Starting phenix.real_space_refine
on Tue Mar  3 14:52:25 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ddo_30655/03_2026/7ddo_30655.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ddo_30655/03_2026/7ddo_30655.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ddo_30655/03_2026/7ddo_30655.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ddo_30655/03_2026/7ddo_30655.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ddo_30655/03_2026/7ddo_30655.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ddo_30655/03_2026/7ddo_30655.cif"
  }
  resolution = 3.4
  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=   0.005
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     S      37      5.16       5
     C    4133      2.51       5
     N    1067      2.21       5
     O    1230      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 65 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6468
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4877
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 597, 4870
          Classifications: {'peptide': 597}
          Link IDs: {'PTRANS': 27, 'TRANS': 569}
      Conformer: "B"
        Number of residues, atoms: 597, 4870
          Classifications: {'peptide': 597}
          Link IDs: {'PTRANS': 27, 'TRANS': 569}
          bond proxies already assigned to first conformer: 4998
    Chain: "C"
      Number of atoms: 1534
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 194, 1534
          Classifications: {'peptide': 194}
          Link IDs: {'PTRANS': 10, 'TRANS': 183}
    Chain: "A"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 43
          Unusual residues: {' ZN': 1, 'NAG': 3}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "C"
      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: 2.44, per 1000 atoms: 0.38
  Number of scatterers: 6468
  At special positions: 0
  Unit cell: (101.362, 96.3937, 106.331, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      1     29.99
     S      37     16.00
     O    1230      8.00
     N    1067      7.00
     C    4133      6.00
    sf(0) = scattering factor at diffraction angle 0.

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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 902 " - " ASN A 546 "
      " NAG A 903 " - " ASN A  90 "
      " NAG A 904 " - " ASN A  53 "
      " NAG C 601 " - " ASN C 343 "
  Time building additional restraints: 0.69
  Conformation dependent library (CDL) restraints added in 418.3 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 901 "
        pdb="ZN    ZN A 901 " - pdb=" NE2 HIS A 378 "
        pdb="ZN    ZN A 901 " - pdb=" NE2 HIS A 374 "


  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1490

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 5 sheets defined
      55.6% alpha, 5.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 53
      removed outlier: 3.599A  pdb=" N   GLN A  24 " --> pdb=" O   THR A  20 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   ASP A  38 " --> pdb=" O   HIS A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 81
      removed outlier: 3.737A  pdb=" N   VAL A  59 " --> pdb=" O   THR A  55 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 82 through 83
      No H-bonds generated for 'chain 'A' and resid 82 through 83'
    Processing helix  chain 'A' and resid 84 through 88
      removed outlier: 3.621A  pdb=" N   GLU A  87 " --> pdb=" O   PRO A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 90 through 101
    Processing helix  chain 'A' and resid 103 through 108
      removed outlier: 3.564A  pdb=" N   SER A 106 " --> pdb=" O   ASN A 103 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   VAL A 107 " --> pdb=" O   GLY A 104 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   LEU A 108 " --> pdb=" O   SER A 105 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 103 through 108'
    Processing helix  chain 'A' and resid 109 through 129
    Processing helix  chain 'A' and resid 143 through 155
      removed outlier: 4.233A  pdb=" N   ASN A 149 " --> pdb=" O   GLU A 145 " (cutoff:3.500A)
      removed outlier: 4.387A  pdb=" N   GLU A 150 " --> pdb=" O   PRO A 146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 194
      removed outlier: 4.192A  pdb=" N   LYS A 174 " --> pdb=" O   SER A 170 " (cutoff:3.500A)
      removed outlier: 4.292A  pdb=" N   GLN A 175 " --> pdb=" O   GLU A 171 " (cutoff:3.500A)
      Proline residue:  A 178  - end of helix
    Processing helix  chain 'A' and resid 198 through 205
    Processing helix  chain 'A' and resid 220 through 252
      Proline residue:  A 235  - end of helix
    Processing helix  chain 'A' and resid 265 through 267
      No H-bonds generated for 'chain 'A' and resid 265 through 267'
    Processing helix  chain 'A' and resid 275 through 279
    Processing helix  chain 'A' and resid 293 through 300
    Processing helix  chain 'A' and resid 303 through 318
      removed outlier: 3.720A  pdb=" N   VAL A 318 " --> pdb=" O   PHE A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 331
      removed outlier: 3.643A  pdb=" N   TRP A 328 " --> pdb=" O   THR A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 385
      removed outlier: 3.591A  pdb=" N   HIS A 373 " --> pdb=" O   PHE A 369 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   TYR A 385 " --> pdb=" O   TYR A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 393
      removed outlier: 3.565A  pdb=" N   ARG A 393 " --> pdb=" O   PHE A 390 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 399 through 413
      removed outlier: 3.666A  pdb=" N   ALA A 403 " --> pdb=" O   GLY A 399 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   MET A 408 " --> pdb=" O   VAL A 404 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   SER A 409 " --> pdb=" O   GLY A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 421
    Processing helix  chain 'A' and resid 431 through 446
    Processing helix  chain 'A' and resid 449 through 465
    Processing helix  chain 'A' and resid 469 through 471
      No H-bonds generated for 'chain 'A' and resid 469 through 471'
    Processing helix  chain 'A' and resid 472 through 485
    Processing helix  chain 'A' and resid 498 through 502
    Processing helix  chain 'A' and resid 503 through 508
    Processing helix  chain 'A' and resid 513 through 533
      removed outlier: 3.619A  pdb=" N   PHE A 523 " --> pdb=" O   THR A 519 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 547 through 559
      removed outlier: 3.780A  pdb=" N   MET A 557 " --> pdb=" O   LYS A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 575
      removed outlier: 3.929A  pdb=" N   VAL A 573 " --> pdb=" O   ALA A 569 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 581 through 599
      Proline residue:  A 590  - end of helix
    Processing helix  chain 'A' and resid 600 through 602
      No H-bonds generated for 'chain 'A' and resid 600 through 602'
    Processing helix  chain 'C' and resid 338 through 343
    Processing helix  chain 'C' and resid 365 through 370
    Processing helix  chain 'C' and resid 416 through 422
    Processing helix  chain 'C' and resid 502 through 506
      removed outlier: 3.715A  pdb=" N   GLN C 506 " --> pdb=" O   VAL C 503 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263
      removed outlier: 5.815A  pdb=" N   LEU A 262 " --> pdb=" O   VAL A 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 352
      removed outlier: 6.174A  pdb=" N   ASP A 355 " --> pdb=" O   LEU A 351 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 354 through 358
      removed outlier: 3.774A  pdb=" N   ASN C 354 " --> pdb=" O   SER C 399 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   ILE C 358 " --> pdb=" O   VAL C 395 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   VAL C 395 " --> pdb=" O   ILE C 358 " (cutoff:3.500A)
      removed outlier: 4.654A  pdb=" N   ASN C 394 " --> pdb=" O   GLU C 516 " (cutoff:3.500A)
      removed outlier: 4.038A  pdb=" N   GLU C 516 " --> pdb=" O   ASN C 394 " (cutoff:3.500A)
      removed outlier: 4.526A  pdb=" N   VAL C 433 " --> pdb=" O   LYS C 378 " (cutoff:3.500A)
      removed outlier: 4.246A  pdb=" N   LYS C 378 " --> pdb=" O   VAL C 433 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 452 through 453
    Processing sheet with id=AA5, first strand: chain 'C' and resid 473 through 474
      removed outlier: 3.815A  pdb=" N   TYR C 489 " --> pdb=" O   TYR C 473 " (cutoff:3.500A)

    304 hydrogen bonds defined for protein.
    875 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: 0.93

  Time building geometry restraints manager: 0.91 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2077
        1.34 -     1.46: 1660
        1.46 -     1.58: 2854
        1.58 -     1.70: 0
        1.70 -     1.81: 58
  Bond restraints: 6649
  Sorted by residual:
  bond pdb=" C1  NAG A 902 "
       pdb=" O5  NAG A 902 "
    ideal  model  delta    sigma   weight residual
    1.406  1.436 -0.030 2.00e-02 2.50e+03 2.27e+00
  bond pdb=" C1  NAG A 903 "
       pdb=" O5  NAG A 903 "
    ideal  model  delta    sigma   weight residual
    1.406  1.436 -0.030 2.00e-02 2.50e+03 2.20e+00
  bond pdb=" C1  NAG A 904 "
       pdb=" O5  NAG A 904 "
    ideal  model  delta    sigma   weight residual
    1.406  1.434 -0.028 2.00e-02 2.50e+03 1.99e+00
  bond pdb=" C1  NAG C 601 "
       pdb=" O5  NAG C 601 "
    ideal  model  delta    sigma   weight residual
    1.406  1.433 -0.027 2.00e-02 2.50e+03 1.78e+00
  bond pdb=" CA  VAL C 524 "
       pdb=" CB  VAL C 524 "
    ideal  model  delta    sigma   weight residual
    1.531  1.545 -0.014 1.11e-02 8.12e+03 1.61e+00
  ... (remaining 6644 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.37: 8752
        1.37 -     2.74: 223
        2.74 -     4.11: 55
        4.11 -     5.48: 9
        5.48 -     6.85: 3
  Bond angle restraints: 9042
  Sorted by residual:
  angle pdb=" N   VAL C 524 "
        pdb=" CA  VAL C 524 "
        pdb=" C   VAL C 524 "
      ideal   model   delta    sigma   weight residual
     106.53  110.71   -4.18 1.41e+00 5.03e-01 8.81e+00
  angle pdb=" N   ILE A 544 "
        pdb=" CA  ILE A 544 "
        pdb=" C   ILE A 544 "
      ideal   model   delta    sigma   weight residual
     113.22  109.75    3.47 1.23e+00 6.61e-01 7.95e+00
  angle pdb=" N   GLU A 589 "
        pdb=" CA  GLU A 589 "
        pdb=" C   GLU A 589 "
      ideal   model   delta    sigma   weight residual
     109.81  115.20   -5.39 2.21e+00 2.05e-01 5.95e+00
  angle pdb=" C   LEU A 144 "
        pdb=" N   GLU A 145 "
        pdb=" CA  GLU A 145 "
      ideal   model   delta    sigma   weight residual
     120.97  124.12   -3.15 1.48e+00 4.57e-01 4.53e+00
  angle pdb=" N   VAL A 506 "
        pdb=" CA  VAL A 506 "
        pdb=" C   VAL A 506 "
      ideal   model   delta    sigma   weight residual
     111.45  109.52    1.93 9.30e-01 1.16e+00 4.30e+00
  ... (remaining 9037 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.31: 3558
       17.31 -    34.63: 319
       34.63 -    51.94: 68
       51.94 -    69.25: 15
       69.25 -    86.56: 12
  Dihedral angle restraints: 3972
    sinusoidal: 1648
      harmonic: 2324
  Sorted by residual:
  dihedral pdb=" CB  CYS C 379 "
           pdb=" SG  CYS C 379 "
           pdb=" SG  CYS C 432 "
           pdb=" CB  CYS C 432 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00    6.44   86.56     1      1.00e+01 1.00e-02 9.02e+01
  dihedral pdb=" CB  CYS C 391 "
           pdb=" SG  CYS C 391 "
           pdb=" SG  CYS C 525 "
           pdb=" CB  CYS C 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   25.85   67.15     1      1.00e+01 1.00e-02 5.87e+01
  dihedral pdb=" CB  CYS A 133 "
           pdb=" SG  CYS A 133 "
           pdb=" SG  CYS A 141 "
           pdb=" CB  CYS A 141 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -22.59  -63.41     1      1.00e+01 1.00e-02 5.30e+01
  ... (remaining 3969 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 571
       0.028 -    0.056: 251
       0.056 -    0.084: 80
       0.084 -    0.111: 51
       0.111 -    0.139: 6
  Chirality restraints: 959
  Sorted by residual:
  chirality pdb=" CA  GLU A 589 "
            pdb=" N   GLU A 589 "
            pdb=" C   GLU A 589 "
            pdb=" CB  GLU A 589 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.85e-01
  chirality pdb=" CA  ILE C 434 "
            pdb=" N   ILE C 434 "
            pdb=" C   ILE C 434 "
            pdb=" CB  ILE C 434 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.71e-01
  chirality pdb=" CA  THR C 372 "
            pdb=" N   THR C 372 "
            pdb=" C   THR C 372 "
            pdb=" CB  THR C 372 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.40    0.12 2.00e-01 2.50e+01 3.69e-01
  ... (remaining 956 not shown)

  Planarity restraints: 1173
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 582 "    0.025 5.00e-02 4.00e+02   3.80e-02 2.31e+00
        pdb=" N   PRO A 583 "   -0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO A 583 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 583 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 234 "    0.024 5.00e-02 4.00e+02   3.67e-02 2.15e+00
        pdb=" N   PRO A 235 "   -0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO A 235 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 235 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS C 462 "    0.021 5.00e-02 4.00e+02   3.23e-02 1.67e+00
        pdb=" N   PRO C 463 "   -0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO C 463 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO C 463 "    0.018 5.00e-02 4.00e+02
  ... (remaining 1170 not shown)

  Histogram of nonbonded interaction distances:
        2.06 -     2.63: 79
        2.63 -     3.20: 5772
        3.20 -     3.76: 10356
        3.76 -     4.33: 14430
        4.33 -     4.90: 23518
  Nonbonded interactions: 54155
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 402 "
            pdb="ZN    ZN A 901 "
     model   vdw
     2.062 2.230
  nonbonded pdb=" OH  TYR A 237 "
            pdb=" O   VAL A 485 "
     model   vdw
     2.167 3.040
  nonbonded pdb=" OH  TYR A 183 "
            pdb=" OD2 ASP A 509 "
     model   vdw
     2.226 3.040
  nonbonded pdb=" O   LEU A 278 "
            pdb=" OG1 THR A 282 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" OE1 GLU C 406 "
            pdb=" OH  TYR C 495 "
     model   vdw
     2.260 3.040
  ... (remaining 54150 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.260
  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:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.690
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.410
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7760
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.162   6662  Z= 0.159
  Angle     :  0.557   6.846   9068  Z= 0.314
  Chirality :  0.039   0.139    959
  Planarity :  0.003   0.038   1169
  Dihedral  : 14.130  86.321   2461
  Min Nonbonded Distance : 2.062

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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 are not related in a simple way.
  whole: -1.39 (0.27), residues: 788
  helix: -0.30 (0.23), residues: 403
  sheet: -1.61 (0.64), residues: 57
  loop : -1.49 (0.31), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 219 
 TYR   0.014   0.001   TYR A 381 
 PHE   0.014   0.001   PHE C 490 
 TRP   0.008   0.001   TRP A 477 
 HIS   0.003   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 6649)
  covalent geometry    : angle       0.54891 ( 9042)
  SS BOND              : bond        0.00150 (    7)
  SS BOND              : angle       2.10156 (   14)
  hydrogen bonds       : bond        0.14490 (  304)
  hydrogen bonds       : angle       5.67191 (  875)
  metal coordination   : bond        0.13450 (    2)
  link_NAG-ASN         : bond        0.00152 (    4)
  link_NAG-ASN         : angle       1.45957 (   12)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 0.269 
Fit side-chains
REVERT: A  190 MET cc_start: 0.8484 (tmm) cc_final: 0.8223 (tmm)
REVERT: A  382 ASP cc_start: 0.8527 (m-30) cc_final: 0.8105 (m-30)
REVERT: C  396 TYR cc_start: 0.6757 (m-80) cc_final: 0.6205 (m-80)
REVERT: C  408 ARG cc_start: 0.8277 (ptp90) cc_final: 0.7999 (ptp-170)
  outliers start: 0
  outliers final: 0
  residues processed: 142
  average time/residue: 0.0785
  time to fit residues: 15.1578
Evaluate side-chains
  114 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    8.9990
   chunk 62 optimal weight:    8.9990
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    0.4980
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    0.5980
   chunk 74 optimal weight:    8.9990
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
A  58 ASN
A 210 ASN
** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 250 ASN
A 338 ASN
A 340 GLN
C 460 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.148153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.116007 restraints weight = 9721.398|
|-----------------------------------------------------------------------------|
r_work (start): 0.3264 rms_B_bonded: 2.41
r_work: 0.3149 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3023 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3023
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3035
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3035 r_free = 0.3035    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3035 r_free = 0.3035    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3035
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7996
moved from start:          0.1062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6662  Z= 0.124
  Angle     :  0.540   6.919   9068  Z= 0.272
  Chirality :  0.041   0.146    959
  Planarity :  0.004   0.032   1169
  Dihedral  :  4.788  43.967    945
  Min Nonbonded Distance : 2.065

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  :  8.76 %
    Favored  : 90.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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 are not related in a simple way.
  whole: -0.20 (0.29), residues: 788
  helix:  0.71 (0.25), residues: 402
  sheet: -1.22 (0.65), residues: 57
  loop : -0.92 (0.33), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 219 
 TYR   0.017   0.001   TYR A 381 
 PHE   0.014   0.001   PHE C 490 
 TRP   0.015   0.001   TRP A 594 
 HIS   0.003   0.001   HIS A 265 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 6649)
  covalent geometry    : angle       0.52929 ( 9042)
  SS BOND              : bond        0.00262 (    7)
  SS BOND              : angle       1.98710 (   14)
  hydrogen bonds       : bond        0.04168 (  304)
  hydrogen bonds       : angle       4.57655 (  875)
  metal coordination   : bond        0.00290 (    2)
  link_NAG-ASN         : bond        0.00115 (    4)
  link_NAG-ASN         : angle       2.18788 (   12)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 115
  time to evaluate  : 0.256 
Fit side-chains
REVERT: A  382 ASP cc_start: 0.8593 (m-30) cc_final: 0.8208 (m-30)
REVERT: A  455 MET cc_start: 0.8850 (tmm) cc_final: 0.8185 (tmm)
REVERT: A  489 GLU cc_start: 0.8748 (pm20) cc_final: 0.8134 (pm20)
REVERT: C  356 LYS cc_start: 0.8102 (mppt) cc_final: 0.7807 (mmtt)
REVERT: C  508 TYR cc_start: 0.8530 (m-80) cc_final: 0.7951 (m-80)
  outliers start: 8
  outliers final: 6
  residues processed: 119
  average time/residue: 0.0677
  time to fit residues: 11.4221
Evaluate side-chains
  114 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 108
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  479 GLU
Chi-restraints excluded: chain C residue  379 CYS
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  489 TYR
Chi-restraints excluded: chain C residue  493 GLN
Chi-restraints excluded: chain C residue  514 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 3 optimal weight:    5.9990
   chunk 56 optimal weight:    0.7980
   chunk 35 optimal weight:    6.9990
   chunk 38 optimal weight:    1.9990
   chunk 67 optimal weight:    3.9990
   chunk 2 optimal weight:    0.7980
   chunk 48 optimal weight:    0.6980
   chunk 59 optimal weight:   10.0000
   chunk 21 optimal weight:    0.9980
   chunk 4 optimal weight:    3.9990
   chunk 1 optimal weight:    0.8980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 340 GLN
A 345 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.149221 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.118443 restraints weight = 18683.453|
|-----------------------------------------------------------------------------|
r_work (start): 0.3311 rms_B_bonded: 3.56
r_work: 0.3079 rms_B_bonded: 4.29 restraints_weight: 0.5000
r_work (final): 0.3079
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3072
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3072 r_free = 0.3072    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3072 r_free = 0.3072    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3072
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7975
moved from start:          0.1303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   6662  Z= 0.109
  Angle     :  0.515   6.980   9068  Z= 0.258
  Chirality :  0.041   0.142    959
  Planarity :  0.004   0.032   1169
  Dihedral  :  4.338  43.158    945
  Min Nonbonded Distance : 2.144

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 10.20 %
    Favored  : 88.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.29 (0.29), residues: 788
  helix:  1.04 (0.25), residues: 409
  sheet: -0.99 (0.64), residues: 55
  loop : -0.61 (0.34), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 219 
 TYR   0.014   0.001   TYR A 381 
 PHE   0.011   0.001   PHE C 490 
 TRP   0.021   0.001   TRP A 594 
 HIS   0.004   0.001   HIS A 345 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 6649)
  covalent geometry    : angle       0.50256 ( 9042)
  SS BOND              : bond        0.00252 (    7)
  SS BOND              : angle       1.84573 (   14)
  hydrogen bonds       : bond        0.03896 (  304)
  hydrogen bonds       : angle       4.36981 (  875)
  metal coordination   : bond        0.00093 (    2)
  link_NAG-ASN         : bond        0.00245 (    4)
  link_NAG-ASN         : angle       2.42480 (   12)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 116
  time to evaluate  : 0.220 
Fit side-chains
REVERT: A  267 LEU cc_start: 0.8541 (mt) cc_final: 0.8287 (mt)
REVERT: A  382 ASP cc_start: 0.8510 (m-30) cc_final: 0.8096 (m-30)
REVERT: A  455 MET cc_start: 0.8793 (tmm) cc_final: 0.8123 (tmm)
REVERT: A  474 MET cc_start: 0.8528 (mmp) cc_final: 0.8186 (mmp)
REVERT: A  489 GLU cc_start: 0.8704 (pm20) cc_final: 0.8086 (pm20)
REVERT: C  343 ASN cc_start: 0.6900 (m-40) cc_final: 0.6499 (p0)
REVERT: C  356 LYS cc_start: 0.8060 (mppt) cc_final: 0.7791 (mmtt)
  outliers start: 9
  outliers final: 5
  residues processed: 121
  average time/residue: 0.0685
  time to fit residues: 11.7649
Evaluate side-chains
  113 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 108
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  379 CYS
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  489 TYR
Chi-restraints excluded: chain C residue  493 GLN
Chi-restraints excluded: chain C residue  514 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 41 optimal weight:    2.9990
   chunk 36 optimal weight:    0.7980
   chunk 10 optimal weight:    1.9990
   chunk 52 optimal weight:    6.9990
   chunk 68 optimal weight:    0.8980
   chunk 11 optimal weight:    4.9990
   chunk 64 optimal weight:   20.0000
   chunk 29 optimal weight:    0.9990
   chunk 32 optimal weight:    0.5980
   chunk 20 optimal weight:    5.9990
   chunk 17 optimal weight:    3.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
A 338 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.149012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.116338 restraints weight = 11877.361|
|-----------------------------------------------------------------------------|
r_work (start): 0.3295 rms_B_bonded: 2.61
r_work: 0.3178 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3178
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3162
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3162 r_free = 0.3162    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3162 r_free = 0.3162    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3162
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7917
moved from start:          0.1504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6662  Z= 0.116
  Angle     :  0.529   6.973   9068  Z= 0.264
  Chirality :  0.041   0.147    959
  Planarity :  0.004   0.032   1169
  Dihedral  :  4.298  35.498    945
  Min Nonbonded Distance : 2.107

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 12.21 %
    Favored  : 86.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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 are not related in a simple way.
  whole:  0.47 (0.30), residues: 788
  helix:  1.21 (0.25), residues: 405
  sheet: -0.79 (0.65), residues: 55
  loop : -0.55 (0.34), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 219 
 TYR   0.019   0.001   TYR A 183 
 PHE   0.011   0.001   PHE C 490 
 TRP   0.022   0.001   TRP A 594 
 HIS   0.003   0.001   HIS A  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 6649)
  covalent geometry    : angle       0.51957 ( 9042)
  SS BOND              : bond        0.00263 (    7)
  SS BOND              : angle       1.88271 (   14)
  hydrogen bonds       : bond        0.03894 (  304)
  hydrogen bonds       : angle       4.32851 (  875)
  metal coordination   : bond        0.00167 (    2)
  link_NAG-ASN         : bond        0.00175 (    4)
  link_NAG-ASN         : angle       1.99981 (   12)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 108
  time to evaluate  : 0.232 
Fit side-chains
REVERT: A  267 LEU cc_start: 0.8463 (mt) cc_final: 0.8198 (mt)
REVERT: A  455 MET cc_start: 0.8735 (tmm) cc_final: 0.8095 (tmm)
REVERT: A  474 MET cc_start: 0.8449 (mmp) cc_final: 0.8053 (mmp)
REVERT: A  489 GLU cc_start: 0.8669 (pm20) cc_final: 0.8267 (pm20)
REVERT: C  356 LYS cc_start: 0.8039 (mppt) cc_final: 0.7823 (mmtt)
REVERT: C  396 TYR cc_start: 0.6996 (m-80) cc_final: 0.6433 (m-80)
REVERT: C  474 GLN cc_start: 0.7598 (tt0) cc_final: 0.7295 (tt0)
  outliers start: 7
  outliers final: 6
  residues processed: 112
  average time/residue: 0.0731
  time to fit residues: 11.4264
Evaluate side-chains
  108 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 102
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain C residue  379 CYS
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  489 TYR
Chi-restraints excluded: chain C residue  493 GLN
Chi-restraints excluded: chain C residue  514 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 34 optimal weight:   10.0000
   chunk 66 optimal weight:    4.9990
   chunk 35 optimal weight:    0.7980
   chunk 29 optimal weight:    0.6980
   chunk 0 optimal weight:   10.0000
   chunk 39 optimal weight:    0.8980
   chunk 24 optimal weight:    4.9990
   chunk 40 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   chunk 63 optimal weight:    7.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
** A 239 HIS ** 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 = 0.3725 r_free = 0.3725 target = 0.147842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.114689 restraints weight = 12315.660|
|-----------------------------------------------------------------------------|
r_work (start): 0.3282 rms_B_bonded: 2.68
r_work: 0.3160 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3160
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3145
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3145 r_free = 0.3145    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3145 r_free = 0.3145    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3145
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7935
moved from start:          0.1674

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6662  Z= 0.128
  Angle     :  0.529   6.764   9068  Z= 0.267
  Chirality :  0.041   0.136    959
  Planarity :  0.004   0.032   1169
  Dihedral  :  4.387  40.648    945
  Min Nonbonded Distance : 2.098

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 12.07 %
    Favored  : 86.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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 are not related in a simple way.
  whole:  0.63 (0.30), residues: 788
  helix:  1.31 (0.26), residues: 405
  sheet: -0.62 (0.66), residues: 55
  loop : -0.46 (0.34), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 219 
 TYR   0.018   0.001   TYR A 183 
 PHE   0.016   0.001   PHE C 490 
 TRP   0.016   0.001   TRP A 594 
 HIS   0.004   0.001   HIS A  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 6649)
  covalent geometry    : angle       0.51758 ( 9042)
  SS BOND              : bond        0.00287 (    7)
  SS BOND              : angle       1.98632 (   14)
  hydrogen bonds       : bond        0.03946 (  304)
  hydrogen bonds       : angle       4.33146 (  875)
  metal coordination   : bond        0.00196 (    2)
  link_NAG-ASN         : bond        0.00269 (    4)
  link_NAG-ASN         : angle       2.28091 (   12)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 104
  time to evaluate  : 0.231 
Fit side-chains
REVERT: A  267 LEU cc_start: 0.8421 (mt) cc_final: 0.8108 (mt)
REVERT: A  474 MET cc_start: 0.8493 (mmp) cc_final: 0.8099 (mmp)
REVERT: A  489 GLU cc_start: 0.8659 (pm20) cc_final: 0.8012 (pm20)
REVERT: C  356 LYS cc_start: 0.8048 (mppt) cc_final: 0.7812 (mmtp)
REVERT: C  396 TYR cc_start: 0.6984 (m-80) cc_final: 0.6356 (m-80)
  outliers start: 10
  outliers final: 8
  residues processed: 111
  average time/residue: 0.0737
  time to fit residues: 11.4047
Evaluate side-chains
  107 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 99
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain C residue  350 VAL
Chi-restraints excluded: chain C residue  379 CYS
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  489 TYR
Chi-restraints excluded: chain C residue  493 GLN
Chi-restraints excluded: chain C residue  514 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 63 optimal weight:    8.9990
   chunk 19 optimal weight:    0.8980
   chunk 8 optimal weight:    2.9990
   chunk 9 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9980
   chunk 75 optimal weight:    6.9990
   chunk 46 optimal weight:    4.9990
   chunk 45 optimal weight:    0.0470
   chunk 44 optimal weight:    0.8980
   chunk 28 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   overall best weight:    0.7478

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

Flipped N/Q/H residues before XYZ refinement:
A 345 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.149487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.118678 restraints weight = 18925.570|
|-----------------------------------------------------------------------------|
r_work (start): 0.3339 rms_B_bonded: 3.54
r_work: 0.3109 rms_B_bonded: 4.31 restraints_weight: 0.5000
r_work (final): 0.3109
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3100
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3100 r_free = 0.3100    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3100 r_free = 0.3100    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3100
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7989
moved from start:          0.1745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   6662  Z= 0.105
  Angle     :  0.516   7.027   9068  Z= 0.260
  Chirality :  0.041   0.136    959
  Planarity :  0.004   0.031   1169
  Dihedral  :  4.207  36.714    945
  Min Nonbonded Distance : 2.114

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 12.07 %
    Favored  : 86.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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 are not related in a simple way.
  whole:  0.79 (0.30), residues: 788
  helix:  1.42 (0.26), residues: 405
  sheet: -0.54 (0.67), residues: 55
  loop : -0.35 (0.35), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 219 
 TYR   0.016   0.001   TYR A 183 
 PHE   0.009   0.001   PHE C 490 
 TRP   0.013   0.001   TRP A 594 
 HIS   0.005   0.001   HIS A 345 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 ( 6649)
  covalent geometry    : angle       0.50597 ( 9042)
  SS BOND              : bond        0.00268 (    7)
  SS BOND              : angle       1.80777 (   14)
  hydrogen bonds       : bond        0.03731 (  304)
  hydrogen bonds       : angle       4.25579 (  875)
  metal coordination   : bond        0.00093 (    2)
  link_NAG-ASN         : bond        0.00190 (    4)
  link_NAG-ASN         : angle       2.04997 (   12)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 108
  time to evaluate  : 0.182 
Fit side-chains
REVERT: A   82 MET cc_start: 0.7920 (mtp) cc_final: 0.7633 (mpp)
REVERT: A  249 MET cc_start: 0.8349 (ptp) cc_final: 0.7928 (ttp)
REVERT: A  267 LEU cc_start: 0.8487 (mt) cc_final: 0.8205 (mt)
REVERT: A  350 ASP cc_start: 0.8063 (t0) cc_final: 0.7342 (p0)
REVERT: A  376 MET cc_start: 0.8612 (mmm) cc_final: 0.8384 (mmm)
REVERT: A  474 MET cc_start: 0.8559 (mmp) cc_final: 0.8186 (mmp)
REVERT: A  489 GLU cc_start: 0.8659 (pm20) cc_final: 0.8234 (pm20)
REVERT: A  589 GLU cc_start: 0.8443 (tm-30) cc_final: 0.8181 (tm-30)
REVERT: C  343 ASN cc_start: 0.7106 (m-40) cc_final: 0.6646 (p0)
REVERT: C  396 TYR cc_start: 0.6993 (m-80) cc_final: 0.6357 (m-80)
REVERT: C  406 GLU cc_start: 0.8335 (tt0) cc_final: 0.8123 (tt0)
REVERT: C  489 TYR cc_start: 0.7408 (OUTLIER) cc_final: 0.5791 (p90)
  outliers start: 9
  outliers final: 6
  residues processed: 113
  average time/residue: 0.0672
  time to fit residues: 10.9131
Evaluate side-chains
  107 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 100
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain C residue  350 VAL
Chi-restraints excluded: chain C residue  379 CYS
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  489 TYR
Chi-restraints excluded: chain C residue  493 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 34 optimal weight:    7.9990
   chunk 50 optimal weight:    3.9990
   chunk 47 optimal weight:    0.5980
   chunk 8 optimal weight:    0.9990
   chunk 17 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   overall best weight:    1.5188

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

Flipped N/Q/H residues before XYZ refinement:
A 345 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.147183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.114314 restraints weight = 11759.715|
|-----------------------------------------------------------------------------|
r_work (start): 0.3274 rms_B_bonded: 2.60
r_work: 0.3157 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3157
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3147
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3147 r_free = 0.3147    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3147 r_free = 0.3147    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3147
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7941
moved from start:          0.1790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6662  Z= 0.140
  Angle     :  0.545   8.187   9068  Z= 0.275
  Chirality :  0.042   0.159    959
  Planarity :  0.004   0.032   1169
  Dihedral  :  4.275  32.556    945
  Min Nonbonded Distance : 2.094

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 12.50 %
    Favored  : 86.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.70 (0.30), residues: 788
  helix:  1.24 (0.25), residues: 411
  sheet: -0.52 (0.69), residues: 56
  loop : -0.27 (0.35), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 518 
 TYR   0.018   0.001   TYR A 183 
 PHE   0.017   0.001   PHE C 490 
 TRP   0.012   0.001   TRP A 477 
 HIS   0.004   0.001   HIS A  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 6649)
  covalent geometry    : angle       0.53475 ( 9042)
  SS BOND              : bond        0.00342 (    7)
  SS BOND              : angle       2.11126 (   14)
  hydrogen bonds       : bond        0.04073 (  304)
  hydrogen bonds       : angle       4.32160 (  875)
  metal coordination   : bond        0.00226 (    2)
  link_NAG-ASN         : bond        0.00197 (    4)
  link_NAG-ASN         : angle       1.98091 (   12)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 102
  time to evaluate  : 0.238 
Fit side-chains
REVERT: A   82 MET cc_start: 0.7914 (mtp) cc_final: 0.7637 (mpp)
REVERT: A  267 LEU cc_start: 0.8445 (mt) cc_final: 0.8101 (mt)
REVERT: A  270 MET cc_start: 0.8443 (tpt) cc_final: 0.7808 (tpt)
REVERT: A  350 ASP cc_start: 0.8043 (t0) cc_final: 0.7271 (p0)
REVERT: A  376 MET cc_start: 0.8644 (mmm) cc_final: 0.8393 (mmm)
REVERT: A  589 GLU cc_start: 0.8377 (tm-30) cc_final: 0.8153 (tm-30)
REVERT: C  343 ASN cc_start: 0.7157 (m-40) cc_final: 0.6580 (p0)
REVERT: C  396 TYR cc_start: 0.6905 (m-80) cc_final: 0.6280 (m-80)
REVERT: C  489 TYR cc_start: 0.7352 (OUTLIER) cc_final: 0.5521 (p90)
  outliers start: 10
  outliers final: 8
  residues processed: 107
  average time/residue: 0.0650
  time to fit residues: 9.9571
Evaluate side-chains
  109 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 100
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  259 ILE
Chi-restraints excluded: chain A residue  487 VAL
Chi-restraints excluded: chain C residue  350 VAL
Chi-restraints excluded: chain C residue  379 CYS
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  489 TYR
Chi-restraints excluded: chain C residue  493 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 41 optimal weight:    3.9990
   chunk 5 optimal weight:    4.9990
   chunk 66 optimal weight:    0.5980
   chunk 34 optimal weight:    6.9990
   chunk 26 optimal weight:    0.1980
   chunk 35 optimal weight:    0.8980
   chunk 59 optimal weight:    0.0050
   chunk 24 optimal weight:    2.9990
   chunk 52 optimal weight:   10.0000
   chunk 37 optimal weight:    0.7980
   chunk 39 optimal weight:    0.8980
   overall best weight:    0.4994

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

Flipped N/Q/H residues before XYZ refinement:
A 345 HIS
C 354 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.150310 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.117408 restraints weight = 12206.633|
|-----------------------------------------------------------------------------|
r_work (start): 0.3297 rms_B_bonded: 2.69
r_work: 0.3180 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3180
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3167
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3167 r_free = 0.3167    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3167 r_free = 0.3167    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3167
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
moved from start:          0.1902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   6662  Z= 0.099
  Angle     :  0.515   7.630   9068  Z= 0.259
  Chirality :  0.041   0.152    959
  Planarity :  0.004   0.031   1169
  Dihedral  :  4.113  32.613    945
  Min Nonbonded Distance : 2.123

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 12.93 %
    Favored  : 85.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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 are not related in a simple way.
  whole:  1.00 (0.30), residues: 788
  helix:  1.59 (0.26), residues: 399
  sheet: -0.26 (0.70), residues: 51
  loop : -0.24 (0.35), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 219 
 TYR   0.016   0.001   TYR A 183 
 PHE   0.011   0.001   PHE C 490 
 TRP   0.011   0.001   TRP A 594 
 HIS   0.004   0.001   HIS A 345 

Details of bonding type rmsd
  covalent geometry    : bond        0.00213 ( 6649)
  covalent geometry    : angle       0.50504 ( 9042)
  SS BOND              : bond        0.00236 (    7)
  SS BOND              : angle       2.03251 (   14)
  hydrogen bonds       : bond        0.03609 (  304)
  hydrogen bonds       : angle       4.20203 (  875)
  metal coordination   : bond        0.00058 (    2)
  link_NAG-ASN         : bond        0.00195 (    4)
  link_NAG-ASN         : angle       1.78852 (   12)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 109
  time to evaluate  : 0.243 
Fit side-chains
REVERT: A   82 MET cc_start: 0.7738 (mtp) cc_final: 0.7477 (mpp)
REVERT: A  249 MET cc_start: 0.8352 (ptp) cc_final: 0.7952 (ttp)
REVERT: A  267 LEU cc_start: 0.8460 (mt) cc_final: 0.8164 (mt)
REVERT: A  350 ASP cc_start: 0.7952 (t0) cc_final: 0.7221 (p0)
REVERT: A  376 MET cc_start: 0.8593 (mmm) cc_final: 0.8343 (mmm)
REVERT: A  474 MET cc_start: 0.8456 (mmp) cc_final: 0.8137 (mmp)
REVERT: A  489 GLU cc_start: 0.8672 (pm20) cc_final: 0.8108 (pm20)
REVERT: A  589 GLU cc_start: 0.8396 (tm-30) cc_final: 0.8191 (tm-30)
REVERT: C  396 TYR cc_start: 0.6959 (m-80) cc_final: 0.6273 (m-80)
REVERT: C  489 TYR cc_start: 0.7159 (OUTLIER) cc_final: 0.5700 (p90)
  outliers start: 10
  outliers final: 6
  residues processed: 115
  average time/residue: 0.0690
  time to fit residues: 11.1803
Evaluate side-chains
  109 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 102
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain C residue  350 VAL
Chi-restraints excluded: chain C residue  379 CYS
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  489 TYR
Chi-restraints excluded: chain C residue  493 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 17 optimal weight:    6.9990
   chunk 14 optimal weight:    3.9990
   chunk 30 optimal weight:    0.0000
   chunk 24 optimal weight:    0.9980
   chunk 57 optimal weight:    0.6980
   chunk 31 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9990
   chunk 6 optimal weight:    0.3980
   chunk 15 optimal weight:    1.9990
   chunk 45 optimal weight:    4.9990
   chunk 8 optimal weight:    0.6980
   overall best weight:    0.5584

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

Flipped N/Q/H residues before XYZ refinement:
A 338 ASN
A 345 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.150557 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.117514 restraints weight = 12373.404|
|-----------------------------------------------------------------------------|
r_work (start): 0.3319 rms_B_bonded: 2.73
r_work: 0.3201 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3172
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3172 r_free = 0.3172    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3172 r_free = 0.3172    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3172
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7892
moved from start:          0.1962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   6662  Z= 0.098
  Angle     :  0.512   7.740   9068  Z= 0.257
  Chirality :  0.040   0.146    959
  Planarity :  0.004   0.031   1169
  Dihedral  :  4.029  31.269    945
  Min Nonbonded Distance : 2.107

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 14.08 %
    Favored  : 84.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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 are not related in a simple way.
  whole:  1.04 (0.30), residues: 788
  helix:  1.61 (0.26), residues: 399
  sheet: -0.33 (0.69), residues: 51
  loop : -0.20 (0.35), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 219 
 TYR   0.010   0.001   TYR A 381 
 PHE   0.009   0.001   PHE C 490 
 TRP   0.010   0.001   TRP A 594 
 HIS   0.004   0.001   HIS A 345 

Details of bonding type rmsd
  covalent geometry    : bond        0.00213 ( 6649)
  covalent geometry    : angle       0.50311 ( 9042)
  SS BOND              : bond        0.00187 (    7)
  SS BOND              : angle       2.02058 (   14)
  hydrogen bonds       : bond        0.03573 (  304)
  hydrogen bonds       : angle       4.17726 (  875)
  metal coordination   : bond        0.00074 (    2)
  link_NAG-ASN         : bond        0.00205 (    4)
  link_NAG-ASN         : angle       1.69081 (   12)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 101
  time to evaluate  : 0.252 
Fit side-chains
REVERT: A   82 MET cc_start: 0.7699 (mtp) cc_final: 0.7440 (mpp)
REVERT: A  249 MET cc_start: 0.8363 (ptp) cc_final: 0.7961 (ttp)
REVERT: A  267 LEU cc_start: 0.8455 (mt) cc_final: 0.8129 (mt)
REVERT: A  270 MET cc_start: 0.8399 (tpt) cc_final: 0.7759 (tpt)
REVERT: A  350 ASP cc_start: 0.7960 (t0) cc_final: 0.7219 (p0)
REVERT: A  376 MET cc_start: 0.8576 (mmm) cc_final: 0.8311 (mmm)
REVERT: A  474 MET cc_start: 0.8408 (mmp) cc_final: 0.8058 (mmp)
REVERT: A  489 GLU cc_start: 0.8661 (pm20) cc_final: 0.8114 (pm20)
REVERT: A  589 GLU cc_start: 0.8389 (tm-30) cc_final: 0.8188 (tm-30)
REVERT: C  396 TYR cc_start: 0.6954 (m-80) cc_final: 0.6279 (m-80)
REVERT: C  489 TYR cc_start: 0.7263 (OUTLIER) cc_final: 0.5739 (p90)
  outliers start: 7
  outliers final: 5
  residues processed: 106
  average time/residue: 0.0668
  time to fit residues: 10.2004
Evaluate side-chains
  103 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 97
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain C residue  350 VAL
Chi-restraints excluded: chain C residue  379 CYS
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  489 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 20 optimal weight:    4.9990
   chunk 19 optimal weight:    0.6980
   chunk 11 optimal weight:    6.9990
   chunk 58 optimal weight:    6.9990
   chunk 25 optimal weight:    0.9980
   chunk 27 optimal weight:    0.6980
   chunk 65 optimal weight:    7.9990
   chunk 54 optimal weight:    0.0370
   chunk 24 optimal weight:    5.9990
   chunk 9 optimal weight:    2.9990
   chunk 70 optimal weight:    4.9990
   overall best weight:    1.0860

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

Flipped N/Q/H residues before XYZ refinement:
** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 338 ASN
A 345 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.149215 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.117284 restraints weight = 11698.085|
|-----------------------------------------------------------------------------|
r_work (start): 0.3296 rms_B_bonded: 2.56
r_work: 0.3179 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3155
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3155 r_free = 0.3155    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3155 r_free = 0.3155    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3155
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.1950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6662  Z= 0.116
  Angle     :  0.518   7.731   9068  Z= 0.262
  Chirality :  0.041   0.147    959
  Planarity :  0.004   0.031   1169
  Dihedral  :  4.085  28.667    945
  Min Nonbonded Distance : 2.108

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 14.37 %
    Favored  : 84.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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 are not related in a simple way.
  whole:  0.99 (0.30), residues: 788
  helix:  1.48 (0.26), residues: 405
  sheet: -0.20 (0.69), residues: 50
  loop : -0.14 (0.35), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 518 
 TYR   0.017   0.001   TYR A 279 
 PHE   0.014   0.001   PHE C 490 
 TRP   0.010   0.001   TRP A 594 
 HIS   0.004   0.001   HIS A 345 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 6649)
  covalent geometry    : angle       0.50854 ( 9042)
  SS BOND              : bond        0.00229 (    7)
  SS BOND              : angle       2.06318 (   14)
  hydrogen bonds       : bond        0.03790 (  304)
  hydrogen bonds       : angle       4.21439 (  875)
  metal coordination   : bond        0.00141 (    2)
  link_NAG-ASN         : bond        0.00202 (    4)
  link_NAG-ASN         : angle       1.77031 (   12)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 99
  time to evaluate  : 0.256 
Fit side-chains
REVERT: A  249 MET cc_start: 0.8377 (ptp) cc_final: 0.7965 (ttp)
REVERT: A  267 LEU cc_start: 0.8490 (mt) cc_final: 0.8162 (mt)
REVERT: A  270 MET cc_start: 0.8464 (tpt) cc_final: 0.7871 (tpt)
REVERT: A  350 ASP cc_start: 0.8011 (t0) cc_final: 0.7225 (p0)
REVERT: A  376 MET cc_start: 0.8572 (mmm) cc_final: 0.8304 (mmm)
REVERT: A  474 MET cc_start: 0.8439 (mmp) cc_final: 0.8082 (mmp)
REVERT: A  489 GLU cc_start: 0.8651 (pm20) cc_final: 0.8343 (pm20)
REVERT: C  396 TYR cc_start: 0.6960 (m-80) cc_final: 0.6333 (m-80)
REVERT: C  489 TYR cc_start: 0.7377 (OUTLIER) cc_final: 0.5641 (p90)
  outliers start: 7
  outliers final: 5
  residues processed: 104
  average time/residue: 0.0701
  time to fit residues: 10.4393
Evaluate side-chains
  102 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 96
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain C residue  350 VAL
Chi-restraints excluded: chain C residue  379 CYS
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  489 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 13 optimal weight:    4.9990
   chunk 46 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 36 optimal weight:    0.6980
   chunk 60 optimal weight:    0.9990
   chunk 24 optimal weight:    0.8980
   chunk 63 optimal weight:    3.9990
   chunk 25 optimal weight:    0.0770
   overall best weight:    0.7340

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

Flipped N/Q/H residues before XYZ refinement:
A 338 ASN
A 345 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.149938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.119259 restraints weight = 17347.156|
|-----------------------------------------------------------------------------|
r_work (start): 0.3352 rms_B_bonded: 3.06
r_work: 0.3141 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3098
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3098 r_free = 0.3098    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3098 r_free = 0.3098    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3098
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7967
moved from start:          0.1995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   6662  Z= 0.105
  Angle     :  0.521   7.208   9068  Z= 0.263
  Chirality :  0.041   0.144    959
  Planarity :  0.004   0.031   1169
  Dihedral  :  4.031  28.063    945
  Min Nonbonded Distance : 2.115

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 14.51 %
    Favored  : 84.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.04 (0.30), residues: 788
  helix:  1.50 (0.26), residues: 405
  sheet: -0.22 (0.68), residues: 50
  loop : -0.08 (0.35), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 219 
 TYR   0.016   0.001   TYR A 279 
 PHE   0.019   0.001   PHE C 490 
 TRP   0.010   0.001   TRP A 594 
 HIS   0.004   0.001   HIS A 345 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 ( 6649)
  covalent geometry    : angle       0.51161 ( 9042)
  SS BOND              : bond        0.00205 (    7)
  SS BOND              : angle       2.00153 (   14)
  hydrogen bonds       : bond        0.03655 (  304)
  hydrogen bonds       : angle       4.17727 (  875)
  metal coordination   : bond        0.00110 (    2)
  link_NAG-ASN         : bond        0.00191 (    4)
  link_NAG-ASN         : angle       1.74688 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1852.58 seconds
wall clock time: 32 minutes 21.79 seconds (1941.79 seconds total)