 -    10.92: 16
       10.92 -    14.56: 3
       14.56 -    18.20: 1
  Bond angle restraints: 10228
  Sorted by residual:
  angle pdb=" CA  PRO B 526 "
        pdb=" N   PRO B 526 "
        pdb=" CD  PRO B 526 "
      ideal   model   delta    sigma   weight residual
     112.00  102.58    9.42 1.40e+00 5.10e-01 4.53e+01
  angle pdb=" CA  PRO A 149 "
        pdb=" N   PRO A 149 "
        pdb=" CD  PRO A 149 "
      ideal   model   delta    sigma   weight residual
     112.00  103.38    8.62 1.40e+00 5.10e-01 3.79e+01
  angle pdb=" CA  LEU A 310 "
        pdb=" CB  LEU A 310 "
        pdb=" CG  LEU A 310 "
      ideal   model   delta    sigma   weight residual
     116.30  134.50  -18.20 3.50e+00 8.16e-02 2.70e+01
  angle pdb=" C   ILE A 129 "
        pdb=" N   MET A 130 "
        pdb=" CA  MET A 130 "
      ideal   model   delta    sigma   weight residual
     122.58  113.49    9.09 2.07e+00 2.33e-01 1.93e+01
  angle pdb=" CA  TYR A 337 "
        pdb=" CB  TYR A 337 "
        pdb=" CG  TYR A 337 "
      ideal   model   delta    sigma   weight residual
     113.90  120.98   -7.08 1.80e+00 3.09e-01 1.55e+01
  ... (remaining 10223 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.22: 4035
       22.22 -    44.43: 472
       44.43 -    66.65: 89
       66.65 -    88.86: 28
       88.86 -   111.08: 12
  Dihedral angle restraints: 4636
    sinusoidal: 2021
      harmonic: 2615
  Sorted by residual:
  dihedral pdb=" CA  LEU A 350 "
           pdb=" C   LEU A 350 "
           pdb=" N   PRO A 351 "
           pdb=" CA  PRO A 351 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -142.44  -37.56     0      5.00e+00 4.00e-02 5.64e+01
  dihedral pdb=" CB  CYS A 154 "
           pdb=" SG  CYS A 154 "
           pdb=" SG  CYS B 109 "
           pdb=" CB  CYS B 109 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -149.89   63.89     1      1.00e+01 1.00e-02 5.37e+01
  dihedral pdb=" CA  ILE A 100 "
           pdb=" C   ILE A 100 "
           pdb=" N   PRO A 101 "
           pdb=" CA  PRO A 101 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -152.05  -27.95     0      5.00e+00 4.00e-02 3.13e+01
  ... (remaining 4633 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.065: 1018
       0.065 -    0.130: 166
       0.130 -    0.196: 22
       0.196 -    0.261: 5
       0.261 -    0.326: 2
  Chirality restraints: 1213
  Sorted by residual:
  chirality pdb=" CG  LEU B 233 "
            pdb=" CB  LEU B 233 "
            pdb=" CD1 LEU B 233 "
            pdb=" CD2 LEU B 233 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.26   -0.33 2.00e-01 2.50e+01 2.66e+00
  chirality pdb=" C5  BMA D   3 "
            pdb=" C4  BMA D   3 "
            pdb=" C6  BMA D   3 "
            pdb=" O5  BMA D   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.55    0.27 2.00e-01 2.50e+01 1.86e+00
  chirality pdb=" C08 AJP A 601 "
            pdb=" C07 AJP A 601 "
            pdb=" C10 AJP A 601 "
            pdb=" O09 AJP A 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.56    2.82   -0.26 2.00e-01 2.50e+01 1.70e+00
  ... (remaining 1210 not shown)

  Planarity restraints: 1254
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 525 "    0.104 5.00e-02 4.00e+02   1.50e-01 3.60e+01
        pdb=" N   PRO B 526 "   -0.259 5.00e-02 4.00e+02
        pdb=" CA  PRO B 526 "    0.080 5.00e-02 4.00e+02
        pdb=" CD  PRO B 526 "    0.076 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 148 "    0.077 5.00e-02 4.00e+02   1.12e-01 2.01e+01
        pdb=" N   PRO A 149 "   -0.194 5.00e-02 4.00e+02
        pdb=" CA  PRO A 149 "    0.057 5.00e-02 4.00e+02
        pdb=" CD  PRO A 149 "    0.060 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 399 "    0.020 2.00e-02 2.50e+03   2.08e-02 8.68e+00
        pdb=" CG  TYR A 399 "   -0.052 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 399 "    0.014 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 399 "    0.013 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 399 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 399 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 399 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR A 399 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1251 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1790
        2.79 -     3.31: 7031
        3.31 -     3.84: 12106
        3.84 -     4.37: 12654
        4.37 -     4.90: 21712
  Nonbonded interactions: 55293
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B 367 "
            pdb=" O   PRO B 386 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" OH  TYR B 149 "
            pdb=" OE2 GLU B 370 "
     model   vdw
     2.289 3.040
  nonbonded pdb=" O   LYS B 315 "
            pdb=" OG1 THR B 319 "
     model   vdw
     2.289 3.040
  nonbonded pdb=" O   GLY A  57 "
            pdb=" OG  SER A  61 "
     model   vdw
     2.289 3.040
  nonbonded pdb=" O   VAL A 279 "
            pdb=" OG1 THR A 283 "
     model   vdw
     2.291 3.040
  ... (remaining 55288 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 'E'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.720
  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:          0.080
  Check model and map are aligned:         0.030
  Set scattering table:                    0.010
  Process input model:                     6.990
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.120
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7534
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.116   7509  Z= 0.213
  Angle     :  0.966  18.202  10254  Z= 0.453
  Chirality :  0.052   0.326   1213
  Planarity :  0.007   0.150   1250
  Dihedral  : 19.802 111.079   2959
  Min Nonbonded Distance : 2.258

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.78 %
    Favored  : 93.22 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  : 41.20 %
    Favored  : 57.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.09 (0.27), residues: 914
  helix:  0.30 (0.23), residues: 483
  sheet: -0.51 (0.67), residues: 59
  loop : -2.15 (0.30), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 346 
 TYR   0.052   0.002   TYR A 399 
 PHE   0.045   0.002   PHE A 440 
 TRP   0.020   0.001   TRP A 316 
 HIS   0.008   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00478 ( 7500)
  covalent geometry    : angle       0.95933 (10228)
  SS BOND              : bond        0.00098 (    1)
  SS BOND              : angle       1.90394 (    2)
  hydrogen bonds       : bond        0.12707 (  363)
  hydrogen bonds       : angle       5.85767 ( 1068)
  link_BETA1-4         : bond        0.00756 (    4)
  link_BETA1-4         : angle       3.11305 (   12)
  link_NAG-ASN         : bond        0.00074 (    4)
  link_NAG-ASN         : angle       1.77583 (   12)

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

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

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 155
  time to evaluate  : 0.194 
Fit side-chains
   revert: symmetry clash
REVERT: A  112 GLU cc_start: 0.7980 (tp30) cc_final: 0.7032 (tm-30)
REVERT: A  140 MET cc_start: 0.8817 (ttm) cc_final: 0.8589 (ttp)
REVERT: A  215 GLU cc_start: 0.7309 (mp0) cc_final: 0.6593 (pm20)
REVERT: A  221 ASN cc_start: 0.7800 (OUTLIER) cc_final: 0.7492 (p0)
  outliers start: 7
  outliers final: 2
  residues processed: 162
  average time/residue: 0.0596
  time to fit residues: 14.2346
Evaluate side-chains
  154 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 151
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  221 ASN
Chi-restraints excluded: chain B residue  357 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    4.9990
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    4.9990
   chunk 74 optimal weight:    0.9980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 264 ASN
** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 428 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.176145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.143892 restraints weight = 13139.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.143636 restraints weight = 9895.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.144813 restraints weight = 9879.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.145598 restraints weight = 7568.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.146237 restraints weight = 7026.714|
|-----------------------------------------------------------------------------|
r_work (final): 0.3698
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
moved from start:          0.0895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   7509  Z= 0.142
  Angle     :  0.684  10.232  10254  Z= 0.324
  Chirality :  0.041   0.207   1213
  Planarity :  0.005   0.091   1250
  Dihedral  : 11.751  96.548   1371
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.13 %
    Favored  : 93.87 %
  Rotamer:
    Outliers :  5.48 %
    Allowed  : 34.68 %
    Favored  : 59.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.29 (0.28), residues: 914
  helix:  1.03 (0.24), residues: 480
  sheet: -0.61 (0.64), residues: 55
  loop : -1.77 (0.32), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 470 
 TYR   0.036   0.002   TYR A 399 
 PHE   0.013   0.001   PHE A 393 
 TRP   0.010   0.001   TRP A 316 
 HIS   0.002   0.001   HIS B 441 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 7500)
  covalent geometry    : angle       0.67416 (10228)
  SS BOND              : bond        0.00150 (    1)
  SS BOND              : angle       1.24690 (    2)
  hydrogen bonds       : bond        0.04099 (  363)
  hydrogen bonds       : angle       4.67574 ( 1068)
  link_BETA1-4         : bond        0.00648 (    4)
  link_BETA1-4         : angle       3.15000 (   12)
  link_NAG-ASN         : bond        0.00143 (    4)
  link_NAG-ASN         : angle       1.63414 (   12)

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

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

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 161
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
REVERT: A  166 MET cc_start: 0.7529 (OUTLIER) cc_final: 0.7242 (mmm)
REVERT: A  215 GLU cc_start: 0.7420 (mp0) cc_final: 0.6853 (pm20)
REVERT: A  356 MET cc_start: 0.6430 (mpp) cc_final: 0.6089 (mpp)
REVERT: B  302 SER cc_start: 0.9404 (OUTLIER) cc_final: 0.9053 (t)
  outliers start: 42
  outliers final: 27
  residues processed: 186
  average time/residue: 0.0514
  time to fit residues: 14.5730
Evaluate side-chains
  182 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 153
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 ILE
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  143 SER
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  155 ILE
Chi-restraints excluded: chain A residue  166 MET
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  208 GLN
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  325 SER
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  396 TYR
Chi-restraints excluded: chain A residue  402 THR
Chi-restraints excluded: chain A residue  428 VAL
Chi-restraints excluded: chain A residue  464 PHE
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  207 LEU
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  290 LEU
Chi-restraints excluded: chain B residue  302 SER
Chi-restraints excluded: chain B residue  325 THR
Chi-restraints excluded: chain B residue  357 PHE
Chi-restraints excluded: chain B residue  373 LEU
Chi-restraints excluded: chain B residue  387 VAL
Chi-restraints excluded: chain B residue  453 ILE
Chi-restraints excluded: chain B residue  513 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 81 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 9 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 10 optimal weight:    0.4980
   chunk 26 optimal weight:    0.7980
   chunk 20 optimal weight:    1.9990
   chunk 30 optimal weight:   10.0000
   chunk 73 optimal weight:    2.9990
   chunk 89 optimal weight:    6.9990
   chunk 55 optimal weight:    6.9990
   overall best weight:    1.4586

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

Flipped N/Q/H residues before XYZ refinement:
** B 381 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 = 0.4052 r_free = 0.4052 target = 0.173601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.137719 restraints weight = 13811.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.139241 restraints weight = 10012.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.140805 restraints weight = 8145.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.141319 restraints weight = 6689.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.141728 restraints weight = 6406.431|
|-----------------------------------------------------------------------------|
r_work (final): 0.3679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
moved from start:          0.1621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7509  Z= 0.190
  Angle     :  0.723   9.405  10254  Z= 0.345
  Chirality :  0.043   0.236   1213
  Planarity :  0.005   0.073   1250
  Dihedral  : 10.396  86.542   1369
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 10.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  8.60 %
    Allowed  : 33.12 %
    Favored  : 58.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.05 (0.28), residues: 914
  helix:  1.21 (0.24), residues: 485
  sheet: -0.28 (0.66), residues: 61
  loop : -1.73 (0.32), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 470 
 TYR   0.030   0.002   TYR A 399 
 PHE   0.016   0.002   PHE A 327 
 TRP   0.012   0.001   TRP A 316 
 HIS   0.005   0.001   HIS B 119 

Details of bonding type rmsd
  covalent geometry    : bond        0.00436 ( 7500)
  covalent geometry    : angle       0.71233 (10228)
  SS BOND              : bond        0.00268 (    1)
  SS BOND              : angle       0.95679 (    2)
  hydrogen bonds       : bond        0.04530 (  363)
  hydrogen bonds       : angle       4.65107 ( 1068)
  link_BETA1-4         : bond        0.00588 (    4)
  link_BETA1-4         : angle       3.35987 (   12)
  link_NAG-ASN         : bond        0.00230 (    4)
  link_NAG-ASN         : angle       1.73172 (   12)

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

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

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 168
  time to evaluate  : 0.174 
Fit side-chains
   revert: symmetry clash
REVERT: A   63 LYS cc_start: 0.8948 (pptt) cc_final: 0.8374 (pttp)
REVERT: A  221 ASN cc_start: 0.8003 (OUTLIER) cc_final: 0.7464 (p0)
REVERT: A  356 MET cc_start: 0.6685 (mpp) cc_final: 0.6380 (mpp)
REVERT: A  360 ARG cc_start: 0.2121 (OUTLIER) cc_final: 0.0866 (ttp-170)
REVERT: B  237 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7923 (mm)
REVERT: B  336 GLN cc_start: 0.8724 (tp40) cc_final: 0.8238 (tp-100)
REVERT: B  432 GLU cc_start: 0.8098 (tp30) cc_final: 0.7831 (tp30)
  outliers start: 66
  outliers final: 37
  residues processed: 210
  average time/residue: 0.0510
  time to fit residues: 16.2039
Evaluate side-chains
  199 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 159
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  143 SER
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  154 CYS
Chi-restraints excluded: chain A residue  155 ILE
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  173 THR
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  208 GLN
Chi-restraints excluded: chain A residue  221 ASN
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  273 ILE
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  360 ARG
Chi-restraints excluded: chain A residue  372 CYS
Chi-restraints excluded: chain A residue  398 CYS
Chi-restraints excluded: chain A residue  402 THR
Chi-restraints excluded: chain A residue  423 ASN
Chi-restraints excluded: chain A residue  428 VAL
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  462 ILE
Chi-restraints excluded: chain B residue  150 LEU
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  207 LEU
Chi-restraints excluded: chain B residue  229 VAL
Chi-restraints excluded: chain B residue  237 LEU
Chi-restraints excluded: chain B residue  249 ILE
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  290 LEU
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  302 SER
Chi-restraints excluded: chain B residue  325 THR
Chi-restraints excluded: chain B residue  339 LEU
Chi-restraints excluded: chain B residue  357 PHE
Chi-restraints excluded: chain B residue  408 VAL
Chi-restraints excluded: chain B residue  417 SER
Chi-restraints excluded: chain B residue  453 ILE
Chi-restraints excluded: chain B residue  513 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 13 optimal weight:    5.9990
   chunk 35 optimal weight:    0.7980
   chunk 60 optimal weight:    0.0980
   chunk 52 optimal weight:    1.9990
   chunk 82 optimal weight:    0.8980
   chunk 36 optimal weight:    0.9980
   chunk 30 optimal weight:    4.9990
   chunk 20 optimal weight:    0.8980
   chunk 18 optimal weight:    1.9990
   chunk 84 optimal weight:    1.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 221 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.175488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.139267 restraints weight = 13987.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.142814 restraints weight = 9455.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.144680 restraints weight = 6828.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.144803 restraints weight = 5659.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.144856 restraints weight = 5540.638|
|-----------------------------------------------------------------------------|
r_work (final): 0.3695
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
moved from start:          0.1706

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7509  Z= 0.133
  Angle     :  0.678   7.831  10254  Z= 0.318
  Chirality :  0.042   0.271   1213
  Planarity :  0.004   0.062   1250
  Dihedral  :  9.635  77.550   1367
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  5.91 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  7.04 %
    Allowed  : 35.59 %
    Favored  : 57.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.15 (0.28), residues: 914
  helix:  1.35 (0.24), residues: 484
  sheet: -0.38 (0.67), residues: 56
  loop : -1.54 (0.33), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 470 
 TYR   0.025   0.002   TYR A 399 
 PHE   0.017   0.001   PHE A 464 
 TRP   0.011   0.001   TRP A 316 
 HIS   0.003   0.001   HIS B 313 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 7500)
  covalent geometry    : angle       0.66608 (10228)
  SS BOND              : bond        0.00132 (    1)
  SS BOND              : angle       0.95612 (    2)
  hydrogen bonds       : bond        0.03999 (  363)
  hydrogen bonds       : angle       4.47562 ( 1068)
  link_BETA1-4         : bond        0.00713 (    4)
  link_BETA1-4         : angle       3.39806 (   12)
  link_NAG-ASN         : bond        0.00147 (    4)
  link_NAG-ASN         : angle       1.67528 (   12)

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

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

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 163
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 LYS cc_start: 0.8855 (pptt) cc_final: 0.8208 (ptmm)
REVERT: A  221 ASN cc_start: 0.7937 (OUTLIER) cc_final: 0.7399 (p0)
REVERT: A  356 MET cc_start: 0.6735 (mpp) cc_final: 0.6461 (mpp)
REVERT: A  360 ARG cc_start: 0.2026 (OUTLIER) cc_final: 0.0928 (ttp-170)
REVERT: B  302 SER cc_start: 0.9372 (OUTLIER) cc_final: 0.8988 (t)
REVERT: B  336 GLN cc_start: 0.8674 (tp40) cc_final: 0.8273 (tp40)
  outliers start: 54
  outliers final: 36
  residues processed: 200
  average time/residue: 0.0492
  time to fit residues: 14.6326
Evaluate side-chains
  195 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 156
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  143 SER
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  154 CYS
Chi-restraints excluded: chain A residue  155 ILE
Chi-restraints excluded: chain A residue  168 CYS
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  208 GLN
Chi-restraints excluded: chain A residue  221 ASN
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  300 ASN
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  325 SER
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  360 ARG
Chi-restraints excluded: chain A residue  372 CYS
Chi-restraints excluded: chain A residue  396 TYR
Chi-restraints excluded: chain A residue  398 CYS
Chi-restraints excluded: chain A residue  423 ASN
Chi-restraints excluded: chain A residue  428 VAL
Chi-restraints excluded: chain B residue   85 LEU
Chi-restraints excluded: chain B residue  150 LEU
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  154 LYS
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  164 HIS
Chi-restraints excluded: chain B residue  207 LEU
Chi-restraints excluded: chain B residue  221 GLN
Chi-restraints excluded: chain B residue  230 LYS
Chi-restraints excluded: chain B residue  281 SER
Chi-restraints excluded: chain B residue  290 LEU
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  302 SER
Chi-restraints excluded: chain B residue  325 THR
Chi-restraints excluded: chain B residue  357 PHE
Chi-restraints excluded: chain B residue  417 SER
Chi-restraints excluded: chain B residue  453 ILE
Chi-restraints excluded: chain B residue  513 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 3 optimal weight:    0.4980
   chunk 55 optimal weight:    7.9990
   chunk 49 optimal weight:    0.4980
   chunk 56 optimal weight:    0.6980
   chunk 50 optimal weight:    1.9990
   chunk 74 optimal weight:    0.0670
   chunk 41 optimal weight:    4.9990
   chunk 35 optimal weight:    0.9980
   chunk 20 optimal weight:    0.5980
   chunk 37 optimal weight:   10.0000
   chunk 66 optimal weight:    0.6980
   overall best weight:    0.4718

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

Flipped N/Q/H residues before XYZ refinement:
** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 221 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.177250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.140801 restraints weight = 13911.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.141189 restraints weight = 9858.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.142560 restraints weight = 8125.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.143886 restraints weight = 7301.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.144094 restraints weight = 6718.886|
|-----------------------------------------------------------------------------|
r_work (final): 0.3675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.1777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7509  Z= 0.121
  Angle     :  0.686  13.931  10254  Z= 0.317
  Chirality :  0.042   0.233   1213
  Planarity :  0.004   0.057   1250
  Dihedral  :  9.005  66.873   1367
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  6.65 %
    Allowed  : 36.11 %
    Favored  : 57.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.34 (0.29), residues: 914
  helix:  1.52 (0.24), residues: 485
  sheet: -0.25 (0.68), residues: 56
  loop : -1.49 (0.33), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 418 
 TYR   0.012   0.001   TYR A 385 
 PHE   0.016   0.001   PHE B 269 
 TRP   0.011   0.001   TRP A 316 
 HIS   0.002   0.000   HIS B 313 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 7500)
  covalent geometry    : angle       0.67435 (10228)
  SS BOND              : bond        0.00150 (    1)
  SS BOND              : angle       0.95708 (    2)
  hydrogen bonds       : bond        0.03789 (  363)
  hydrogen bonds       : angle       4.39384 ( 1068)
  link_BETA1-4         : bond        0.00759 (    4)
  link_BETA1-4         : angle       3.42728 (   12)
  link_NAG-ASN         : bond        0.00117 (    4)
  link_NAG-ASN         : angle       1.61058 (   12)

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

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

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 167
  time to evaluate  : 0.215 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 LYS cc_start: 0.8761 (pptt) cc_final: 0.8246 (pttp)
REVERT: A  140 MET cc_start: 0.8766 (ttm) cc_final: 0.8552 (ttp)
REVERT: A  221 ASN cc_start: 0.7854 (OUTLIER) cc_final: 0.7269 (p0)
REVERT: A  258 MET cc_start: 0.6689 (OUTLIER) cc_final: 0.5708 (mmt)
REVERT: A  270 PHE cc_start: 0.6062 (m-80) cc_final: 0.5465 (m-80)
REVERT: A  294 GLN cc_start: 0.9164 (tp40) cc_final: 0.8936 (mm-40)
REVERT: A  360 ARG cc_start: 0.1856 (OUTLIER) cc_final: 0.1272 (ttp-170)
REVERT: B  237 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8373 (mm)
REVERT: B  302 SER cc_start: 0.9358 (OUTLIER) cc_final: 0.9023 (t)
REVERT: B  336 GLN cc_start: 0.8627 (tp40) cc_final: 0.8050 (tp-100)
  outliers start: 51
  outliers final: 34
  residues processed: 201
  average time/residue: 0.0575
  time to fit residues: 16.5683
Evaluate side-chains
  200 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 161
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  154 CYS
Chi-restraints excluded: chain A residue  155 ILE
Chi-restraints excluded: chain A residue  168 CYS
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  208 GLN
Chi-restraints excluded: chain A residue  221 ASN
Chi-restraints excluded: chain A residue  258 MET
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  300 ASN
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  360 ARG
Chi-restraints excluded: chain A residue  396 TYR
Chi-restraints excluded: chain A residue  398 CYS
Chi-restraints excluded: chain A residue  423 ASN
Chi-restraints excluded: chain A residue  464 PHE
Chi-restraints excluded: chain B residue   85 LEU
Chi-restraints excluded: chain B residue  150 LEU
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  154 LYS
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  156 LYS
Chi-restraints excluded: chain B residue  164 HIS
Chi-restraints excluded: chain B residue  207 LEU
Chi-restraints excluded: chain B residue  230 LYS
Chi-restraints excluded: chain B residue  237 LEU
Chi-restraints excluded: chain B residue  249 ILE
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  281 SER
Chi-restraints excluded: chain B residue  290 LEU
Chi-restraints excluded: chain B residue  302 SER
Chi-restraints excluded: chain B residue  357 PHE
Chi-restraints excluded: chain B residue  417 SER
Chi-restraints excluded: chain B residue  453 ILE
Chi-restraints excluded: chain B residue  465 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 43 optimal weight:    8.9990
   chunk 41 optimal weight:    0.6980
   chunk 83 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9980
   chunk 40 optimal weight:    3.9990
   chunk 58 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 47 optimal weight:    2.9990
   chunk 76 optimal weight:    5.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** B 166 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 = 0.4078 r_free = 0.4078 target = 0.175947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.139964 restraints weight = 13892.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.140493 restraints weight = 9460.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.141642 restraints weight = 7703.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.142266 restraints weight = 7079.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.142841 restraints weight = 6481.867|
|-----------------------------------------------------------------------------|
r_work (final): 0.3683
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7782
moved from start:          0.1901

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7509  Z= 0.139
  Angle     :  0.701  12.987  10254  Z= 0.326
  Chirality :  0.043   0.304   1213
  Planarity :  0.004   0.054   1250
  Dihedral  :  8.434  57.299   1367
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 9.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.46 %
    Favored  : 93.54 %
  Rotamer:
    Outliers :  7.56 %
    Allowed  : 35.20 %
    Favored  : 57.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.38 (0.29), residues: 914
  helix:  1.60 (0.24), residues: 483
  sheet: -0.21 (0.68), residues: 56
  loop : -1.54 (0.32), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 418 
 TYR   0.030   0.002   TYR A 399 
 PHE   0.015   0.001   PHE A 464 
 TRP   0.011   0.001   TRP A 316 
 HIS   0.003   0.001   HIS B 313 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 7500)
  covalent geometry    : angle       0.69012 (10228)
  SS BOND              : bond        0.00164 (    1)
  SS BOND              : angle       1.01008 (    2)
  hydrogen bonds       : bond        0.03883 (  363)
  hydrogen bonds       : angle       4.37986 ( 1068)
  link_BETA1-4         : bond        0.00869 (    4)
  link_BETA1-4         : angle       3.39938 (   12)
  link_NAG-ASN         : bond        0.00079 (    4)
  link_NAG-ASN         : angle       1.61859 (   12)

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

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

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 169
  time to evaluate  : 0.203 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 LYS cc_start: 0.8857 (pptt) cc_final: 0.8362 (pttp)
REVERT: A  221 ASN cc_start: 0.7823 (OUTLIER) cc_final: 0.7251 (p0)
REVERT: A  258 MET cc_start: 0.6779 (OUTLIER) cc_final: 0.5789 (mmt)
REVERT: A  270 PHE cc_start: 0.6071 (m-80) cc_final: 0.5478 (m-80)
REVERT: A  291 MET cc_start: 0.7280 (mtt) cc_final: 0.6992 (mtt)
REVERT: A  354 LEU cc_start: 0.8178 (tp) cc_final: 0.7967 (tp)
REVERT: A  356 MET cc_start: 0.6642 (mpp) cc_final: 0.6386 (mpp)
REVERT: A  360 ARG cc_start: 0.1986 (OUTLIER) cc_final: 0.1070 (ttp-170)
REVERT: B  234 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8023 (pm20)
REVERT: B  302 SER cc_start: 0.9393 (OUTLIER) cc_final: 0.9133 (t)
REVERT: B  315 LYS cc_start: 0.8283 (tppt) cc_final: 0.8020 (tppt)
REVERT: B  336 GLN cc_start: 0.8628 (tp40) cc_final: 0.8222 (tp40)
REVERT: B  496 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7824 (tp)
  outliers start: 58
  outliers final: 42
  residues processed: 208
  average time/residue: 0.0561
  time to fit residues: 17.1784
Evaluate side-chains
  206 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 158
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  143 SER
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  154 CYS
Chi-restraints excluded: chain A residue  155 ILE
Chi-restraints excluded: chain A residue  168 CYS
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  208 GLN
Chi-restraints excluded: chain A residue  221 ASN
Chi-restraints excluded: chain A residue  258 MET
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  272 SER
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  360 ARG
Chi-restraints excluded: chain A residue  372 CYS
Chi-restraints excluded: chain A residue  396 TYR
Chi-restraints excluded: chain A residue  398 CYS
Chi-restraints excluded: chain A residue  423 ASN
Chi-restraints excluded: chain A residue  428 VAL
Chi-restraints excluded: chain A residue  456 ILE
Chi-restraints excluded: chain A residue  464 PHE
Chi-restraints excluded: chain B residue   85 LEU
Chi-restraints excluded: chain B residue  150 LEU
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  154 LYS
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  156 LYS
Chi-restraints excluded: chain B residue  164 HIS
Chi-restraints excluded: chain B residue  207 LEU
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  230 LYS
Chi-restraints excluded: chain B residue  234 GLU
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  281 SER
Chi-restraints excluded: chain B residue  290 LEU
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  302 SER
Chi-restraints excluded: chain B residue  325 THR
Chi-restraints excluded: chain B residue  339 LEU
Chi-restraints excluded: chain B residue  357 PHE
Chi-restraints excluded: chain B residue  417 SER
Chi-restraints excluded: chain B residue  453 ILE
Chi-restraints excluded: chain B residue  456 TRP
Chi-restraints excluded: chain B residue  465 VAL
Chi-restraints excluded: chain B residue  496 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 17 optimal weight:    8.9990
   chunk 31 optimal weight:    8.9990
   chunk 71 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.6980
   chunk 76 optimal weight:    7.9990
   chunk 49 optimal weight:    0.7980
   chunk 78 optimal weight:    0.8980
   chunk 18 optimal weight:    6.9990
   chunk 59 optimal weight:    4.9990
   chunk 63 optimal weight:    6.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** B 166 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 = 0.4081 r_free = 0.4081 target = 0.175993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.138378 restraints weight = 13942.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.140782 restraints weight = 9529.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.141853 restraints weight = 7203.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.142272 restraints weight = 6825.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.142658 restraints weight = 6293.466|
|-----------------------------------------------------------------------------|
r_work (final): 0.3667
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7784
moved from start:          0.2012

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   7509  Z= 0.142
  Angle     :  0.718  11.565  10254  Z= 0.335
  Chirality :  0.043   0.295   1213
  Planarity :  0.004   0.053   1250
  Dihedral  :  8.117  57.448   1367
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.46 %
    Favored  : 93.54 %
  Rotamer:
    Outliers :  7.69 %
    Allowed  : 35.20 %
    Favored  : 57.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.43 (0.29), residues: 914
  helix:  1.65 (0.24), residues: 480
  sheet: -0.18 (0.68), residues: 56
  loop : -1.49 (0.33), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 108 
 TYR   0.030   0.002   TYR A 399 
 PHE   0.028   0.001   PHE A 433 
 TRP   0.013   0.001   TRP A 316 
 HIS   0.002   0.000   HIS B 119 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 7500)
  covalent geometry    : angle       0.70739 (10228)
  SS BOND              : bond        0.00149 (    1)
  SS BOND              : angle       0.98829 (    2)
  hydrogen bonds       : bond        0.03945 (  363)
  hydrogen bonds       : angle       4.40453 ( 1068)
  link_BETA1-4         : bond        0.00872 (    4)
  link_BETA1-4         : angle       3.32243 (   12)
  link_NAG-ASN         : bond        0.00071 (    4)
  link_NAG-ASN         : angle       1.67896 (   12)

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

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

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 171
  time to evaluate  : 0.204 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 LYS cc_start: 0.8833 (pptt) cc_final: 0.8303 (pttp)
REVERT: A  221 ASN cc_start: 0.7862 (OUTLIER) cc_final: 0.7282 (p0)
REVERT: A  258 MET cc_start: 0.6711 (OUTLIER) cc_final: 0.5720 (mmt)
REVERT: A  270 PHE cc_start: 0.6050 (m-80) cc_final: 0.5472 (m-80)
REVERT: A  291 MET cc_start: 0.7355 (mtt) cc_final: 0.7064 (mtt)
REVERT: A  354 LEU cc_start: 0.8112 (tp) cc_final: 0.7905 (tp)
REVERT: A  356 MET cc_start: 0.6639 (mpp) cc_final: 0.6364 (mpp)
REVERT: B  234 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.7999 (pm20)
REVERT: B  302 SER cc_start: 0.9354 (OUTLIER) cc_final: 0.9062 (t)
REVERT: B  336 GLN cc_start: 0.8631 (tp40) cc_final: 0.8080 (tp-100)
REVERT: B  496 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7790 (tp)
  outliers start: 59
  outliers final: 44
  residues processed: 209
  average time/residue: 0.0512
  time to fit residues: 16.0019
Evaluate side-chains
  213 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 164
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  143 SER
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  154 CYS
Chi-restraints excluded: chain A residue  155 ILE
Chi-restraints excluded: chain A residue  168 CYS
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  208 GLN
Chi-restraints excluded: chain A residue  221 ASN
Chi-restraints excluded: chain A residue  258 MET
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  300 ASN
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  372 CYS
Chi-restraints excluded: chain A residue  396 TYR
Chi-restraints excluded: chain A residue  398 CYS
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  423 ASN
Chi-restraints excluded: chain A residue  428 VAL
Chi-restraints excluded: chain A residue  456 ILE
Chi-restraints excluded: chain A residue  464 PHE
Chi-restraints excluded: chain B residue   85 LEU
Chi-restraints excluded: chain B residue  150 LEU
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  154 LYS
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  156 LYS
Chi-restraints excluded: chain B residue  160 LEU
Chi-restraints excluded: chain B residue  164 HIS
Chi-restraints excluded: chain B residue  207 LEU
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  230 LYS
Chi-restraints excluded: chain B residue  234 GLU
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  281 SER
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  302 SER
Chi-restraints excluded: chain B residue  303 TYR
Chi-restraints excluded: chain B residue  325 THR
Chi-restraints excluded: chain B residue  339 LEU
Chi-restraints excluded: chain B residue  357 PHE
Chi-restraints excluded: chain B residue  373 LEU
Chi-restraints excluded: chain B residue  417 SER
Chi-restraints excluded: chain B residue  453 ILE
Chi-restraints excluded: chain B residue  496 LEU
Chi-restraints excluded: chain B residue  513 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 56 optimal weight:    0.9990
   chunk 10 optimal weight:    0.6980
   chunk 68 optimal weight:    1.9990
   chunk 44 optimal weight:    0.4980
   chunk 64 optimal weight:    3.9990
   chunk 62 optimal weight:    0.8980
   chunk 89 optimal weight:    3.9990
   chunk 11 optimal weight:    0.0570
   chunk 61 optimal weight:    0.8980
   chunk 33 optimal weight:    0.7980
   chunk 7 optimal weight:    7.9990
   overall best weight:    0.5898

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

Flipped N/Q/H residues before XYZ refinement:
** B 166 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 = 0.4090 r_free = 0.4090 target = 0.176891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.141258 restraints weight = 13964.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.141629 restraints weight = 9555.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.142651 restraints weight = 7673.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.143460 restraints weight = 7081.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.143850 restraints weight = 6467.213|
|-----------------------------------------------------------------------------|
r_work (final): 0.3681
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7760
moved from start:          0.2057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7509  Z= 0.129
  Angle     :  0.724  11.562  10254  Z= 0.332
  Chirality :  0.044   0.253   1213
  Planarity :  0.004   0.051   1250
  Dihedral  :  7.875  57.530   1367
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.13 %
    Favored  : 93.87 %
  Rotamer:
    Outliers :  6.78 %
    Allowed  : 35.98 %
    Favored  : 57.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.37 (0.29), residues: 914
  helix:  1.60 (0.24), residues: 482
  sheet: -0.17 (0.67), residues: 56
  loop : -1.55 (0.33), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 108 
 TYR   0.030   0.002   TYR A 399 
 PHE   0.022   0.001   PHE A 463 
 TRP   0.013   0.001   TRP A 316 
 HIS   0.003   0.001   HIS B 313 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 7500)
  covalent geometry    : angle       0.71397 (10228)
  SS BOND              : bond        0.00128 (    1)
  SS BOND              : angle       1.00704 (    2)
  hydrogen bonds       : bond        0.03801 (  363)
  hydrogen bonds       : angle       4.36968 ( 1068)
  link_BETA1-4         : bond        0.00861 (    4)
  link_BETA1-4         : angle       3.22074 (   12)
  link_NAG-ASN         : bond        0.00090 (    4)
  link_NAG-ASN         : angle       1.70323 (   12)

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

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

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 175
  time to evaluate  : 0.261 
Fit side-chains
   revert: symmetry clash
REVERT: A  140 MET cc_start: 0.8713 (ttm) cc_final: 0.8480 (ttp)
REVERT: A  221 ASN cc_start: 0.7815 (OUTLIER) cc_final: 0.7262 (p0)
REVERT: A  253 TYR cc_start: 0.7778 (m-80) cc_final: 0.7085 (m-80)
REVERT: A  258 MET cc_start: 0.6633 (OUTLIER) cc_final: 0.5667 (mmt)
REVERT: A  270 PHE cc_start: 0.6000 (m-80) cc_final: 0.5431 (m-80)
REVERT: A  291 MET cc_start: 0.7404 (mtt) cc_final: 0.7100 (mtt)
REVERT: A  354 LEU cc_start: 0.8028 (tp) cc_final: 0.7824 (tp)
REVERT: A  356 MET cc_start: 0.6580 (mpp) cc_final: 0.6304 (mpp)
REVERT: B  206 ASP cc_start: 0.8685 (p0) cc_final: 0.8470 (p0)
REVERT: B  234 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8020 (pm20)
REVERT: B  302 SER cc_start: 0.9326 (OUTLIER) cc_final: 0.9025 (t)
REVERT: B  336 GLN cc_start: 0.8621 (tp40) cc_final: 0.8078 (tp-100)
REVERT: B  496 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7805 (tp)
  outliers start: 52
  outliers final: 39
  residues processed: 211
  average time/residue: 0.0510
  time to fit residues: 16.1164
Evaluate side-chains
  208 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 164
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  143 SER
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  154 CYS
Chi-restraints excluded: chain A residue  155 ILE
Chi-restraints excluded: chain A residue  168 CYS
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  208 GLN
Chi-restraints excluded: chain A residue  213 HIS
Chi-restraints excluded: chain A residue  221 ASN
Chi-restraints excluded: chain A residue  258 MET
Chi-restraints excluded: chain A residue  272 SER
Chi-restraints excluded: chain A residue  300 ASN
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  372 CYS
Chi-restraints excluded: chain A residue  396 TYR
Chi-restraints excluded: chain A residue  398 CYS
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  423 ASN
Chi-restraints excluded: chain A residue  456 ILE
Chi-restraints excluded: chain A residue  464 PHE
Chi-restraints excluded: chain B residue   85 LEU
Chi-restraints excluded: chain B residue  150 LEU
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  156 LYS
Chi-restraints excluded: chain B residue  160 LEU
Chi-restraints excluded: chain B residue  164 HIS
Chi-restraints excluded: chain B residue  207 LEU
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  234 GLU
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  281 SER
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  302 SER
Chi-restraints excluded: chain B residue  339 LEU
Chi-restraints excluded: chain B residue  357 PHE
Chi-restraints excluded: chain B residue  417 SER
Chi-restraints excluded: chain B residue  453 ILE
Chi-restraints excluded: chain B residue  496 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 55 optimal weight:    7.9990
   chunk 38 optimal weight:    0.9980
   chunk 17 optimal weight:    0.5980
   chunk 86 optimal weight:    7.9990
   chunk 88 optimal weight:    0.9990
   chunk 24 optimal weight:    0.8980
   chunk 35 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 31 optimal weight:    8.9990
   chunk 56 optimal weight:    0.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A 252 ASN
** B 166 ASN ** 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 = 0.4081 r_free = 0.4081 target = 0.176097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.139030 restraints weight = 13819.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.139942 restraints weight = 9897.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.141232 restraints weight = 7884.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.142100 restraints weight = 7434.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.142164 restraints weight = 6704.366|
|-----------------------------------------------------------------------------|
r_work (final): 0.3668
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.2228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7509  Z= 0.148
  Angle     :  0.755  11.454  10254  Z= 0.352
  Chirality :  0.044   0.235   1213
  Planarity :  0.004   0.050   1250
  Dihedral  :  7.840  57.363   1367
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 10.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.35 %
    Favored  : 93.65 %
  Rotamer:
    Outliers :  7.04 %
    Allowed  : 35.85 %
    Favored  : 57.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.37 (0.29), residues: 914
  helix:  1.59 (0.24), residues: 482
  sheet: -0.21 (0.67), residues: 56
  loop : -1.53 (0.33), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 418 
 TYR   0.015   0.002   TYR A 337 
 PHE   0.023   0.002   PHE A 393 
 TRP   0.014   0.001   TRP A 316 
 HIS   0.008   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 7500)
  covalent geometry    : angle       0.74574 (10228)
  SS BOND              : bond        0.00158 (    1)
  SS BOND              : angle       1.07509 (    2)
  hydrogen bonds       : bond        0.03933 (  363)
  hydrogen bonds       : angle       4.44313 ( 1068)
  link_BETA1-4         : bond        0.00829 (    4)
  link_BETA1-4         : angle       3.15325 (   12)
  link_NAG-ASN         : bond        0.00102 (    4)
  link_NAG-ASN         : angle       1.76155 (   12)

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

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

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 167
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
REVERT: A   63 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8410 (pttp)
REVERT: A  221 ASN cc_start: 0.7866 (OUTLIER) cc_final: 0.7307 (p0)
REVERT: A  258 MET cc_start: 0.6581 (OUTLIER) cc_final: 0.5660 (mmt)
REVERT: A  270 PHE cc_start: 0.6008 (m-80) cc_final: 0.5418 (m-80)
REVERT: A  291 MET cc_start: 0.7461 (mtt) cc_final: 0.7172 (mtt)
REVERT: A  354 LEU cc_start: 0.8055 (tp) cc_final: 0.7848 (tp)
REVERT: A  356 MET cc_start: 0.6611 (mpp) cc_final: 0.6333 (mpp)
REVERT: B  234 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8019 (pm20)
REVERT: B  302 SER cc_start: 0.9308 (OUTLIER) cc_final: 0.8934 (t)
REVERT: B  336 GLN cc_start: 0.8624 (tp40) cc_final: 0.8076 (tp-100)
REVERT: B  496 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7853 (tp)
  outliers start: 54
  outliers final: 44
  residues processed: 200
  average time/residue: 0.0524
  time to fit residues: 15.5848
Evaluate side-chains
  211 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 161
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 LYS
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  137 VAL
Chi-restraints excluded: chain A residue  143 SER
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  154 CYS
Chi-restraints excluded: chain A residue  155 ILE
Chi-restraints excluded: chain A residue  168 CYS
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  208 GLN
Chi-restraints excluded: chain A residue  221 ASN
Chi-restraints excluded: chain A residue  258 MET
Chi-restraints excluded: chain A residue  272 SER
Chi-restraints excluded: chain A residue  300 ASN
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  372 CYS
Chi-restraints excluded: chain A residue  396 TYR
Chi-restraints excluded: chain A residue  398 CYS
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  423 ASN
Chi-restraints excluded: chain A residue  428 VAL
Chi-restraints excluded: chain A residue  456 ILE
Chi-restraints excluded: chain A residue  464 PHE
Chi-restraints excluded: chain B residue   85 LEU
Chi-restraints excluded: chain B residue  150 LEU
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  156 LYS
Chi-restraints excluded: chain B residue  160 LEU
Chi-restraints excluded: chain B residue  164 HIS
Chi-restraints excluded: chain B residue  207 LEU
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  230 LYS
Chi-restraints excluded: chain B residue  234 GLU
Chi-restraints excluded: chain B residue  249 ILE
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  281 SER
Chi-restraints excluded: chain B residue  290 LEU
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  299 LEU
Chi-restraints excluded: chain B residue  302 SER
Chi-restraints excluded: chain B residue  339 LEU
Chi-restraints excluded: chain B residue  357 PHE
Chi-restraints excluded: chain B residue  373 LEU
Chi-restraints excluded: chain B residue  417 SER
Chi-restraints excluded: chain B residue  453 ILE
Chi-restraints excluded: chain B residue  496 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 66 optimal weight:    0.8980
   chunk 14 optimal weight:    0.0060
   chunk 71 optimal weight:    0.2980
   chunk 74 optimal weight:    0.6980
   chunk 40 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 28 optimal weight:    0.5980
   chunk 33 optimal weight:    0.9980
   chunk 64 optimal weight:    0.7980
   chunk 75 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9980
   overall best weight:    0.4796

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

Flipped N/Q/H residues before XYZ refinement:
A 252 ASN
** B 166 ASN ** 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 = 0.4097 r_free = 0.4097 target = 0.177603 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.142704 restraints weight = 13931.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.142604 restraints weight = 9260.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.143714 restraints weight = 8389.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.144493 restraints weight = 7211.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.144715 restraints weight = 6993.816|
|-----------------------------------------------------------------------------|
r_work (final): 0.3705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7747
moved from start:          0.2292

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   7509  Z= 0.129
  Angle     :  0.751  11.422  10254  Z= 0.347
  Chirality :  0.044   0.222   1213
  Planarity :  0.004   0.050   1250
  Dihedral  :  7.709  57.611   1367
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 10.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.24 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  6.00 %
    Allowed  : 37.03 %
    Favored  : 56.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.32 (0.29), residues: 914
  helix:  1.54 (0.24), residues: 487
  sheet: -0.10 (0.68), residues: 56
  loop : -1.60 (0.33), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 524 
 TYR   0.031   0.002   TYR A 399 
 PHE   0.022   0.001   PHE A 393 
 TRP   0.014   0.001   TRP A 316 
 HIS   0.006   0.001   HIS B 313 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 7500)
  covalent geometry    : angle       0.74251 (10228)
  SS BOND              : bond        0.00037 (    1)
  SS BOND              : angle       0.98632 (    2)
  hydrogen bonds       : bond        0.03765 (  363)
  hydrogen bonds       : angle       4.38184 ( 1068)
  link_BETA1-4         : bond        0.00816 (    4)
  link_BETA1-4         : angle       3.04140 (   12)
  link_NAG-ASN         : bond        0.00076 (    4)
  link_NAG-ASN         : angle       1.77547 (   12)

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

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

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 168
  time to evaluate  : 0.195 
Fit side-chains
   revert: symmetry clash
REVERT: A  215 GLU cc_start: 0.7391 (mp0) cc_final: 0.6519 (pm20)
REVERT: A  221 ASN cc_start: 0.7890 (OUTLIER) cc_final: 0.7366 (p0)
REVERT: A  258 MET cc_start: 0.6615 (OUTLIER) cc_final: 0.5684 (mmt)
REVERT: A  270 PHE cc_start: 0.5980 (m-80) cc_final: 0.5412 (m-80)
REVERT: A  291 MET cc_start: 0.7374 (mtt) cc_final: 0.7047 (mtt)
REVERT: A  354 LEU cc_start: 0.7987 (tp) cc_final: 0.7781 (tp)
REVERT: A  356 MET cc_start: 0.6588 (mpp) cc_final: 0.6337 (mpp)
REVERT: B  234 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.7952 (pm20)
REVERT: B  336 GLN cc_start: 0.8650 (tp40) cc_final: 0.8344 (tp-100)
  outliers start: 46
  outliers final: 38
  residues processed: 200
  average time/residue: 0.0487
  time to fit residues: 14.6918
Evaluate side-chains
  204 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 163
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  143 SER
Chi-restraints excluded: chain A residue  154 CYS
Chi-restraints excluded: chain A residue  155 ILE
Chi-restraints excluded: chain A residue  168 CYS
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  208 GLN
Chi-restraints excluded: chain A residue  221 ASN
Chi-restraints excluded: chain A residue  252 ASN
Chi-restraints excluded: chain A residue  258 MET
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  272 SER
Chi-restraints excluded: chain A residue  300 ASN
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  372 CYS
Chi-restraints excluded: chain A residue  396 TYR
Chi-restraints excluded: chain A residue  398 CYS
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  423 ASN
Chi-restraints excluded: chain A residue  456 ILE
Chi-restraints excluded: chain A residue  464 PHE
Chi-restraints excluded: chain B residue   85 LEU
Chi-restraints excluded: chain B residue  150 LEU
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  156 LYS
Chi-restraints excluded: chain B residue  164 HIS
Chi-restraints excluded: chain B residue  207 LEU
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  230 LYS
Chi-restraints excluded: chain B residue  234 GLU
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  357 PHE
Chi-restraints excluded: chain B residue  373 LEU
Chi-restraints excluded: chain B residue  417 SER
Chi-restraints excluded: chain B residue  453 ILE
Chi-restraints excluded: chain B residue  456 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 56 optimal weight:    0.8980
   chunk 54 optimal weight:    0.8980
   chunk 82 optimal weight:    0.3980
   chunk 55 optimal weight:    3.9990
   chunk 24 optimal weight:    0.5980
   chunk 76 optimal weight:    0.8980
   chunk 41 optimal weight:    3.9990
   chunk 21 optimal weight:    5.9990
   chunk 66 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9980
   chunk 14 optimal weight:    6.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 252 ASN
** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 458 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.177199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.141507 restraints weight = 13699.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.141704 restraints weight = 9474.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.143052 restraints weight = 7765.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.144162 restraints weight = 7055.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.144242 restraints weight = 6454.163|
|-----------------------------------------------------------------------------|
r_work (final): 0.3672
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7753
moved from start:          0.2289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.100   7509  Z= 0.182
  Angle     :  1.057  59.199  10254  Z= 0.596
  Chirality :  0.046   0.424   1213
  Planarity :  0.004   0.049   1250
  Dihedral  :  7.760  57.441   1367
  Min Nonbonded Distance : 2.238

Molprobity Statistics.
  All-atom Clashscore : 11.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.46 %
    Favored  : 93.54 %
  Rotamer:
    Outliers :  6.00 %
    Allowed  : 37.42 %
    Favored  : 56.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.31 (0.29), residues: 914
  helix:  1.53 (0.24), residues: 487
  sheet: -0.10 (0.68), residues: 56
  loop : -1.60 (0.33), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 418 
 TYR   0.016   0.002   TYR A 399 
 PHE   0.018   0.001   PHE A 393 
 TRP   0.013   0.001   TRP A 316 
 HIS   0.006   0.001   HIS B 313 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 7500)
  covalent geometry    : angle       1.05144 (10228)
  SS BOND              : bond        0.00324 (    1)
  SS BOND              : angle       0.77932 (    2)
  hydrogen bonds       : bond        0.03770 (  363)
  hydrogen bonds       : angle       4.38427 ( 1068)
  link_BETA1-4         : bond        0.00740 (    4)
  link_BETA1-4         : angle       3.09197 (   12)
  link_NAG-ASN         : bond        0.00071 (    4)
  link_NAG-ASN         : angle       1.77404 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1174.82 seconds
wall clock time: 21 minutes 1.02 seconds (1261.02 seconds total)