Starting phenix.real_space_refine
on Fri Sep 11 01:55:16 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7t9l_25761/09_2026/7t9l_25761.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7t9l_25761/09_2026/7t9l_25761.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.66
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/cci-nas-00/data/ceres_data/7t9l_25761/09_2026/7t9l_25761.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7t9l_25761/09_2026/7t9l_25761.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7t9l_25761/09_2026/7t9l_25761.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7t9l_25761/09_2026/7t9l_25761.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7t9l_25761/09_2026/7t9l_25761.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7t9l_25761/09_2026/7t9l_25761.map"
  }
  resolution = 2.66
  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=  -0.001 sd=   0.016
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      37      5.16       5
     C    4203      2.51       5
     N    1084      2.21       5
     O    1243      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 6567
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1612
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1612
          Classifications: {'peptide': 201}
          Link IDs: {'PTRANS': 12, 'TRANS': 188}
    Chain: "D"
      Number of atoms: 4857
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 595, 4857
          Classifications: {'peptide': 595}
          Link IDs: {'PTRANS': 27, 'TRANS': 567}
    Chain: "A"
      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 chiralities: 1
    Chain: "D"
      Number of atoms: 84
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 84
          Unusual residues: {'NAG': 6}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen chiralities: 6
  Time building chain proxies: 1.59, per 1000 atoms: 0.24
  Number of scatterers: 6567
  At special positions: 0
  Unit cell: (78, 86, 122, 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      37     16.00
     O    1243      8.00
     N    1084      7.00
     C    4203      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 133 " - pdb=" SG  CYS D 141 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 530 " - pdb=" SG  CYS D 542 " distance=2.02

  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 A1301 " - " ASN A 343 "
      " NAG D 701 " - " ASN D  53 "
      " NAG D 702 " - " ASN D  90 "
      " NAG D 703 " - " ASN D 103 "
      " NAG D 704 " - " ASN D 322 "
      " NAG D 705 " - " ASN D 432 "
      " NAG D 706 " - " ASN D 546 "
  Time building additional restraints: 0.59
  Conformation dependent library (CDL) restraints added in 370.8 milliseconds
  

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1504

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 5 sheets defined
      56.4% alpha, 5.5% 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 338 through 343
    Processing helix  chain 'A' and resid 365 through 370
    Processing helix  chain 'A' and resid 384 through 389
      removed outlier: 3.680A  pdb=" N   LEU A 387 " --> pdb=" O   PRO A 384 " (cutoff:3.500A)
      removed outlier: 4.206A  pdb=" N   ASN A 388 " --> pdb=" O   THR A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 422
    Processing helix  chain 'A' and resid 438 through 443
      removed outlier: 3.679A  pdb=" N   SER A 443 " --> pdb=" O   ASN A 439 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 20 through 52
    Processing helix  chain 'D' and resid 55 through 81
    Processing helix  chain 'D' and resid 90 through 101
    Processing helix  chain 'D' and resid 103 through 108
      removed outlier: 4.206A  pdb=" N   VAL D 107 " --> pdb=" O   GLY D 104 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   LEU D 108 " --> pdb=" O   SER D 105 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 109 through 129
    Processing helix  chain 'D' and resid 147 through 155
      removed outlier: 3.622A  pdb=" N   SER D 155 " --> pdb=" O   ILE D 151 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 157 through 194
      Proline residue:  D 178  - end of helix
      removed outlier: 3.809A  pdb=" N   VAL D 185 " --> pdb=" O   GLU D 181 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 198 through 205
    Processing helix  chain 'D' and resid 206 through 208
      No H-bonds generated for 'chain 'D' and resid 206 through 208'
    Processing helix  chain 'D' and resid 220 through 252
      removed outlier: 4.532A  pdb=" N   GLU D 224 " --> pdb=" O   GLY D 220 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   GLU D 232 " --> pdb=" O   HIS D 228 " (cutoff:3.500A)
      Proline residue:  D 235  - end of helix
    Processing helix  chain 'D' and resid 265 through 267
      No H-bonds generated for 'chain 'D' and resid 265 through 267'
    Processing helix  chain 'D' and resid 275 through 279
      removed outlier: 3.767A  pdb=" N   TYR D 279 " --> pdb=" O   THR D 276 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 293 through 300
    Processing helix  chain 'D' and resid 303 through 319
    Processing helix  chain 'D' and resid 324 through 331
      removed outlier: 3.500A  pdb=" N   TRP D 328 " --> pdb=" O   THR D 324 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 365 through 385
      removed outlier: 3.721A  pdb=" N   TYR D 385 " --> pdb=" O   TYR D 381 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 386 through 388
      No H-bonds generated for 'chain 'D' and resid 386 through 388'
    Processing helix  chain 'D' and resid 389 through 393
    Processing helix  chain 'D' and resid 397 through 413
      removed outlier: 4.352A  pdb=" N   HIS D 401 " --> pdb=" O   ASN D 397 " (cutoff:3.500A)
      removed outlier: 4.661A  pdb=" N   GLU D 402 " --> pdb=" O   GLU D 398 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   GLY D 405 " --> pdb=" O   HIS D 401 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   MET D 408 " --> pdb=" O   VAL D 404 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   ALA D 413 " --> pdb=" O   SER D 409 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 414 through 421
    Processing helix  chain 'D' and resid 431 through 447
      removed outlier: 3.518A  pdb=" N   GLU D 435 " --> pdb=" O   ASP D 431 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 448 through 466
      removed outlier: 4.389A  pdb=" N   PHE D 452 " --> pdb=" O   GLY D 448 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 469 through 471
      No H-bonds generated for 'chain 'D' and resid 469 through 471'
    Processing helix  chain 'D' and resid 472 through 484
    Processing helix  chain 'D' and resid 499 through 502
      removed outlier: 3.826A  pdb=" N   SER D 502 " --> pdb=" O   ASP D 499 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 499 through 502'
    Processing helix  chain 'D' and resid 503 through 508
    Processing helix  chain 'D' and resid 512 through 533
      removed outlier: 4.344A  pdb=" N   TYR D 516 " --> pdb=" O   PHE D 512 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   PHE D 523 " --> pdb=" O   THR D 519 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 538 through 542
    Processing helix  chain 'D' and resid 547 through 559
      removed outlier: 4.000A  pdb=" N   MET D 557 " --> pdb=" O   LYS D 553 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 565 through 575
    Processing helix  chain 'D' and resid 581 through 588
    Processing helix  chain 'D' and resid 588 through 599
    Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358
    Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474
    Processing sheet with id=AA4, first strand: chain 'D' and resid 262 through 263
      removed outlier: 5.972A  pdb=" N   LEU D 262 " --> pdb=" O   VAL D 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'D' and resid 347 through 352
      removed outlier: 6.218A  pdb=" N   ASP D 355 " --> pdb=" O   LEU D 351 " (cutoff:3.500A)

    315 hydrogen bonds defined for protein.
    906 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: 0.85

  Time building geometry restraints manager: 0.83 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2050
        1.34 -     1.46: 1710
        1.46 -     1.58: 2934
        1.58 -     1.70: 0
        1.70 -     1.82: 58
  Bond restraints: 6752
  Sorted by residual:
  bond pdb=" CG  LEU D 558 "
       pdb=" CD1 LEU D 558 "
    ideal  model  delta    sigma   weight residual
    1.521  1.443  0.078 3.30e-02 9.18e+02 5.55e+00
  bond pdb=" C1  NAG D 706 "
       pdb=" O5  NAG D 706 "
    ideal  model  delta    sigma   weight residual
    1.406  1.450 -0.044 2.00e-02 2.50e+03 4.80e+00
  bond pdb=" C1  NAG D 705 "
       pdb=" O5  NAG D 705 "
    ideal  model  delta    sigma   weight residual
    1.406  1.446 -0.040 2.00e-02 2.50e+03 4.08e+00
  bond pdb=" C1  NAG D 701 "
       pdb=" O5  NAG D 701 "
    ideal  model  delta    sigma   weight residual
    1.406  1.446 -0.040 2.00e-02 2.50e+03 4.05e+00
  bond pdb=" C1  NAG D 702 "
       pdb=" O5  NAG D 702 "
    ideal  model  delta    sigma   weight residual
    1.406  1.445 -0.039 2.00e-02 2.50e+03 3.90e+00
  ... (remaining 6747 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.65: 8952
        2.65 -     5.31: 188
        5.31 -     7.96: 25
        7.96 -    10.62: 8
       10.62 -    13.27: 3
  Bond angle restraints: 9176
  Sorted by residual:
  angle pdb=" CB  LYS D 534 "
        pdb=" CG  LYS D 534 "
        pdb=" CD  LYS D 534 "
      ideal   model   delta    sigma   weight residual
     111.30  121.60  -10.30 2.30e+00 1.89e-01 2.00e+01
  angle pdb=" CB  MET D 152 "
        pdb=" CG  MET D 152 "
        pdb=" SD  MET D 152 "
      ideal   model   delta    sigma   weight residual
     112.70  125.97  -13.27 3.00e+00 1.11e-01 1.96e+01
  angle pdb=" C   SER A 359 "
        pdb=" N   ASN A 360 "
        pdb=" CA  ASN A 360 "
      ideal   model   delta    sigma   weight residual
     122.46  128.55   -6.09 1.41e+00 5.03e-01 1.86e+01
  angle pdb=" CB  MET D 323 "
        pdb=" CG  MET D 323 "
        pdb=" SD  MET D 323 "
      ideal   model   delta    sigma   weight residual
     112.70  125.10  -12.40 3.00e+00 1.11e-01 1.71e+01
  angle pdb=" CB  LYS D 600 "
        pdb=" CG  LYS D 600 "
        pdb=" CD  LYS D 600 "
      ideal   model   delta    sigma   weight residual
     111.30  119.94   -8.64 2.30e+00 1.89e-01 1.41e+01
  ... (remaining 9171 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.94: 3537
       17.94 -    35.89: 328
       35.89 -    53.83: 52
       53.83 -    71.78: 11
       71.78 -    89.72: 6
  Dihedral angle restraints: 3934
    sinusoidal: 1593
      harmonic: 2341
  Sorted by residual:
  dihedral pdb=" CB  CYS D 133 "
           pdb=" SG  CYS D 133 "
           pdb=" SG  CYS D 141 "
           pdb=" CB  CYS D 141 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   38.00   55.00     1      1.00e+01 1.00e-02 4.09e+01
  dihedral pdb=" CA  GLN D 139 "
           pdb=" C   GLN D 139 "
           pdb=" N   GLU D 140 "
           pdb=" CA  GLU D 140 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.63   21.37     0      5.00e+00 4.00e-02 1.83e+01
  dihedral pdb=" CA  ALA D 396 "
           pdb=" C   ALA D 396 "
           pdb=" N   ASN D 397 "
           pdb=" CA  ASN D 397 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.15   20.85     0      5.00e+00 4.00e-02 1.74e+01
  ... (remaining 3931 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 644
       0.048 -    0.095: 230
       0.095 -    0.143: 85
       0.143 -    0.191: 14
       0.191 -    0.239: 7
  Chirality restraints: 980
  Sorted by residual:
  chirality pdb=" CG  LEU D 267 "
            pdb=" CB  LEU D 267 "
            pdb=" CD1 LEU D 267 "
            pdb=" CD2 LEU D 267 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.35   -0.24 2.00e-01 2.50e+01 1.42e+00
  chirality pdb=" CB  VAL D 581 "
            pdb=" CA  VAL D 581 "
            pdb=" CG1 VAL D 581 "
            pdb=" CG2 VAL D 581 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.40   -0.22 2.00e-01 2.50e+01 1.26e+00
  chirality pdb=" CB  ILE A 332 "
            pdb=" CA  ILE A 332 "
            pdb=" CG1 ILE A 332 "
            pdb=" CG2 ILE A 332 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.44    0.20 2.00e-01 2.50e+01 1.04e+00
  ... (remaining 977 not shown)

  Planarity restraints: 1186
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS D  68 "    0.022 2.00e-02 2.50e+03   4.47e-02 2.00e+01
        pdb=" C   LYS D  68 "   -0.077 2.00e-02 2.50e+03
        pdb=" O   LYS D  68 "    0.029 2.00e-02 2.50e+03
        pdb=" N   TRP D  69 "    0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS D 241 "   -0.017 2.00e-02 2.50e+03   3.34e-02 1.11e+01
        pdb=" C   HIS D 241 "    0.058 2.00e-02 2.50e+03
        pdb=" O   HIS D 241 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   ALA D 242 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU D 240 "   -0.016 2.00e-02 2.50e+03   3.25e-02 1.05e+01
        pdb=" C   LEU D 240 "    0.056 2.00e-02 2.50e+03
        pdb=" O   LEU D 240 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   HIS D 241 "   -0.019 2.00e-02 2.50e+03
  ... (remaining 1183 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 1755
        2.80 -     3.33: 5984
        3.33 -     3.85: 11578
        3.85 -     4.38: 13246
        4.38 -     4.90: 22673
  Nonbonded interactions: 55236
  Sorted by model distance:
  nonbonded pdb=" OH  TYR D 183 "
            pdb=" OD1 ASP D 509 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" OH  TYR D 217 "
            pdb=" OD2 ASP D 225 "
     model   vdw
     2.329 3.040
  nonbonded pdb=" NZ  LYS D 475 "
            pdb=" OE1 GLU D 495 "
     model   vdw
     2.333 3.120
  nonbonded pdb=" OG  SER D 170 "
            pdb=" NZ  LYS D 174 "
     model   vdw
     2.341 3.120
  nonbonded pdb=" NH1 ARG A 457 "
            pdb=" OD2 ASP A 467 "
     model   vdw
     2.360 3.120
  ... (remaining 55231 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             6.230
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.790
  Find NCS groups from input model:        0.030
  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:6.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.190
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8384
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      :  0.006   0.078   6765  Z= 0.276
  Angle     :  0.963  13.272   9209  Z= 0.498
  Chirality :  0.058   0.239    980
  Planarity :  0.009   0.076   1179
  Dihedral  : 14.260  89.721   2412
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 3.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  2.42 %
    Favored  : 97.44 %
  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: -1.53 (0.26), residues: 792
  helix: -1.05 (0.22), residues: 393
  sheet:  0.51 (0.73), residues: 44
  loop : -1.02 (0.30), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG D 582 
 TYR   0.029   0.002   TYR D 385 
 PHE   0.038   0.003   PHE A 347 
 TRP   0.016   0.002   TRP D 594 
 HIS   0.009   0.002   HIS D 401 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00620 /  0.28 ( 6752)
  covalent geometry    : angle       0.95564 /  0.50 ( 9176)
  SS BOND              : bond        0.00399 /  0.28 (    6)
  SS BOND              : angle       1.60971 /  0.94 (   12)
  hydrogen bonds       : bond        0.13902 /  8.79 (  315)
  hydrogen bonds       : angle       6.75111 /  4.81 (  906)
  link_NAG-ASN         : bond        0.00532 /  0.17 (    7)
  link_NAG-ASN         : angle       2.46026 /  1.93 (   21)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 185
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
REVERT: A  390 LEU cc_start: 0.8386 (tp) cc_final: 0.8131 (tt)
REVERT: D  110 GLU cc_start: 0.8260 (tp30) cc_final: 0.7953 (tp30)
REVERT: D  114 LYS cc_start: 0.9112 (ttpp) cc_final: 0.8730 (tppt)
REVERT: D  291 ILE cc_start: 0.8288 (mt) cc_final: 0.7977 (mm)
REVERT: D  366 MET cc_start: 0.8645 (ttp) cc_final: 0.8381 (ttp)
REVERT: D  435 GLU cc_start: 0.7712 (mt-10) cc_final: 0.7390 (mm-30)
REVERT: D  471 ASP cc_start: 0.8816 (p0) cc_final: 0.8579 (p0)
REVERT: D  472 GLN cc_start: 0.8345 (mm110) cc_final: 0.7892 (mm-40)
REVERT: D  579 MET cc_start: 0.8879 (mtm) cc_final: 0.8644 (ttm)
REVERT: D  582 ARG cc_start: 0.8043 (mmm160) cc_final: 0.7712 (mmm160)
  outliers start: 1
  outliers final: 1
  residues processed: 185
  average time/residue: 0.6042
  time to fit residues: 116.9612
Evaluate side-chains
  119 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 118
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  339 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    0.6980
   chunk 74 optimal weight:    0.8980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D  42 GLN
D 175 GLN
D 374 HIS
D 472 GLN
D 598 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.104705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.078539 restraints weight = 12010.023|
|-----------------------------------------------------------------------------|
r_work (start): 0.3105 rms_B_bonded: 2.82
r_work: 0.2976 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.2976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8493
moved from start:          0.2484

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   6765  Z= 0.188
  Angle     :  0.660  10.538   9209  Z= 0.335
  Chirality :  0.045   0.168    980
  Planarity :  0.005   0.038   1179
  Dihedral  :  6.058 119.514    868
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 14.53 %
    Favored  : 82.62 %
  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:  0.12 (0.29), residues: 792
  helix:  0.49 (0.26), residues: 390
  sheet:  0.13 (0.73), residues: 49
  loop : -0.25 (0.32), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 466 
 TYR   0.017   0.001   TYR D  41 
 PHE   0.019   0.002   PHE D 400 
 TRP   0.017   0.002   TRP D 165 
 HIS   0.006   0.001   HIS D 241 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00424 /  0.19 ( 6752)
  covalent geometry    : angle       0.64948 /  0.33 ( 9176)
  SS BOND              : bond        0.00910 /  0.53 (    6)
  SS BOND              : angle       2.70564 /  1.11 (   12)
  hydrogen bonds       : bond        0.05289 /  3.50 (  315)
  hydrogen bonds       : angle       4.95779 /  3.48 (  906)
  link_NAG-ASN         : bond        0.00272 /  0.10 (    7)
  link_NAG-ASN         : angle       1.56545 /  1.23 (   21)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 118
  time to evaluate  : 0.241 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  390 LEU cc_start: 0.8510 (tp) cc_final: 0.8252 (tt)
REVERT: A  444 LYS cc_start: 0.8867 (mttt) cc_final: 0.8472 (mttp)
REVERT: D  114 LYS cc_start: 0.9279 (ttpp) cc_final: 0.8938 (tppt)
REVERT: D  287 GLN cc_start: 0.9172 (mm-40) cc_final: 0.8811 (tm-30)
REVERT: D  297 MET cc_start: 0.9205 (mtm) cc_final: 0.8803 (mtp)
REVERT: D  366 MET cc_start: 0.8546 (ttp) cc_final: 0.8334 (ttp)
REVERT: D  435 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7948 (mm-30)
REVERT: D  579 MET cc_start: 0.9187 (mtm) cc_final: 0.8782 (ttm)
  outliers start: 20
  outliers final: 6
  residues processed: 127
  average time/residue: 0.5239
  time to fit residues: 70.1773
Evaluate side-chains
  104 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 98
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  380 TYR
Chi-restraints excluded: chain A residue  503 VAL
Chi-restraints excluded: chain D residue  162 LEU
Chi-restraints excluded: chain D residue  238 GLU
Chi-restraints excluded: chain D residue  359 LEU
Chi-restraints excluded: chain D residue  604 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 47 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9990
   chunk 8 optimal weight:    0.8980
   chunk 56 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9980
   chunk 14 optimal weight:    0.5980
   chunk 12 optimal weight:    0.3980
   chunk 19 optimal weight:    4.9990
   chunk 21 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   overall best weight:    0.7782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D 134 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.103495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.077097 restraints weight = 12021.515|
|-----------------------------------------------------------------------------|
r_work (start): 0.3076 rms_B_bonded: 2.83
r_work: 0.2944 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.2944
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8465
moved from start:          0.2879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6765  Z= 0.178
  Angle     :  0.636   9.741   9209  Z= 0.323
  Chirality :  0.045   0.234    980
  Planarity :  0.004   0.037   1179
  Dihedral  :  4.349  18.336    866
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 17.24 %
    Favored  : 79.91 %
  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:  0.60 (0.29), residues: 792
  helix:  0.88 (0.26), residues: 396
  sheet:  0.12 (0.71), residues: 49
  loop :  0.03 (0.33), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 466 
 TYR   0.017   0.001   TYR D 385 
 PHE   0.018   0.002   PHE D 400 
 TRP   0.013   0.001   TRP D 165 
 HIS   0.004   0.001   HIS D 241 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00401 /  0.18 ( 6752)
  covalent geometry    : angle       0.62332 /  0.32 ( 9176)
  SS BOND              : bond        0.00582 /  0.37 (    6)
  SS BOND              : angle       3.25443 /  2.22 (   12)
  hydrogen bonds       : bond        0.05099 /  3.38 (  315)
  hydrogen bonds       : angle       4.75553 /  3.34 (  906)
  link_NAG-ASN         : bond        0.00257 /  0.08 (    7)
  link_NAG-ASN         : angle       1.32928 /  1.02 (   21)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 104
  time to evaluate  : 0.277 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  500 THR cc_start: 0.9395 (p) cc_final: 0.9194 (p)
REVERT: D  115 ARG cc_start: 0.8278 (tpm-80) cc_final: 0.7815 (tpm-80)
REVERT: D  123 MET cc_start: 0.7917 (OUTLIER) cc_final: 0.7379 (mtt)
REVERT: D  189 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8533 (tp30)
REVERT: D  510 TYR cc_start: 0.8629 (m-80) cc_final: 0.8393 (m-80)
REVERT: D  579 MET cc_start: 0.9222 (mtm) cc_final: 0.8875 (ttm)
  outliers start: 20
  outliers final: 7
  residues processed: 115
  average time/residue: 0.5539
  time to fit residues: 67.1070
Evaluate side-chains
  105 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 96
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  380 TYR
Chi-restraints excluded: chain A residue  391 CYS
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  503 VAL
Chi-restraints excluded: chain D residue  123 MET
Chi-restraints excluded: chain D residue  162 LEU
Chi-restraints excluded: chain D residue  189 GLU
Chi-restraints excluded: chain D residue  359 LEU
Chi-restraints excluded: chain D residue  604 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 7 optimal weight:    0.4980
   chunk 5 optimal weight:    0.9990
   chunk 24 optimal weight:    0.7980
   chunk 64 optimal weight:    2.9990
   chunk 15 optimal weight:    0.0370
   chunk 68 optimal weight:    0.9980
   chunk 19 optimal weight:    4.9990
   chunk 46 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 26 optimal weight:    0.8980
   overall best weight:    0.6458

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D 175 GLN
D 598 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.103547 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.077240 restraints weight = 12034.841|
|-----------------------------------------------------------------------------|
r_work (start): 0.3085 rms_B_bonded: 2.84
r_work: 0.2956 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.2956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8446
moved from start:          0.3223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   6765  Z= 0.159
  Angle     :  0.636  11.524   9209  Z= 0.316
  Chirality :  0.044   0.245    980
  Planarity :  0.004   0.036   1179
  Dihedral  :  4.224  17.876    866
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 18.23 %
    Favored  : 78.35 %
  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:  0.98 (0.30), residues: 792
  helix:  1.19 (0.26), residues: 391
  sheet: -0.09 (0.65), residues: 59
  loop :  0.32 (0.34), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 466 
 TYR   0.015   0.001   TYR D 385 
 PHE   0.015   0.001   PHE D 369 
 TRP   0.011   0.001   TRP D 165 
 HIS   0.003   0.001   HIS D 241 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00359 /  0.16 ( 6752)
  covalent geometry    : angle       0.62343 /  0.31 ( 9176)
  SS BOND              : bond        0.00770 /  0.53 (    6)
  SS BOND              : angle       3.23391 /  2.29 (   12)
  hydrogen bonds       : bond        0.04810 /  3.20 (  315)
  hydrogen bonds       : angle       4.66736 /  3.28 (  906)
  link_NAG-ASN         : bond        0.00224 /  0.07 (    7)
  link_NAG-ASN         : angle       1.16108 /  0.88 (   21)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 105
  time to evaluate  : 0.207 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  500 THR cc_start: 0.9367 (p) cc_final: 0.9149 (p)
REVERT: D  114 LYS cc_start: 0.8977 (mmpt) cc_final: 0.8467 (tppt)
REVERT: D  115 ARG cc_start: 0.8277 (tpm-80) cc_final: 0.7781 (tpm-80)
REVERT: D  123 MET cc_start: 0.7889 (OUTLIER) cc_final: 0.7426 (mtt)
REVERT: D  287 GLN cc_start: 0.9186 (mm-40) cc_final: 0.8936 (tm-30)
REVERT: D  297 MET cc_start: 0.9090 (mtm) cc_final: 0.8722 (mtp)
REVERT: D  383 MET cc_start: 0.9024 (mtp) cc_final: 0.8814 (mtm)
REVERT: D  440 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8495 (tp)
REVERT: D  470 LYS cc_start: 0.8771 (tppp) cc_final: 0.8558 (tppp)
REVERT: D  497 TYR cc_start: 0.8109 (m-80) cc_final: 0.7725 (m-10)
REVERT: D  510 TYR cc_start: 0.8633 (m-80) cc_final: 0.8424 (m-80)
REVERT: D  579 MET cc_start: 0.9234 (mtm) cc_final: 0.8950 (ttm)
REVERT: D  596 LYS cc_start: 0.9109 (OUTLIER) cc_final: 0.8696 (mttm)
  outliers start: 24
  outliers final: 7
  residues processed: 119
  average time/residue: 0.5268
  time to fit residues: 66.1509
Evaluate side-chains
  102 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 92
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  380 TYR
Chi-restraints excluded: chain A residue  391 CYS
Chi-restraints excluded: chain A residue  503 VAL
Chi-restraints excluded: chain D residue  123 MET
Chi-restraints excluded: chain D residue  162 LEU
Chi-restraints excluded: chain D residue  318 VAL
Chi-restraints excluded: chain D residue  359 LEU
Chi-restraints excluded: chain D residue  440 LEU
Chi-restraints excluded: chain D residue  596 LYS
Chi-restraints excluded: chain D residue  604 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 16 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   chunk 48 optimal weight:    0.9980
   chunk 67 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 0 optimal weight:    0.5980
   chunk 47 optimal weight:    0.5980
   chunk 38 optimal weight:    1.9990
   chunk 76 optimal weight:    0.7980
   chunk 77 optimal weight:    0.5980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 360 ASN
D 175 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.103215 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.076904 restraints weight = 12280.173|
|-----------------------------------------------------------------------------|
r_work (start): 0.3057 rms_B_bonded: 2.85
r_work: 0.2914 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.2914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8474
moved from start:          0.3394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   6765  Z= 0.164
  Angle     :  0.630  10.439   9209  Z= 0.317
  Chirality :  0.044   0.274    980
  Planarity :  0.004   0.034   1179
  Dihedral  :  4.149  18.180    866
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 18.52 %
    Favored  : 77.49 %
  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:  1.12 (0.30), residues: 792
  helix:  1.27 (0.26), residues: 398
  sheet: -0.16 (0.63), residues: 59
  loop :  0.46 (0.36), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 466 
 TYR   0.015   0.001   TYR D 385 
 PHE   0.015   0.001   PHE D 369 
 TRP   0.009   0.001   TRP D 271 
 HIS   0.003   0.001   HIS D 241 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00372 /  0.16 ( 6752)
  covalent geometry    : angle       0.61692 /  0.31 ( 9176)
  SS BOND              : bond        0.00808 /  0.55 (    6)
  SS BOND              : angle       3.36717 /  2.47 (   12)
  hydrogen bonds       : bond        0.04832 /  3.21 (  315)
  hydrogen bonds       : angle       4.65136 /  3.27 (  906)
  link_NAG-ASN         : bond        0.00219 /  0.07 (    7)
  link_NAG-ASN         : angle       1.11735 /  0.84 (   21)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 103
  time to evaluate  : 0.261 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  500 THR cc_start: 0.9381 (p) cc_final: 0.9163 (p)
REVERT: D  115 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.7831 (tpm-80)
REVERT: D  123 MET cc_start: 0.7919 (OUTLIER) cc_final: 0.7365 (mtt)
REVERT: D  287 GLN cc_start: 0.9190 (mm-40) cc_final: 0.8875 (tm-30)
REVERT: D  291 ILE cc_start: 0.8164 (OUTLIER) cc_final: 0.7707 (tp)
REVERT: D  297 MET cc_start: 0.9152 (mtm) cc_final: 0.8789 (mtp)
REVERT: D  383 MET cc_start: 0.9108 (mtp) cc_final: 0.8844 (mtm)
REVERT: D  440 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8513 (tp)
REVERT: D  470 LYS cc_start: 0.8784 (tppp) cc_final: 0.8515 (tppp)
REVERT: D  475 LYS cc_start: 0.8756 (ttpp) cc_final: 0.8508 (ttpp)
REVERT: D  510 TYR cc_start: 0.8633 (m-80) cc_final: 0.8414 (m-80)
REVERT: D  579 MET cc_start: 0.9230 (OUTLIER) cc_final: 0.8963 (ttm)
REVERT: D  596 LYS cc_start: 0.9113 (OUTLIER) cc_final: 0.8712 (mttm)
  outliers start: 28
  outliers final: 11
  residues processed: 122
  average time/residue: 0.4741
  time to fit residues: 61.4554
Evaluate side-chains
  123 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 106
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  380 TYR
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  503 VAL
Chi-restraints excluded: chain D residue   91 LEU
Chi-restraints excluded: chain D residue  115 ARG
Chi-restraints excluded: chain D residue  123 MET
Chi-restraints excluded: chain D residue  148 LEU
Chi-restraints excluded: chain D residue  162 LEU
Chi-restraints excluded: chain D residue  291 ILE
Chi-restraints excluded: chain D residue  318 VAL
Chi-restraints excluded: chain D residue  359 LEU
Chi-restraints excluded: chain D residue  401 HIS
Chi-restraints excluded: chain D residue  440 LEU
Chi-restraints excluded: chain D residue  579 MET
Chi-restraints excluded: chain D residue  596 LYS
Chi-restraints excluded: chain D residue  604 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 30 optimal weight:    0.9990
   chunk 17 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9990
   chunk 36 optimal weight:    0.7980
   chunk 37 optimal weight:    0.3980
   chunk 0 optimal weight:    2.9990
   chunk 55 optimal weight:    0.5980
   chunk 49 optimal weight:    0.7980
   chunk 34 optimal weight:    0.6980
   chunk 76 optimal weight:    0.8980
   chunk 52 optimal weight:    2.9990
   overall best weight:    0.6580

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.103380 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.077112 restraints weight = 12150.884|
|-----------------------------------------------------------------------------|
r_work (start): 0.3079 rms_B_bonded: 2.83
r_work: 0.2948 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.2948
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8453
moved from start:          0.3534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6765  Z= 0.162
  Angle     :  0.642  11.004   9209  Z= 0.320
  Chirality :  0.044   0.291    980
  Planarity :  0.004   0.033   1179
  Dihedral  :  4.111  18.060    866
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 19.52 %
    Favored  : 77.07 %
  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:  1.22 (0.30), residues: 792
  helix:  1.34 (0.26), residues: 398
  sheet: -0.18 (0.64), residues: 59
  loop :  0.53 (0.36), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 466 
 TYR   0.015   0.001   TYR D 385 
 PHE   0.015   0.001   PHE D 369 
 TRP   0.010   0.001   TRP D 165 
 HIS   0.003   0.001   HIS D 241 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00366 /  0.16 ( 6752)
  covalent geometry    : angle       0.62871 /  0.31 ( 9176)
  SS BOND              : bond        0.00866 /  0.60 (    6)
  SS BOND              : angle       3.52409 /  2.68 (   12)
  hydrogen bonds       : bond        0.04827 /  3.19 (  315)
  hydrogen bonds       : angle       4.60930 /  3.24 (  906)
  link_NAG-ASN         : bond        0.00219 /  0.07 (    7)
  link_NAG-ASN         : angle       1.09257 /  0.82 (   21)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 107
  time to evaluate  : 0.215 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  500 THR cc_start: 0.9384 (p) cc_final: 0.9166 (p)
REVERT: D  114 LYS cc_start: 0.8963 (mmpt) cc_final: 0.8485 (tppt)
REVERT: D  115 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.7832 (tpm-80)
REVERT: D  123 MET cc_start: 0.7882 (OUTLIER) cc_final: 0.7479 (mtt)
REVERT: D  189 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8520 (tp30)
REVERT: D  291 ILE cc_start: 0.8155 (OUTLIER) cc_final: 0.7700 (tp)
REVERT: D  297 MET cc_start: 0.9120 (mtm) cc_final: 0.8789 (mtp)
REVERT: D  383 MET cc_start: 0.9087 (mtp) cc_final: 0.8851 (mtm)
REVERT: D  440 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8480 (tp)
REVERT: D  470 LYS cc_start: 0.8829 (tppp) cc_final: 0.8552 (tppp)
REVERT: D  475 LYS cc_start: 0.8755 (ttpp) cc_final: 0.8547 (ttpp)
REVERT: D  497 TYR cc_start: 0.7960 (m-80) cc_final: 0.7679 (m-10)
REVERT: D  510 TYR cc_start: 0.8594 (m-80) cc_final: 0.8365 (m-80)
REVERT: D  579 MET cc_start: 0.9234 (OUTLIER) cc_final: 0.8957 (ttm)
REVERT: D  596 LYS cc_start: 0.9096 (OUTLIER) cc_final: 0.8675 (mttm)
  outliers start: 24
  outliers final: 10
  residues processed: 122
  average time/residue: 0.4791
  time to fit residues: 62.0800
Evaluate side-chains
  119 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 102
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  380 TYR
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  503 VAL
Chi-restraints excluded: chain D residue   91 LEU
Chi-restraints excluded: chain D residue  115 ARG
Chi-restraints excluded: chain D residue  123 MET
Chi-restraints excluded: chain D residue  162 LEU
Chi-restraints excluded: chain D residue  189 GLU
Chi-restraints excluded: chain D residue  291 ILE
Chi-restraints excluded: chain D residue  318 VAL
Chi-restraints excluded: chain D residue  359 LEU
Chi-restraints excluded: chain D residue  401 HIS
Chi-restraints excluded: chain D residue  440 LEU
Chi-restraints excluded: chain D residue  579 MET
Chi-restraints excluded: chain D residue  596 LYS
Chi-restraints excluded: chain D residue  604 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 46 optimal weight:    0.0370
   chunk 22 optimal weight:    0.5980
   chunk 64 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 74 optimal weight:    0.6980
   chunk 77 optimal weight:    0.6980
   chunk 38 optimal weight:    0.7980
   chunk 39 optimal weight:    1.9990
   chunk 17 optimal weight:    0.3980
   chunk 62 optimal weight:    0.5980
   chunk 4 optimal weight:    0.9990
   overall best weight:    0.4658

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 414 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.104299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.078056 restraints weight = 12065.500|
|-----------------------------------------------------------------------------|
r_work (start): 0.3092 rms_B_bonded: 2.82
r_work: 0.2960 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.2960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8447
moved from start:          0.3574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6765  Z= 0.139
  Angle     :  0.647  14.510   9209  Z= 0.317
  Chirality :  0.044   0.299    980
  Planarity :  0.003   0.034   1179
  Dihedral  :  4.037  17.127    866
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 20.94 %
    Favored  : 75.93 %
  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:  1.27 (0.30), residues: 792
  helix:  1.44 (0.26), residues: 396
  sheet: -0.21 (0.64), residues: 59
  loop :  0.49 (0.36), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 306 
 TYR   0.013   0.001   TYR D 385 
 PHE   0.014   0.001   PHE D 369 
 TRP   0.010   0.001   TRP D 165 
 HIS   0.003   0.001   HIS A 519 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00312 /  0.14 ( 6752)
  covalent geometry    : angle       0.63208 /  0.31 ( 9176)
  SS BOND              : bond        0.00747 /  0.51 (    6)
  SS BOND              : angle       3.65418 /  2.87 (   12)
  hydrogen bonds       : bond        0.04645 /  3.07 (  315)
  hydrogen bonds       : angle       4.57075 /  3.21 (  906)
  link_NAG-ASN         : bond        0.00203 /  0.06 (    7)
  link_NAG-ASN         : angle       1.04969 /  0.79 (   21)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 105
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  334 ASN cc_start: 0.7892 (t0) cc_final: 0.7634 (t0)
REVERT: D  115 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7879 (tpm-80)
REVERT: D  123 MET cc_start: 0.7934 (OUTLIER) cc_final: 0.7511 (mtt)
REVERT: D  189 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8520 (tp30)
REVERT: D  287 GLN cc_start: 0.9128 (mm-40) cc_final: 0.8914 (tm-30)
REVERT: D  291 ILE cc_start: 0.8128 (OUTLIER) cc_final: 0.7681 (tp)
REVERT: D  297 MET cc_start: 0.9129 (mtm) cc_final: 0.8792 (mtp)
REVERT: D  470 LYS cc_start: 0.8792 (tppp) cc_final: 0.8500 (tppp)
REVERT: D  475 LYS cc_start: 0.8776 (ttpp) cc_final: 0.8547 (ttpp)
REVERT: D  497 TYR cc_start: 0.7973 (m-80) cc_final: 0.7606 (m-10)
REVERT: D  510 TYR cc_start: 0.8577 (m-80) cc_final: 0.8341 (m-80)
REVERT: D  579 MET cc_start: 0.9231 (OUTLIER) cc_final: 0.8928 (ttm)
REVERT: D  596 LYS cc_start: 0.9103 (OUTLIER) cc_final: 0.8730 (mttm)
  outliers start: 22
  outliers final: 8
  residues processed: 119
  average time/residue: 0.5070
  time to fit residues: 63.9195
Evaluate side-chains
  111 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 97
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  380 TYR
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  503 VAL
Chi-restraints excluded: chain D residue  115 ARG
Chi-restraints excluded: chain D residue  123 MET
Chi-restraints excluded: chain D residue  162 LEU
Chi-restraints excluded: chain D residue  189 GLU
Chi-restraints excluded: chain D residue  291 ILE
Chi-restraints excluded: chain D residue  318 VAL
Chi-restraints excluded: chain D residue  359 LEU
Chi-restraints excluded: chain D residue  367 ASP
Chi-restraints excluded: chain D residue  579 MET
Chi-restraints excluded: chain D residue  596 LYS
Chi-restraints excluded: chain D residue  604 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 21 optimal weight:    0.7980
   chunk 14 optimal weight:    0.8980
   chunk 67 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9990
   chunk 16 optimal weight:    0.8980
   chunk 53 optimal weight:    2.9990
   chunk 11 optimal weight:    0.8980
   chunk 2 optimal weight:    0.6980
   chunk 20 optimal weight:    0.6980
   chunk 18 optimal weight:    0.8980
   chunk 26 optimal weight:    0.5980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D 175 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.103691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.077105 restraints weight = 12136.672|
|-----------------------------------------------------------------------------|
r_work (start): 0.3077 rms_B_bonded: 2.85
r_work: 0.2945 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.2945
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8459
moved from start:          0.3685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6765  Z= 0.176
  Angle     :  0.676  12.520   9209  Z= 0.338
  Chirality :  0.045   0.329    980
  Planarity :  0.004   0.033   1179
  Dihedral  :  4.129  17.889    866
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 21.37 %
    Favored  : 75.64 %
  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:  1.23 (0.30), residues: 792
  helix:  1.40 (0.26), residues: 397
  sheet: -0.33 (0.63), residues: 59
  loop :  0.50 (0.36), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 169 
 TYR   0.013   0.001   TYR D 385 
 PHE   0.015   0.001   PHE D 369 
 TRP   0.009   0.001   TRP D 165 
 HIS   0.004   0.001   HIS D 241 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00403 /  0.18 ( 6752)
  covalent geometry    : angle       0.65996 /  0.33 ( 9176)
  SS BOND              : bond        0.00853 /  0.60 (    6)
  SS BOND              : angle       3.88977 /  3.05 (   12)
  hydrogen bonds       : bond        0.04885 /  3.21 (  315)
  hydrogen bonds       : angle       4.62104 /  3.24 (  906)
  link_NAG-ASN         : bond        0.00207 /  0.08 (    7)
  link_NAG-ASN         : angle       1.09552 /  0.83 (   21)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 97
  time to evaluate  : 0.258 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  334 ASN cc_start: 0.7861 (t0) cc_final: 0.7570 (t0)
REVERT: D   55 THR cc_start: 0.7835 (OUTLIER) cc_final: 0.7344 (p)
REVERT: D  115 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.7820 (tpm-80)
REVERT: D  123 MET cc_start: 0.7934 (OUTLIER) cc_final: 0.7503 (mtt)
REVERT: D  189 GLU cc_start: 0.8828 (OUTLIER) cc_final: 0.8516 (tp30)
REVERT: D  287 GLN cc_start: 0.9179 (mm-40) cc_final: 0.8910 (tm-30)
REVERT: D  291 ILE cc_start: 0.8067 (OUTLIER) cc_final: 0.7647 (tp)
REVERT: D  297 MET cc_start: 0.9146 (mtm) cc_final: 0.8592 (mtp)
REVERT: D  470 LYS cc_start: 0.8808 (tppp) cc_final: 0.8501 (tppp)
REVERT: D  510 TYR cc_start: 0.8596 (m-80) cc_final: 0.8314 (m-80)
REVERT: D  579 MET cc_start: 0.9237 (OUTLIER) cc_final: 0.8950 (ttm)
REVERT: D  596 LYS cc_start: 0.9094 (OUTLIER) cc_final: 0.8712 (mttm)
  outliers start: 21
  outliers final: 9
  residues processed: 110
  average time/residue: 0.5133
  time to fit residues: 59.8908
Evaluate side-chains
  107 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 91
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  380 TYR
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  503 VAL
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain D residue   55 THR
Chi-restraints excluded: chain D residue   91 LEU
Chi-restraints excluded: chain D residue  115 ARG
Chi-restraints excluded: chain D residue  123 MET
Chi-restraints excluded: chain D residue  162 LEU
Chi-restraints excluded: chain D residue  189 GLU
Chi-restraints excluded: chain D residue  291 ILE
Chi-restraints excluded: chain D residue  318 VAL
Chi-restraints excluded: chain D residue  359 LEU
Chi-restraints excluded: chain D residue  579 MET
Chi-restraints excluded: chain D residue  596 LYS
Chi-restraints excluded: chain D residue  604 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9990
   chunk 69 optimal weight:    2.9990
   chunk 26 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 43 optimal weight:    0.4980
   chunk 57 optimal weight:    0.5980
   chunk 45 optimal weight:    0.3980
   overall best weight:    0.6782

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.103471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.077127 restraints weight = 12283.366|
|-----------------------------------------------------------------------------|
r_work (start): 0.3076 rms_B_bonded: 2.86
r_work: 0.2946 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.2946
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8455
moved from start:          0.3708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6765  Z= 0.169
  Angle     :  0.697  14.192   9209  Z= 0.347
  Chirality :  0.045   0.348    980
  Planarity :  0.003   0.033   1179
  Dihedral  :  4.143  17.671    866
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 21.79 %
    Favored  : 75.21 %
  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:  1.20 (0.30), residues: 792
  helix:  1.38 (0.26), residues: 397
  sheet: -0.36 (0.63), residues: 59
  loop :  0.48 (0.36), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 169 
 TYR   0.015   0.001   TYR D 497 
 PHE   0.015   0.001   PHE D 369 
 TRP   0.009   0.001   TRP D 165 
 HIS   0.003   0.001   HIS D 241 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00388 /  0.17 ( 6752)
  covalent geometry    : angle       0.67996 /  0.34 ( 9176)
  SS BOND              : bond        0.00914 /  0.64 (    6)
  SS BOND              : angle       4.09528 /  3.24 (   12)
  hydrogen bonds       : bond        0.04845 /  3.19 (  315)
  hydrogen bonds       : angle       4.62249 /  3.24 (  906)
  link_NAG-ASN         : bond        0.00206 /  0.07 (    7)
  link_NAG-ASN         : angle       1.08888 /  0.83 (   21)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 92
  time to evaluate  : 0.320 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  334 ASN cc_start: 0.7778 (t0) cc_final: 0.7500 (t0)
REVERT: D   55 THR cc_start: 0.7802 (OUTLIER) cc_final: 0.7334 (p)
REVERT: D  115 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.7882 (tpm-80)
REVERT: D  123 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.7558 (mtt)
REVERT: D  189 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8509 (tp30)
REVERT: D  287 GLN cc_start: 0.9211 (mm-40) cc_final: 0.8880 (tm-30)
REVERT: D  291 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7650 (tp)
REVERT: D  297 MET cc_start: 0.9148 (mtm) cc_final: 0.8749 (mtp)
REVERT: D  470 LYS cc_start: 0.8803 (tppp) cc_final: 0.8474 (tppp)
REVERT: D  510 TYR cc_start: 0.8599 (m-80) cc_final: 0.8317 (m-80)
REVERT: D  579 MET cc_start: 0.9242 (OUTLIER) cc_final: 0.8964 (ttm)
REVERT: D  596 LYS cc_start: 0.9092 (OUTLIER) cc_final: 0.8705 (mttm)
  outliers start: 21
  outliers final: 10
  residues processed: 106
  average time/residue: 0.4842
  time to fit residues: 54.6889
Evaluate side-chains
  107 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 90
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  380 TYR
Chi-restraints excluded: chain A residue  392 PHE
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  503 VAL
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain D residue   55 THR
Chi-restraints excluded: chain D residue   91 LEU
Chi-restraints excluded: chain D residue  115 ARG
Chi-restraints excluded: chain D residue  123 MET
Chi-restraints excluded: chain D residue  162 LEU
Chi-restraints excluded: chain D residue  189 GLU
Chi-restraints excluded: chain D residue  291 ILE
Chi-restraints excluded: chain D residue  318 VAL
Chi-restraints excluded: chain D residue  359 LEU
Chi-restraints excluded: chain D residue  579 MET
Chi-restraints excluded: chain D residue  596 LYS
Chi-restraints excluded: chain D residue  604 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 63 optimal weight:    0.9980
   chunk 40 optimal weight:    0.2980
   chunk 59 optimal weight:    0.5980
   chunk 27 optimal weight:    0.7980
   chunk 42 optimal weight:    0.6980
   chunk 72 optimal weight:    2.9990
   chunk 51 optimal weight:    0.6980
   chunk 67 optimal weight:    0.2980
   chunk 30 optimal weight:    0.6980
   chunk 55 optimal weight:    0.5980
   chunk 58 optimal weight:    0.5980
   overall best weight:    0.4780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D 154 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.104490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.078161 restraints weight = 12135.963|
|-----------------------------------------------------------------------------|
r_work (start): 0.3098 rms_B_bonded: 2.85
r_work: 0.2967 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.2967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8438
moved from start:          0.3756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6765  Z= 0.147
  Angle     :  0.682  16.768   9209  Z= 0.341
  Chirality :  0.044   0.335    980
  Planarity :  0.003   0.033   1179
  Dihedral  :  4.073  20.239    866
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 21.94 %
    Favored  : 75.07 %
  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:  1.30 (0.30), residues: 792
  helix:  1.56 (0.26), residues: 384
  sheet:  0.12 (0.66), residues: 53
  loop :  0.33 (0.35), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 169 
 TYR   0.021   0.001   TYR D 497 
 PHE   0.018   0.001   PHE A 374 
 TRP   0.009   0.001   TRP D 165 
 HIS   0.007   0.001   HIS D 493 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00335 /  0.15 ( 6752)
  covalent geometry    : angle       0.66314 /  0.33 ( 9176)
  SS BOND              : bond        0.00850 /  0.60 (    6)
  SS BOND              : angle       4.27642 /  3.46 (   12)
  hydrogen bonds       : bond        0.04666 /  3.08 (  315)
  hydrogen bonds       : angle       4.60116 /  3.21 (  906)
  link_NAG-ASN         : bond        0.00199 /  0.06 (    7)
  link_NAG-ASN         : angle       1.07270 /  0.82 (   21)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 95
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  334 ASN cc_start: 0.7779 (t0) cc_final: 0.7512 (t0)
REVERT: D   55 THR cc_start: 0.7780 (OUTLIER) cc_final: 0.7224 (p)
REVERT: D  115 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.7856 (tpm-80)
REVERT: D  123 MET cc_start: 0.7979 (OUTLIER) cc_final: 0.7541 (mtt)
REVERT: D  189 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8504 (tp30)
REVERT: D  287 GLN cc_start: 0.9201 (mm-40) cc_final: 0.8868 (tm-30)
REVERT: D  291 ILE cc_start: 0.8105 (OUTLIER) cc_final: 0.7681 (tp)
REVERT: D  297 MET cc_start: 0.9118 (mtm) cc_final: 0.8570 (mtp)
REVERT: D  341 LYS cc_start: 0.8134 (tppt) cc_final: 0.7883 (tppt)
REVERT: D  470 LYS cc_start: 0.8804 (tppp) cc_final: 0.8496 (tppp)
REVERT: D  510 TYR cc_start: 0.8569 (m-80) cc_final: 0.8288 (m-80)
REVERT: D  579 MET cc_start: 0.9225 (OUTLIER) cc_final: 0.8962 (ttm)
REVERT: D  596 LYS cc_start: 0.9082 (OUTLIER) cc_final: 0.8736 (mttm)
  outliers start: 21
  outliers final: 12
  residues processed: 109
  average time/residue: 0.4779
  time to fit residues: 55.5864
Evaluate side-chains
  109 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 90
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  380 TYR
Chi-restraints excluded: chain A residue  392 PHE
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  503 VAL
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain D residue   55 THR
Chi-restraints excluded: chain D residue   91 LEU
Chi-restraints excluded: chain D residue  115 ARG
Chi-restraints excluded: chain D residue  123 MET
Chi-restraints excluded: chain D residue  162 LEU
Chi-restraints excluded: chain D residue  189 GLU
Chi-restraints excluded: chain D residue  291 ILE
Chi-restraints excluded: chain D residue  318 VAL
Chi-restraints excluded: chain D residue  359 LEU
Chi-restraints excluded: chain D residue  367 ASP
Chi-restraints excluded: chain D residue  579 MET
Chi-restraints excluded: chain D residue  596 LYS
Chi-restraints excluded: chain D residue  604 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 74 optimal weight:    0.5980
   chunk 13 optimal weight:    0.3980
   chunk 62 optimal weight:    1.9990
   chunk 17 optimal weight:    0.0870
   chunk 59 optimal weight:    0.7980
   chunk 14 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9990
   chunk 39 optimal weight:    0.5980
   chunk 27 optimal weight:    0.5980
   chunk 34 optimal weight:    0.9990
   overall best weight:    0.4558

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.104717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.078414 restraints weight = 12033.070|
|-----------------------------------------------------------------------------|
r_work (start): 0.3098 rms_B_bonded: 2.85
r_work: 0.2968 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.2968
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8430
moved from start:          0.3806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6765  Z= 0.144
  Angle     :  0.693  15.944   9209  Z= 0.346
  Chirality :  0.044   0.345    980
  Planarity :  0.003   0.033   1179
  Dihedral  :  4.089  23.024    866
  Min Nonbonded Distance : 2.312

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 22.51 %
    Favored  : 74.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.28 (0.30), residues: 792
  helix:  1.54 (0.26), residues: 384
  sheet:  0.13 (0.67), residues: 53
  loop :  0.33 (0.35), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 169 
 TYR   0.020   0.001   TYR D 497 
 PHE   0.015   0.001   PHE D 369 
 TRP   0.009   0.001   TRP D 165 
 HIS   0.005   0.001   HIS D 493 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00326 /  0.14 ( 6752)
  covalent geometry    : angle       0.67430 /  0.34 ( 9176)
  SS BOND              : bond        0.00734 /  0.51 (    6)
  SS BOND              : angle       4.35594 /  3.40 (   12)
  hydrogen bonds       : bond        0.04710 /  3.10 (  315)
  hydrogen bonds       : angle       4.59292 /  3.20 (  906)
  link_NAG-ASN         : bond        0.00202 /  0.06 (    7)
  link_NAG-ASN         : angle       1.06643 /  0.81 (   21)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2407.05 seconds
wall clock time: 41 minutes 52.60 seconds (2512.60 seconds total)